sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P36871 and applied mutation signature D263G to reconstruct the assayed variant sequence.

assay_conditions_summary: pH 7.4; 298.15 K; cofactor NAD+

column_label: Table 2 (Kinetic parameters and phosphorylation state of WT PGM1 and missense variants), body row D263G; column 'kcat' with printed unit s^-1 = 3.0; column 'Km' with printed unit uM = 115; column 'kcat/Km' with printed unit uM^-1 s^-1 = 0.026.

normalized_value_unit_evidence: kcat: printed Table 2 cell 3.0 in the column unit s^-1; the column prints reciprocal seconds, so no unit conversion applies and the value carries over as 3.0 s^(-1). Km: printed Table 2 cell 115 in the column unit uM; 1 uM is 0.001 mM, so 115 / 1000 = 0.115 mM. kcat/Km: printed Table 2 cell 0.026 in the column unit uM^-1 s^-1; 1 uM^-1 s^-1 is 1000 s^-1 mM^-1, so 0.026 x 1000 = 26.0 s^(-1)*mM^(-1), while the catalog carries 26.08695652173913 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table 2, body row D263G: kcat = 3.0 s^-1; Km = 115 uM; printed kcat/Km = 0.026 uM^-1 s^-1.

row_label: Table 2, body row D263G

table_label: Table 2: Kinetic parameters and phosphorylation state of WT PGM1 and missense variants (J. Biol. Chem. 2014, 289(46):32010-32019)


organism: Homo sapiens

substrate_name: alpha-D-Glucose 1-phosphate

source_db: oed

verification_status: corrected

ki_display: Not reported

protein_accession_database: UniProt

source_license: CC BY 4.0

km_unit: mM

sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P36871 and applied mutation signature D263Y to reconstruct the assayed variant sequence.

mutation_type: substitution

column_label: Table 2 (Kinetic parameters and phosphorylation state of WT PGM1 and missense variants), body row D263Y; column 'kcat' with printed unit s^-1 = 1.54; column 'Km' with printed unit uM = 170; column 'kcat/Km' with printed unit uM^-1 s^-1 = 0.0091.

normalized_value_unit_evidence: kcat: printed Table 2 cell 1.54 in the column unit s^-1; the column prints reciprocal seconds, so no unit conversion applies and the value carries over as 1.54 s^(-1). Km: printed Table 2 cell 170 in the column unit uM; 1 uM is 0.001 mM, so 170 / 1000 = 0.17 mM. kcat/Km: printed Table 2 cell 0.0091 in the column unit uM^-1 s^-1; 1 uM^-1 s^-1 is 1000 s^-1 mM^-1, so 0.0091 x 1000 = 9.1 s^(-1)*mM^(-1), while the catalog carries 9.058823529411764 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table 2, body row D263Y: kcat = 1.54 s^-1; Km = 170 uM; printed kcat/Km = 0.0091 uM^-1 s^-1.

row_label: Table 2, body row D263Y

data_origin: experimental

substrate: alpha-D-Glucose 1-phosphate

status: corrected

source: oed


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P36871 and applied mutation signature D62H to reconstruct the assayed variant sequence.

column_label: Table 2 (Kinetic parameters and phosphorylation state of WT PGM1 and missense variants), body row D62H; column 'kcat' with printed unit s^-1 = 0.197; column 'Km' with printed unit uM = 23.3; column 'kcat/Km' with printed unit uM^-1 s^-1 = 0.0085.

normalized_value_unit_evidence: kcat: printed Table 2 cell 0.197 in the column unit s^-1; the column prints reciprocal seconds, so no unit conversion applies and the value carries over as 0.197 s^(-1). Km: printed Table 2 cell 23.3 in the column unit uM; 1 uM is 0.001 mM, so 23.3 / 1000 = 0.0233 mM. kcat/Km: printed Table 2 cell 0.0085 in the column unit uM^-1 s^-1; 1 uM^-1 s^-1 is 1000 s^-1 mM^-1, so 0.0085 x 1000 = 8.5 s^(-1)*mM^(-1), while the catalog carries 8.565217391304348 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table 2, body row D62H: kcat = 0.197 s^-1; Km = 23.3 uM; printed kcat/Km = 0.0085 uM^-1 s^-1.

row_label: Table 2, body row D62H


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P36871 and applied mutation signature G121R to reconstruct the assayed variant sequence.

column_label: Table 2 (Kinetic parameters and phosphorylation state of WT PGM1 and missense variants), body row G121R; column 'kcat' with printed unit s^-1 = 0.368; column 'Km' with printed unit uM = 56; column 'kcat/Km' with printed unit uM^-1 s^-1 = 0.0066.

normalized_value_unit_evidence: kcat: printed Table 2 cell 0.368 in the column unit s^-1; the column prints reciprocal seconds, so no unit conversion applies and the value carries over as 0.368 s^(-1). Km: printed Table 2 cell 56 in the column unit uM; 1 uM is 0.001 mM, so 56 / 1000 = 0.056 mM. kcat/Km: printed Table 2 cell 0.0066 in the column unit uM^-1 s^-1; 1 uM^-1 s^-1 is 1000 s^-1 mM^-1, so 0.0066 x 1000 = 6.6 s^(-1)*mM^(-1), while the catalog carries 6.571428571428571 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table 2, body row G121R: kcat = 0.368 s^-1; Km = 56 uM; printed kcat/Km = 0.0066 uM^-1 s^-1.

row_label: Table 2, body row G121R


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P36871 and applied mutation signature K68M to reconstruct the assayed variant sequence.

column_label: Table 2 (Kinetic parameters and phosphorylation state of WT PGM1 and missense variants), body row K68M; column 'kcat' with printed unit s^-1 = 153; column 'Km' with printed unit uM = 63.8; column 'kcat/Km' with printed unit uM^-1 s^-1 = 2.40.

normalized_value_unit_evidence: kcat: printed Table 2 cell 153 in the column unit s^-1; the column prints reciprocal seconds, so no unit conversion applies and the value carries over as 153.0 s^(-1). Km: printed Table 2 cell 63.8 in the column unit uM; 1 uM is 0.001 mM, so 63.8 / 1000 = 0.0638 mM. kcat/Km: printed Table 2 cell 2.40 in the column unit uM^-1 s^-1; 1 uM^-1 s^-1 is 1000 s^-1 mM^-1, so 2.40 x 1000 = 2400.0 s^(-1)*mM^(-1), while the catalog carries 2390.625 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table 2, body row K68M: kcat = 153 s^-1; Km = 63.8 uM; printed kcat/Km = 2.40 uM^-1 s^-1.

row_label: Table 2, body row K68M


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P36871 and applied mutation signature R221C to reconstruct the assayed variant sequence.

column_label: Table 2 (Kinetic parameters and phosphorylation state of WT PGM1 and missense variants), body row R221C; column 'kcat' with printed unit s^-1 = 200; column 'Km' with printed unit uM = 94; column 'kcat/Km' with printed unit uM^-1 s^-1 = 2.1.

normalized_value_unit_evidence: kcat: printed Table 2 cell 200 in the column unit s^-1; the column prints reciprocal seconds, so no unit conversion applies and the value carries over as 200.0 s^(-1). Km: printed Table 2 cell 94 in the column unit uM; 1 uM is 0.001 mM, so 94 / 1000 = 0.094 mM. kcat/Km: printed Table 2 cell 2.1 in the column unit uM^-1 s^-1; 1 uM^-1 s^-1 is 1000 s^-1 mM^-1, so 2.1 x 1000 = 2100.0 s^(-1)*mM^(-1), while the catalog carries 2127.659574468085 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table 2, body row R221C: kcat = 200 s^-1; Km = 94 uM; printed kcat/Km = 2.1 uM^-1 s^-1.

row_label: Table 2, body row R221C


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P36871 and applied mutation signature T115A to reconstruct the assayed variant sequence.

column_label: Table 2 (Kinetic parameters and phosphorylation state of WT PGM1 and missense variants), body row T115A; column 'kcat' with printed unit s^-1 = 36.0; column 'Km' with printed unit uM = 41; column 'kcat/Km' with printed unit uM^-1 s^-1 = 0.88.

normalized_value_unit_evidence: kcat: printed Table 2 cell 36.0 in the column unit s^-1; the column prints reciprocal seconds, so no unit conversion applies and the value carries over as 36.0 s^(-1). Km: printed Table 2 cell 41 in the column unit uM; 1 uM is 0.001 mM, so 41 / 1000 = 0.041 mM. kcat/Km: printed Table 2 cell 0.88 in the column unit uM^-1 s^-1; 1 uM^-1 s^-1 is 1000 s^-1 mM^-1, so 0.88 x 1000 = 880.0 s^(-1)*mM^(-1), while the catalog carries 878.0487804878048 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table 2, body row T115A: kcat = 36.0 s^-1; Km = 41 uM; printed kcat/Km = 0.88 uM^-1 s^-1.

row_label: Table 2, body row T115A


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P36871 and applied mutation signature T19A to reconstruct the assayed variant sequence.

column_label: Table 2 (Kinetic parameters and phosphorylation state of WT PGM1 and missense variants), body row T19A; column 'kcat' with printed unit s^-1 = 0.685; column 'Km' with printed unit uM = 130; column 'kcat/Km' with printed unit uM^-1 s^-1 = 0.0053.

normalized_value_unit_evidence: kcat: printed Table 2 cell 0.685 in the column unit s^-1; the column prints reciprocal seconds, so no unit conversion applies and the value carries over as 0.685 s^(-1). Km: printed Table 2 cell 130 in the column unit uM; 1 uM is 0.001 mM, so 130 / 1000 = 0.13 mM. kcat/Km: printed Table 2 cell 0.0053 in the column unit uM^-1 s^-1; 1 uM^-1 s^-1 is 1000 s^-1 mM^-1, so 0.0053 x 1000 = 5.3 s^(-1)*mM^(-1), while the catalog carries 5.269230769230769 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table 2, body row T19A: kcat = 0.685 s^-1; Km = 130 uM; printed kcat/Km = 0.0053 uM^-1 s^-1.

row_label: Table 2, body row T19A


mutation_signature: Unknown

sequence_variant_note: Sequence is treated as wild-type because the source explicitly marked the record as wild-type.

column_label: Table 2 (Kinetic parameters and phosphorylation state of WT PGM1 and missense variants), body row WT; column 'kcat' with printed unit s^-1 = 143; column 'Km' with printed unit uM = 80; column 'kcat/Km' with printed unit uM^-1 s^-1 = 1.8.

normalized_value_unit_evidence: kcat: printed Table 2 cell 143 in the column unit s^-1; the column prints reciprocal seconds, so no unit conversion applies and the value carries over as 143.0 s^(-1). Km: printed Table 2 cell 80 in the column unit uM; 1 uM is 0.001 mM, so 80 / 1000 = 0.08 mM. kcat/Km: printed Table 2 cell 1.8 in the column unit uM^-1 s^-1; 1 uM^-1 s^-1 is 1000 s^-1 mM^-1, so 1.8 x 1000 = 1800.0 s^(-1)*mM^(-1), while the catalog carries 1787.5 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table 2, body row WT: kcat = 143 s^-1; Km = 80 uM; printed kcat/Km = 1.8 uM^-1 s^-1.

row_label: Table 2, body row WT


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P36871 and applied mutation signature Y420H to reconstruct the assayed variant sequence.

column_label: Table 2 (Kinetic parameters and phosphorylation state of WT PGM1 and missense variants), body row Y420H; column 'kcat' with printed unit s^-1 = 162; column 'Km' with printed unit uM = 75; column 'kcat/Km' with printed unit uM^-1 s^-1 = 2.1.

normalized_value_unit_evidence: kcat: printed Table 2 cell 162 in the column unit s^-1; the column prints reciprocal seconds, so no unit conversion applies and the value carries over as 162.0 s^(-1). Km: printed Table 2 cell 75 in the column unit uM; 1 uM is 0.001 mM, so 75 / 1000 = 0.075 mM. kcat/Km: printed Table 2 cell 2.1 in the column unit uM^-1 s^-1; 1 uM^-1 s^-1 is 1000 s^-1 mM^-1, so 2.1 x 1000 = 2100.0 s^(-1)*mM^(-1), while the catalog carries 2160.0 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table 2, body row Y420H: kcat = 162 s^-1; Km = 75 uM; printed kcat/Km = 2.1 uM^-1 s^-1.

row_label: Table 2, body row Y420H


organism: Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)

substrate_name: 2-deoxyribose 1-phosphate

source_db: uniprot

proof_lines: kcat is 575 sec(-1) with glucose 1-phosphate as substrate. kcat is 330 sec(-1) with mannose 1-phosphate as substrate. kcat is 190 sec(-1) with 2-deoxyribose 1-phosphate as substrate.

substrate: 2-deoxyribose 1-phosphate

source: uniprot


organism: Thermococcus kodakarensis

source_db: brenda

sequence_source: multiple

source_databases_merged: brenda uniprot

source: brenda


organism: Acetobacter xylinus

substrate_name: D-Glucose 1,6-bisphosphate

kcat_over_km_origin: calculated

substrate: D-Glucose 1,6-bisphosphate


substrate_name: D-Glucose 1-phosphate

verification_status: unverified

substrate: D-Glucose 1-phosphate

status: unverified


substrate_name: Glycerate 1,3-bisphosphate; D-Glucose 1-phosphate

kcat_over_km_display: Not reported

source_license: SABIO-RK terms (free for academic use; see sabiork.h-its.org)


substrate_name: H2O; alpha-D-Glucose 1,6-bisphosphate

kcat_display: Not reported

substrate: H2O; alpha-D-Glucose 1,6-bisphosphate


substrate_name: alpha-D-Glucose 1,6-bisphosphate; H2O

source_license: CC BY 4.0; SABIO-RK terms (free for academic use; see sabiork.h-its.org)

substrate: alpha-D-Glucose 1,6-bisphosphate; H2O


enzyme_display_name: phosphoglucomutase

organism: Rattus norvegicus

enzyme: phosphoglucomutase


substrate_name: alpha-D-Glucose 6-phosphate

substrate: alpha-D-Glucose 6-phosphate


substrate_name: Glucose 1-phosphate

substrate: Glucose 1-phosphate


substrate_name: 2-deoxy-alpha-D-ribose 1-phosphate

substrate: 2-deoxy-alpha-D-ribose 1-phosphate


organism: Drosophila melanogaster


assay_conditions_summary: pH 6


organism: Arabidopsis thaliana


organism: Saccharomyces cerevisiae


substrate_name: alpha-D-Ribose 1-phosphate

ki_unit: mM

substrate: alpha-D-Ribose 1-phosphate


organism: Lactococcus lactis subsp. cremoris

sequence_variant_note: Sequence identity was resolved, but no explicit wild-type or mutant call was captured.


organism: Escherichia coli (strain K12)


organism: Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)

substrate_name: glucose 6-phosphate

proof_lines: kcat is 3000 min(-1) for glucose 1-phosphate and 1350 min(-1) for mannose 1-phosphate.

substrate: glucose 6-phosphate


substrate_name: mannose 6-phosphate

substrate: mannose 6-phosphate


enzyme_display_name: 2-methylfumaryl-CoA isomerase

organism: Chloroflexus aurantiacus

assay_conditions_summary: 328.15 K; cofactor CoA

proof_lines: 55°C, pH not specified in the publication

proof_lines: kcat is 840 sec(-1) for isomerase activity with 2-methylfumaryl-CoA.

enzyme: 2-methylfumaryl-CoA isomerase


organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

substrate_name: alpha-D-glucose 1,6-diphosphate

verification_status: verified

column_label: Abstract reports Km values for glucose 1-phosphate and glucose 1,6-bisphosphate were 2.34 times 10(-5) M and 2.24 times 10(-6) M, respectively.

raw_value_unit_evidence: Km raw_value=2.24 x 10(-6) M raw_unit=M

row_label: Fleischmann yeast phosphoglucomutase / glucose 1,6-bisphosphate

table_label: PubMed XML abstract PMID 1100398

substrate: alpha-D-glucose 1,6-diphosphate

status: verified


organism: Pseudomonas aeruginosa

substrate_name: alpha-D-glucose 1-phosphate

sequence_variant_note: Mutation context is present, but no sequence was resolved for this record.

substrate: alpha-D-glucose 1-phosphate


proof_lines:
R247A mutant
mutant R247A


organism: Mycobacterium tuberculosis


organism: Triticum aestivum


organism: Bacillus subtilis


enzyme_display_name: thromboxane-A synthase

organism: Sus scrofa

substrate_name: prostaglandin H2

column_label: PubMed abstract states the enzyme reaction has a Km for 15-hydroxy-9 alpha, 11 alpha-peroxidoprosta-5, 13-dienoic acid of 12 microM, with optimal pH 7.5 and 30 degrees C.

raw_value_unit_evidence: Km raw_value=12 raw_unit=microM

row_label: porcine lung thromboxane synthase with 15-hydroxy-9 alpha,11 alpha-peroxidoprosta-5,13-dienoic acid (prostaglandin H2)

table_label: PubMed abstract PMID 3745158

enzyme: thromboxane-A synthase

substrate: prostaglandin H2


enzyme_display_name: ribonuclease T2

organism: Aspergillus oryzae

sequence_variant_note: No sequence was resolved for this record, so variant-aware sequence handling could not be applied.

enzyme: ribonuclease T2


enzyme_display_name: Delta(3)-Delta(2)-enoyl-CoA isomerase

assay_conditions_summary: cofactor CoA

proof_lines:
pI 6.83 enzyme
pI 7.01 enzyme
pI 6.57 enzyme

enzyme: Delta(3)-Delta(2)-enoyl-CoA isomerase


proof_lines:
pI 6.83 enzyme
pI 7.01 enzyme


smiles: CCCCCCC#CCC(=O)N(CCS)C(=O)C

proof_lines:
pI 6.57 enzyme
pI 7.01 enzyme
pI 6.83 enzyme


smiles: CCCCCCCCCC#CC(=O)C(CNC(=O)C)S


smiles: CCCCCC#CC(=O)C(CNC(=O)C)S

proof_lines:
pI 7.01 enzyme
pI 6.57 enzyme
pI 6.83 enzyme


enzyme_display_name: protoporphyrin ferrochelatase

proof_lines: wild type enzyme, in 100 mM tris(hydroxymethyl)aminomethane-HCl, pH 7.4, temperature not specified in the publication

enzyme: protoporphyrin ferrochelatase


proof_lines: mutant enzyme Y13M, in 100 mM tris(hydroxymethyl)aminomethane-HCl, pH 7.4, temperature not specified in the publication


proof_lines: wild-type, in the presence of 4 mM Mg2+, pH 7.4, room temperature


enzyme_display_name: pancreatic ribonuclease

organism: Bos taurus

substrate_name: cytidine-2',3'-cyclic monophosphate

enzyme: pancreatic ribonuclease

substrate: cytidine-2',3'-cyclic monophosphate


enzyme_display_name: prostaglandin-D synthase

organism: Homo sapiens

proof_lines: mutant enzyme L79A, in 100 mM Tris-HCl (pH 8.0), 100 mM NaCl, and 1 mM dithiothreitol, at 25°C

enzyme: prostaglandin-D synthase


proof_lines: mutant enzyme M64A, in 100 mM Tris-HCl (pH 8.0), 100 mM NaCl, and 1 mM dithiothreitol, at 25°C


proof_lines: mutant enzyme L131A, in 100 mM Tris-HCl (pH 8.0), 100 mM NaCl, and 1 mM dithiothreitol, at 25°C


proof_lines: mutant enzyme F83A, in 100 mM Tris-HCl (pH 8.0), 100 mM NaCl, and 1 mM dithiothreitol, at 25°C


proof_lines: mutant enzyme S45A, in 100 mM Tris-HCl (pH 8.0), 100 mM NaCl, and 1 mM dithiothreitol, at 25°C


proof_lines: mutant enzyme M94A, in 100 mM Tris-HCl (pH 8.0), 100 mM NaCl, and 1 mM dithiothreitol, at 25°C


proof_lines: mutant enzyme W54A, in 100 mM Tris-HCl (pH 8.0), 100 mM NaCl, and 1 mM dithiothreitol, at 25°C


proof_lines: wild type enzyme, in 100 mM Tris-HCl (pH 8.0), 100 mM NaCl, and 1 mM dithiothreitol, at 25°C


proof_lines: mutant enzyme S81A, in 100 mM Tris-HCl (pH 8.0), 100 mM NaCl, and 1 mM dithiothreitol, at 25°C


proof_lines: mutant enzyme T147A, in 100 mM Tris-HCl (pH 8.0), 100 mM NaCl, and 1 mM dithiothreitol, at 25°C


proof_lines: mutant enzyme K59A, in 100 mM Tris-HCl (pH 8.0), 100 mM NaCl, and 1 mM dithiothreitol, at 25°C


organism: Aspergillus phoenicis

substrate_name: ApA

substrate: ApA


substrate_name: ApG

substrate: ApG


organism: Caulobacter vibrioides


substrate_name: mesoporphyrin IX

substrate: mesoporphyrin IX


enzyme_display_name: methionine gamma-lyase

organism: Citrobacter freundii

substrate_name: L-methionine

smiles: CSCCC(C(=O)O)N

enzyme: methionine gamma-lyase

substrate: L-methionine


substrate_name: mesoporphyrin

substrate: mesoporphyrin


substrate_name: protoporphyrin

substrate: protoporphyrin


enzyme_display_name: protein disulfide-isomerase

substrate_name: dithiothreitol

smiles: C(C(C(CS)O)O)S

proof_lines: with scrambled ribonuclease as substrate

enzyme: protein disulfide-isomerase

substrate: dithiothreitol


smiles: C(CS)O


substrate_name: cysteine

smiles: C(C(C(=O)O)N)S

proof_lines: glutathione, with scrambled ribonuclease as substrate

substrate: cysteine


substrate_name: GSH

smiles: C(CC(=O)NC(CS)C(=O)NCC(=O)O)C(C(=O)O)N

substrate: GSH


substrate_name: methiin

smiles: CS(=O)CC(C(=O)O)N

proof_lines: PEGylated mutant enzyme C115H, at pH 8.0 and 30°C

proof_lines: liposomes and polymeric vesicles-bound mutant enzyme C115H, at pH 8.0 and 30°C

substrate: methiin


substrate_name: alliin

smiles: C=CCS(=O)CC(C(=O)O)N

substrate: alliin


substrate_name: propiin

smiles: CCCS(=O)CC(C(=O)O)N

proof_lines: free mutant enzyme C115H, at pH 8.0 and 30°C

substrate: propiin


substrate_name: S-methyl-L-cysteine

smiles: CSCC(C(=O)O)N

substrate: S-methyl-L-cysteine


proof_lines: mutant H388A, co-expressed with wild-type, 37°C

proof_lines: mutant C395delta, co-expressed with wild-type, 37°C


proof_lines: mutant H263A, co-expressed with wild-type, 37°C

proof_lines: mutant I186T, co-expressed with wild-type, 37°C


enzyme_display_name: cysteine-S-conjugate beta-lyase

organism: Escherichia coli

substrate_name: L-cystathionine

smiles: C(CSCC(C(=O)O)N)C(C(=O)O)N

enzyme: cysteine-S-conjugate beta-lyase

substrate: L-cystathionine


proof_lines: pH 8.5, 25°C, recombinant chimeric mutant enzyme eCGS-sC-eCBL

proof_lines: pH 8.5, 25°C, recombinant chimeric mutant enzyme eCGS-sN-eCBL


enzyme_display_name: leukotriene-C4 synthase

substrate_name: glutathione

enzyme: leukotriene-C4 synthase

substrate: glutathione


substrate_name: leukotriene A4

substrate: leukotriene A4


km_display: Not reported


substrate_name: D-ribose 1-phosphate

column_label: Table 3 row Pgm2 under ribose-1-phosphate has Vmax, km, and kcat/km columns; values are 0.32, 530, and 0.63 respectively

raw_value_unit_evidence: Ribose-1-phosphate columns report Vmax=0.32 +/- 0.01 umol/(min mgprot), km=530 +/- 3 uM, kcat/km=0.63

row_label: Pgm2 / ribose-1-phosphate

table_label: Table 3. Kinetic parameters of purified His-tagged Pgm proteins on glucose-1-phosphate and ribose-1-phosphate

substrate: D-ribose 1-phosphate


organism: Lacticaseibacillus casei

substrate_name: L-cysteine

proof_lines:
Ctl2, at pH 5.5 and 37°C
Ctl1, at pH 5.5 and 37°C

substrate: L-cysteine


assay_conditions_summary: pH 5.5; 310.15 K; buffer sodium phosphate

proof_lines: Ctl2, in sodium phosphate buffer, at pH 5.5 and 37°C

proof_lines: Ctl1, in sodium phosphate buffer, at pH 5.5 and 37°C

proof_lines: Ctl1, in sodium phosphate buffer, at pH 6.8 and 37°C


substrate_name: DL-homocysteine

smiles: C(CS)C(C(=O)O)N

substrate: DL-homocysteine


proof_lines:
Ctl1, at pH 5.5 and 37°C
Ctl2, at pH 5.5 and 37°C


organism: Myxococcus xanthus


substrate_name: mesoporphyrin IX

substrate: mesoporphyrin IX


organism: Trypanosoma brucei

proof_lines: 37°C, pH 8, 50 mM sodium phosphate, Q81N


proof_lines: 37°C, pH 8, 50 mM sodium phosphate, wild-type


organism: Mus musculus

substrate_name: protoporphyrin IX

proof_lines: wild-type, under strictly anaerobic conditions

substrate: protoporphyrin IX


proof_lines: mutant P255R, under strictly anaerobic conditions


enzyme_display_name: adenylate cyclase

organism: Bordetella pertussis

substrate_name: ATP

assay_conditions_summary: pH 8; 303.15 K; cofactor ATP

proof_lines: mutant enzyme R338A/D360A, at pH 8.0 and 30°C

enzyme: adenylate cyclase

substrate: ATP


enzyme_display_name: UniProt P77366

substrate_name: beta-D-glucose 6-phosphate

source_db: skid

source_license: CC BY-NC-ND 4.0

enzyme: UniProt P77366

substrate: beta-D-glucose 6-phosphate

source: skid


enzyme_display_name: UniProt Q818Z9

organism: Bacillus cereus

substrate_name: D-ribose 5-phosphate

enzyme: UniProt Q818Z9

substrate: D-ribose 5-phosphate


enzyme_display_name: phosphomannomutase

organism: Saccharina japonica

substrate_name: alpha-D-glucose 1-phosphate

enzyme: phosphomannomutase

substrate: alpha-D-glucose 1-phosphate


organism: Amorphophallus konjac

substrate_name: mannose 1-phosphate

substrate: mannose 1-phosphate


enzyme_display_name: UniProt P56839

organism: Mytilus edulis

enzyme: UniProt P56839


enzyme_display_name: L-3-cyanoalanine synthase

organism: Solanum tuberosum

substrate_name: CN-

enzyme: L-3-cyanoalanine synthase

substrate: CN-


substrate_name: O-acetyl-L-serine

smiles: CC(=O)OCC(C(=O)O)N

substrate: O-acetyl-L-serine


organism: Porphyromonas gingivalis

substrate_name: S-ethyl-L-homocysteine

smiles: CCSCCC(C(=O)O)N

substrate: S-ethyl-L-homocysteine


substrate_name: L-methionine sulfoxide

smiles: CS(=O)CCC(C(=O)O)N

substrate: L-methionine sulfoxide


substrate_name: S-Benzyl-L-cysteine

substrate: S-Benzyl-L-cysteine


substrate_name: S-ethyl-L-cysteine

smiles: CCSCC(C(=O)O)N

substrate: S-ethyl-L-cysteine


organism: Cavia porcellus

substrate_name: leukotriene A4

substrate: leukotriene A4


substrate_name: 14,15-Leukotriene A4 methyl ester

substrate: 14,15-Leukotriene A4 methyl ester


substrate_name: 14,15-Leukotriene A4

substrate: 14,15-Leukotriene A4


organism: Bos taurus


substrate_name: cytidine-2',3'-cyclic monophosphate

substrate: cytidine-2',3'-cyclic monophosphate


enzyme_display_name: phosphopentomutase

organism: Rattus norvegicus

substrate_name: deoxyribose 1-phosphate

enzyme: phosphopentomutase

substrate: deoxyribose 1-phosphate


substrate_name: ribose 1-phosphate

substrate: ribose 1-phosphate


enzyme_display_name: beta-phosphoglucomutase

organism: Pyrococcus sp.

substrate_name: beta-D-glucose 1-phosphate

proof_lines:
Raw SKiD Env: Temp=90°C, pH=6
Raw SKiD Env: Temp=90°C, pH=-----

enzyme: beta-phosphoglucomutase

substrate: beta-D-glucose 1-phosphate


enzyme_display_name: phosphoglucomutase (glucose-cofactor)

assay_conditions_summary: cofactor NADPH

proof_lines: direct assay with unreacted glucose 1-phosphate

proof_lines: assay coupled with glucose-6-phosphate dehydrogenase, following NADPH formation

enzyme: phosphoglucomutase (glucose-cofactor)


substrate_name: alpha-D-glucose

substrate: alpha-D-glucose


enzyme_display_name: phosphoacetylglucosamine mutase

organism: Blastocladiella emersonii

substrate_name: N-acetylglucosamine 6-phosphate

enzyme: phosphoacetylglucosamine mutase

substrate: N-acetylglucosamine 6-phosphate


enzyme_display_name: protoporphyrin ferrochelatase

substrate_name: hematoporphyrin

enzyme: protoporphyrin ferrochelatase

substrate: hematoporphyrin


organism: Euglena gracilis

substrate_name: beta-D-Glucose 1-phosphate

substrate: beta-D-Glucose 1-phosphate


organism: Senna corymbosa

substrate_name: D-mannose 1-phosphate

substrate: D-mannose 1-phosphate


substrate_name: D-mannose 6-phosphate

substrate: D-mannose 6-phosphate


organism: Pyrococcus horikoshii

proof_lines:
isoenzyme PH0923, 37°C
isoenzyme PH0923, 65°C
isoenzyme PH0923S101A, 65°C


proof_lines: 90°C, pH not specified in the publication


organism: Giardia duodenalis


organism: Mus musculus

substrate_name: prostaglandin H2

mutation_signature: Δ1

sequence_variant_note: Resolved canonical sequence from identity matching and applied mutation signature Δ1 to reconstruct the assayed variant sequence.

mutation_type: deletion

substrate: prostaglandin H2


sequence_variant_note: Resolved canonical sequence from identity matching and applied mutation signature S45A/S81A to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from identity matching and applied mutation signature H111A to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from identity matching and applied mutation signature H116A to reconstruct the assayed variant sequence.


enzyme_display_name: pancreatic ribonuclease

enzyme: pancreatic ribonuclease


substrate_name: alpha-D-mannose 1-phosphate

proof_lines: in 50 mM HEPES, pH 7.1, 5 mM MgCl2, at 30°C

substrate: alpha-D-mannose 1-phosphate


enzyme_display_name: phosphoenolpyruvate mutase

sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_mutation_ranked_match and applied mutation signature E114A with inferred residue-numbering offset -10 to reconstruct the assayed variant sequence.

enzyme: phosphoenolpyruvate mutase


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_mutation_ranked_match and applied mutation signature D58N to reconstruct the assayed variant sequence.

proof_lines:
mutant enzyme D58N, at pH 7.5 and 25°C
mutant D58N, 25°C, pH 7.5


substrate_name: cyclic 2',3'-cytidine monophosphate

sequence_variant_note: Resolved sequence already matches the mutant residue(s) after applying an inferred residue-numbering offset +26, so it is treated as a source-provided variant sequence.

proof_lines:
mutant K7H/R10H, pH 5.5, 25°C
mutant K7H/R10H, pH 7.0

substrate: cyclic 2',3'-cytidine monophosphate


proof_lines:
wild-type, pH 5.5, 25°C
wild-type, pH 7.0
wild-type, pH7.0


substrate_name: pentacytidylic acid

assay_conditions_summary: pH 7

substrate: pentacytidylic acid


organism: Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)

substrate_name: glucose 6-phosphate

proof_lines: kcat is 3000 min(-1) for glucose 1-phosphate and 1350 min(-1) for mannose 1-phosphate.

substrate: glucose 6-phosphate


substrate_name: mannose 6-phosphate

smiles: C(C(C(C(C(C=O)O)O)O)O)OP(=O)(O)O

substrate: mannose 6-phosphate


organism: Arabidopsis thaliana

column_label: Figure 4 caption reports mannose-1-phosphate reaction Km 29.7 uM for recombinant AtPMM

raw_value_unit_evidence: Figure 4 Km raw_value=29.7 raw_unit=uM

row_label: Recombinant Arabidopsis phosphomannomutase AtPMM

table_label: Wiley full text Figure 4


column_label: Figure 4 caption reports glucose-1-phosphate reaction Km 65.4 uM for recombinant AtPMM

raw_value_unit_evidence: Figure 4 Km raw_value=65.4 raw_unit=uM


organism: Homo sapiens

substrate_name: alpha-D-Glucose 1-phosphate

source_license: CC BY 4.0; SABIO-RK terms (free for academic use; see sabiork.h-its.org); CC BY-NC-ND 4.0

proof_lines:
isoform alpha-PMM1, pH 6.5, 25°C
recombinant enzyme PMM1
isoform PMM1, at pH 7.5 and 32°C

source_databases_merged: sabio_rk brenda skid uniprot

substrate: alpha-D-Glucose 1-phosphate


organism: Thermococcus kodakarensis

proof_lines: kcat is 575 sec(-1) with glucose 1-phosphate as substrate. kcat is 330 sec(-1) with mannose 1-phosphate as substrate. kcat is 190 sec(-1) with 2-deoxyribose 1-phosphate as substrate.


enzyme_display_name: phosphoglucosamine mutase

organism: Escherichia coli (strain K12)

sequence_variant_note: Source notes indicate a mutant or variant enzyme, but no machine-applicable substitution signature was available.

enzyme: phosphoglucosamine mutase


organism: Sus scrofa

substrate_name: galactose 1,6-diphosphate

substrate: galactose 1,6-diphosphate


enzyme_display_name: bisphosphoglycerate mutase

organism: Gallus gallus

substrate_name: H2O; 2,3-Bisphosphoglycerate

enzyme: bisphosphoglycerate mutase

substrate: H2O; 2,3-Bisphosphoglycerate


organism: Escherichia coli


organism: Lactococcus lactis subsp. lactis

substrate_name: H2O; 4-Nitrophenyl phosphate

substrate: H2O; 4-Nitrophenyl phosphate


substrate_name: deoxy-ribose 1-phosphate

substrate: deoxy-ribose 1-phosphate


substrate_name: 2-deoxy-D-ribose 1-phosphate

proof_lines: kcat is 173 sec(-1) (at 90 degrees Celsius).

substrate: 2-deoxy-D-ribose 1-phosphate


organism: Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)

substrate_name: Unknown

substrate: Unknown


proof_lines: Glucose-1,6-bisphosphate is essential for activity.


substrate_name: D-Glucose 1,6-bisphosphate; D-Mannose 6-phosphate


organism: Plasmodium falciparum (isolate 3D7)

sequence_variant_note: Mutation context was captured, but conflicting substitutions targeted the same residue position.

proof_lines: kcat is 0.00017 sec(-1) for the conversion of mannose 6-phosphate (M6P) to mannose 1-phosphate (M1P) in the presence of glucose-1,6-bisphosphate (G-1,6-P) (at room temperature). kcat is 0.0000078 sec(-1) for the conversion of glucose 1-phos


organism: Tetrahymena pyriformis


substrate_name: N-Acetylglucosamine 6-phosphate

substrate: N-Acetylglucosamine 6-phosphate


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature D276E to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature H65R to reconstruct the assayed variant sequence.


substrate_name: beta-D-glucose 1-phosphate (using beta-D-glucose 1,6-(bis)phosphate as an activator, at pH 8.0, 30 degrees Celsius)

sequence_variant_note: Mutation signature G1P/G6P could not be applied safely because the resolved sequence does not match the expected reference residue(s).

proof_lines: kcat is 21 sec(-1) for conversion of G1P to G6P, kcat is 0.5 sec(-1) for conversion of G6P to G1P.


sequence_variant_note: Sequence is treated as wild-type because the source explicitly marked the record as wild-type.


organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature D280A to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature D70A with inferred residue-numbering offset +7 to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature G277A to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature G499A to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature G58A to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature G72A to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature K74A to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature N66A with inferred residue-numbering offset +5 to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature P67A with inferred residue-numbering offset +11 to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature R496A to reconstruct the assayed variant sequence.


substrate_name: mannose 6-phosphate (M6P) (at room temperature)


substrate_name: glucose 1-phosphate (G1P) (at room temperature)


sequence_variant_note: Mutation signature R498A could not be applied safely because the resolved sequence does not match the expected reference residue(s).


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature T500A to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature T62A to reconstruct the assayed variant sequence.


substrate_name: beta-D-Glucose 1,6-bisphosphate

sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature H20A to reconstruct the assayed variant sequence.

column_label: Table 4. beta-PGM-catalyzed betaG1,6bisP hydrolysis kinetic constants; row L. lactis H20A / betaG1,6bisP hydrolysis; column kcat (s^-1); metric kcat; normalized value 0.0197 s^-1 | Table 4. beta-PGM-catalyzed betaG1,6bisP hydrolysis kinetic constants; row L. lactis H20A / betaG1,6bisP hydrolysis; column Km (uM); metric km; normalized value 0.0026 mM | Table 4. beta-PGM-catalyzed betaG1,6bisP hydrolysis kinetic constants; row L. lactis H20A / betaG1,6bisP hydrolysis; column Computed from exact kcat and Km cells; metric kcat_over_km; normalized value 7.5769230769230775 s^-1*mM^-1

normalized_value_unit_evidence: kcat normalized_value=0.0197 normalized_unit=s^-1; km normalized_value=0.0026 normalized_unit=mM; kcat_over_km normalized_value=7.5769230769230775 normalized_unit=s^-1*mM^-1

raw_value_unit_evidence: kcat raw_value=0.0197 raw_unit=s^-1; km raw_value=2.6 raw_unit=uM; kcat_over_km raw_value=0.0197/0.0026 raw_unit=s^-1*mM^-1; computed from explicit kcat and Km cells

substrate: beta-D-Glucose 1,6-bisphosphate


sequence_variant_note: Resolved canonical sequence from package_local_exact_accession:P71447 and applied mutation signature H20N to reconstruct the assayed variant sequence.

column_label: Table 4. beta-PGM-catalyzed betaG1,6bisP hydrolysis kinetic constants; row L. lactis H20N / betaG1,6bisP hydrolysis; column kcat (s^-1); metric kcat; normalized value 0.0303 s^-1 | Table 4. beta-PGM-catalyzed betaG1,6bisP hydrolysis kinetic constants; row L. lactis H20N / betaG1,6bisP hydrolysis; column Km (uM); metric km; normalized value 0.00149 mM | Table 4. beta-PGM-catalyzed betaG1,6bisP hydrolysis kinetic constants; row L. lactis H20N / betaG1,6bisP hydrolysis; column Computed from exact kcat and Km cells; metric kcat_over_km; normalized value 20.335570469798657 s^-1*mM^-1

normalized_value_unit_evidence: kcat normalized_value=0.0303 normalized_unit=s^-1; km normalized_value=0.00149 normalized_unit=mM; kcat_over_km normalized_value=20.335570469798657 normalized_unit=s^-1*mM^-1

raw_value_unit_evidence: kcat raw_value=0.0303 raw_unit=s^-1; km raw_value=1.49 raw_unit=uM; kcat_over_km raw_value=0.0303/0.00149 raw_unit=s^-1*mM^-1; computed from explicit kcat and Km cells


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature T16P to reconstruct the assayed variant sequence.

column_label: Table 4. beta-PGM-catalyzed betaG1,6bisP hydrolysis kinetic constants; row L. lactis T16P / betaG1,6bisP hydrolysis; column kcat (s^-1); metric kcat; normalized value 0.38 s^-1 | Table 4. beta-PGM-catalyzed betaG1,6bisP hydrolysis kinetic constants; row L. lactis T16P / betaG1,6bisP hydrolysis; column Km (uM); metric km; normalized value 0.010 mM | Table 4. beta-PGM-catalyzed betaG1,6bisP hydrolysis kinetic constants; row L. lactis T16P / betaG1,6bisP hydrolysis; column Computed from exact kcat and Km cells; metric kcat_over_km; normalized value 38.0 s^-1*mM^-1

normalized_value_unit_evidence: kcat normalized_value=0.38 normalized_unit=s^-1; km normalized_value=0.010 normalized_unit=mM; kcat_over_km normalized_value=38.0 normalized_unit=s^-1*mM^-1

raw_value_unit_evidence: kcat raw_value=0.38 raw_unit=s^-1; km raw_value=10 raw_unit=uM; kcat_over_km raw_value=0.38/0.010 raw_unit=s^-1*mM^-1; computed from explicit kcat and Km cells


substrate_name: beta-D-Glucose 1-phosphate

column_label: Table 2. Steady state kinetic constants for wild type and mutant beta-PGM; row L. lactis H20A / betaG1P mutase reaction; column kcat (s^-1); metric kcat; normalized value 0.026 s^-1 | Table 2. Steady state kinetic constants for wild type and mutant beta-PGM; row L. lactis H20A / betaG1P mutase reaction; column Km (uM); metric km; normalized value 0.041 mM | Table 2. Steady state kinetic constants for wild type and mutant beta-PGM; row L. lactis H20A / betaG1P mutase reaction; column Computed from exact kcat and Km cells; metric kcat_over_km; normalized value 0.6341463414634145 s^-1*mM^-1

normalized_value_unit_evidence: kcat normalized_value=0.026 normalized_unit=s^-1; km normalized_value=0.041 normalized_unit=mM; kcat_over_km normalized_value=0.6341463414634145 normalized_unit=s^-1*mM^-1

raw_value_unit_evidence: kcat raw_value=0.026 raw_unit=s^-1; km raw_value=41 raw_unit=uM; kcat_over_km raw_value=0.026/0.041 raw_unit=s^-1*mM^-1; computed from explicit kcat and Km cells

substrate: beta-D-Glucose 1-phosphate


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P71447 and applied mutation signature H20N to reconstruct the assayed variant sequence.

column_label: Table 2. Steady state kinetic constants for wild type and mutant beta-PGM; row L. lactis H20N / betaG1P mutase reaction; column kcat (s^-1); metric kcat; normalized value 0.62 s^-1 | Table 2. Steady state kinetic constants for wild type and mutant beta-PGM; row L. lactis H20N / betaG1P mutase reaction; column Km (uM); metric km; normalized value 0.170 mM | Table 2. Steady state kinetic constants for wild type and mutant beta-PGM; row L. lactis H20N / betaG1P mutase reaction; column Computed from exact kcat and Km cells; metric kcat_over_km; normalized value 3.6470588235294117 s^-1*mM^-1

normalized_value_unit_evidence: kcat normalized_value=0.62 normalized_unit=s^-1; km normalized_value=0.170 normalized_unit=mM; kcat_over_km normalized_value=3.6470588235294117 normalized_unit=s^-1*mM^-1

raw_value_unit_evidence: kcat raw_value=0.62 raw_unit=s^-1; km raw_value=170 raw_unit=uM; kcat_over_km raw_value=0.62/0.170 raw_unit=s^-1*mM^-1; computed from explicit kcat and Km cells


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P71447 and applied mutation signature H20Q to reconstruct the assayed variant sequence.

column_label: Table 2. Steady state kinetic constants for wild type and mutant beta-PGM; row L. lactis H20Q / betaG1P mutase reaction; column kcat (s^-1); metric kcat; normalized value 21.9 s^-1 | Table 2. Steady state kinetic constants for wild type and mutant beta-PGM; row L. lactis H20Q / betaG1P mutase reaction; column Km (uM); metric km; normalized value 0.045 mM | Table 2. Steady state kinetic constants for wild type and mutant beta-PGM; row L. lactis H20Q / betaG1P mutase reaction; column Computed from exact kcat and Km cells; metric kcat_over_km; normalized value 486.66666666666663 s^-1*mM^-1

normalized_value_unit_evidence: kcat normalized_value=21.9 normalized_unit=s^-1; km normalized_value=0.045 normalized_unit=mM; kcat_over_km normalized_value=486.66666666666663 normalized_unit=s^-1*mM^-1

raw_value_unit_evidence: kcat raw_value=21.9 raw_unit=s^-1; km raw_value=45 raw_unit=uM; kcat_over_km raw_value=21.9/0.045 raw_unit=s^-1*mM^-1; computed from explicit kcat and Km cells


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature K76A to reconstruct the assayed variant sequence.

column_label: Table 2. Steady state kinetic constants for wild type and mutant beta-PGM; row L. lactis K76A / betaG1P mutase reaction; column kcat (s^-1); metric kcat; normalized value 1.56 s^-1 | Table 2. Steady state kinetic constants for wild type and mutant beta-PGM; row L. lactis K76A / betaG1P mutase reaction; column Km (uM); metric km; normalized value 0.066 mM | Table 2. Steady state kinetic constants for wild type and mutant beta-PGM; row L. lactis K76A / betaG1P mutase reaction; column Computed from exact kcat and Km cells; metric kcat_over_km; normalized value 23.636363636363637 s^-1*mM^-1

normalized_value_unit_evidence: kcat normalized_value=1.56 normalized_unit=s^-1; km normalized_value=0.066 normalized_unit=mM; kcat_over_km normalized_value=23.636363636363637 normalized_unit=s^-1*mM^-1

raw_value_unit_evidence: kcat raw_value=1.56 raw_unit=s^-1; km raw_value=66 raw_unit=uM; kcat_over_km raw_value=1.56/0.066 raw_unit=s^-1*mM^-1; computed from explicit kcat and Km cells


column_label: Table 2. Steady state kinetic constants for wild type and mutant beta-PGM; row L. lactis T16P / betaG1P mutase reaction; column kcat (s^-1); metric kcat; normalized value 0.026 s^-1 | Table 2. Steady state kinetic constants for wild type and mutant beta-PGM; row L. lactis T16P / betaG1P mutase reaction; column Km (uM); metric km; normalized value 0.0048 mM | Table 2. Steady state kinetic constants for wild type and mutant beta-PGM; row L. lactis T16P / betaG1P mutase reaction; column Computed from exact kcat and Km cells; metric kcat_over_km; normalized value 5.416666666666667 s^-1*mM^-1

normalized_value_unit_evidence: kcat normalized_value=0.026 normalized_unit=s^-1; km normalized_value=0.0048 normalized_unit=mM; kcat_over_km normalized_value=5.416666666666667 normalized_unit=s^-1*mM^-1

raw_value_unit_evidence: kcat raw_value=0.026 raw_unit=s^-1; km raw_value=4.8 raw_unit=uM; kcat_over_km raw_value=0.026/0.0048 raw_unit=s^-1*mM^-1; computed from explicit kcat and Km cells


sequence_variant_note: Sequence is treated as wild-type because the source explicitly marked the record as wild-type.

proof_lines:
Raw SKiD Env: Temp=25°C, pH=6.5
Raw SKiD Env: Temp=32°C, pH=7.5

source_databases_merged: sabio_rk skid uniprot


substrate_name: alpha-D-Mannose 1-phosphate

substrate: alpha-D-Mannose 1-phosphate


substrate_name: D-glucosamine 1-phosphate

substrate: D-glucosamine 1-phosphate


substrate_name: D-glucose 1-phosphate

substrate: D-glucose 1-phosphate


substrate_name: fructose 1,6-diphosphate

substrate: fructose 1,6-diphosphate


substrate_name: glucose 1,6-diphosphate

substrate: glucose 1,6-diphosphate


organism: Galdieria sulphuraria

proof_lines: Glucose-1,6-bisphosphate or mannose-1,6-biphosphate are essential for activity.


organism: Saccharomyces cerevisiae

substrate_name: D-Ribose 1-phosphate

sequence_variant_note: Sequence identity was resolved, but no explicit wild-type or mutant call was captured.

column_label: Table 3 row Pgm3 under ribose-1-phosphate has Vmax, km, and kcat/km columns; values are 0.29, 750, and 0.46 respectively

raw_value_unit_evidence: Ribose-1-phosphate columns report Vmax=0.29 +/- 0.06 umol/(min mgprot), km=750 +/- 35 uM, kcat/km=0.46

row_label: Pgm3 / ribose-1-phosphate

source_databases_merged: sabio_rk brenda uniprot

substrate: D-Ribose 1-phosphate


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature G46A to reconstruct the assayed variant sequence.


sequence_variant_note: Mutation signature G46P could not be applied safely because the resolved sequence does not match the expected reference residue(s).


sequence_variant_note: Mutation signature G46V could not be applied safely because the resolved sequence does not match the expected reference residue(s).


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature K45A to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature K45R to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature R49A to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature R49K to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature S52A to reconstruct the assayed variant sequence.


substrate_name: beta-D-glucose 1,6-(bis)phosphate

sequence_variant_note: Mutation signature G1P/G6P could not be applied safely because the resolved sequence does not match the expected reference residue(s).

substrate: beta-D-glucose 1,6-(bis)phosphate


organism: Mytilus edulis

sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_mutation_ranked_match and applied mutation signature L124A to reconstruct the assayed variant sequence.

proof_lines:
mutant L124A, pH 7.5, 25°C
mutant enzyme L124A, at pH 7.5 and 25°C


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_mutation_ranked_match and applied mutation signature K120R to reconstruct the assayed variant sequence.

proof_lines:
mutant K120R, pH 7.5, 25°C
mutant enzyme K120R, at pH 7.5 and 25°C


substrate_name: Phosphonopyruvate

mutation_signature: truncated enzyme truncated enzyme

sequence_variant_note: Mutation context was captured, but the signature could not be translated into an exact residue substitution safely.

mutation_type: truncation

substrate: Phosphonopyruvate


mutation_signature: truncated enzyme


substrate_name: 2-Deoxy-D-ribose 1-phosphate

substrate: 2-Deoxy-D-ribose 1-phosphate


substrate_name: Ribose 1-phosphate

substrate: Ribose 1-phosphate


substrate_name: alpha-D-glucose 1-phosphate

substrate: alpha-D-glucose 1-phosphate


substrate_name: 2-deoxyribose 1-phosphate

substrate: 2-deoxyribose 1-phosphate


proof_lines: GlmM was also capable of catalysing the interconversion of glucose-1-phosphate and glucose-6-phosphate isomers


substrate_name: ATP

assay_conditions_summary: cofactor ATP

substrate: ATP


organism: Triticum aestivum

substrate_name: alpha-D-mannose 1-phosphate

proof_lines: isoform PMM-D1, 30°C, pH not specified in the publication

proof_lines: isoform PMM-A1, 37°C, pH not specified in the publication

proof_lines: isoform PMM-D2, 30°C, pH not specified in the publication

substrate: alpha-D-mannose 1-phosphate


substrate_name: D-Glucosamine 1-phosphate

proof_lines: GlmM interconverts glucosamine-6-phosphate and glucosamine-1-phosphate

substrate: D-Glucosamine 1-phosphate


substrate_name: D-Glucosamine 6-phosphate

substrate: D-Glucosamine 6-phosphate


substrate_name: beta-D-Glucose 1-phosphate

proof_lines: GlmM also catalyzes glucose-1-phosphate and glucose-6-phosphate isomerization

substrate: beta-D-Glucose 1-phosphate


substrate_name: Glucosamine 1,6-diphosphate

proof_lines: GlcN-1,6-diphosphate intermediate in the GlmM mechanism

substrate: Glucosamine 1,6-diphosphate


substrate_name: Glucose 1,6-diphosphate

proof_lines: Glc-1,6-diphosphate-dependent low-activity phosphoglucomutase activity

substrate: Glucose 1,6-diphosphate


source_license: SABIO-RK terms (free for academic use; see sabiork.h-its.org); CC BY-NC-ND 4.0


substrate_name: 4-Nitrophenyl phosphate

normalized_value_unit_evidence: kcat: printed (1.78 ( 0.01) × 10-2 s-1 is (1.78 +/- 0.01) x 10^-2 s^-1 = 0.0178 s^(-1); the export stores kcat at three decimal places, and 0.0178 rounds to the stored 0.018 s^(-1), a precision-only difference. Km: printed 14.3 ( 0.3 mM is 14.3 +/- 0.3 mM = 14.3 mM exactly as stored. kcat/Km: the paper prints no efficiency ratio for pNPP; the export value is the quotient of the export-stored kcat and the printed Km, 0.018 s^-1 / 14.3 mM = 0.0012587412587412585 s^-1 mM^-1. The same quotient computed from the fully printed kcat, 0.0178 / 14.3 = 0.0012447552447552448 s^-1 mM^-1, agrees with it once the kcat is taken at the export's stored precision; the gap is printed precision only. OCR quirks: ) renders =, ( renders +/-, × 10-2 is x 10^-2, s-1 is s^-1.

raw_value_unit_evidence: Results sentence on p 9413 (section: Specificity of Phospho-beta-PGM for the Phosphoryl Group Acceptor): the steady-state constants measured using 2 uM beta-PGM in 2 mM MgCl2 and 50 mM K+Hepes (pH 7.0 and 25 C) read kcat = (1.78 +/- 0.01) x 10^-2 s^-1 and pNPP Km = 14.3 +/- 0.3 mM. In the OCR text the sentence is split across the two right-column lines `follows: kcat ) (1.78 ( 0.01) × 10-2 s-1 and pNPP Km )` and `14.3 ( 0.3 mM.`, interleaved with the left-column line `phosphatase because of its ability to discriminate between`. The BT4131 values printed directly after (kcat 8.3 x 10-2 s-1, Km 0.77 mM) belong to the different enzyme BT4131 at 37 C and are not used.

substrate: 4-Nitrophenyl phosphate


substrate_name: Acetyl phosphate

smiles: CC(=O)OP(=O)(O)O

normalized_value_unit_evidence: kcat: printed 16.6 ( 0.3 s-1 is 16.6 +/- 0.3 s^-1 = 16.6 s^(-1) exactly as stored. Km: printed 800 ( 30 µM is 800 +/- 30 uM = 0.8 mM (1 uM = 0.001 mM), exactly as stored. kcat/Km: the paper prints no efficiency ratio for acetyl phosphate; the export value is the quotient of this sentence's own printed values, 16.6 s^-1 / 0.8 mM = 20.75 s^-1 mM^-1. OCR quirks: ) renders =, ( renders +/-, s-1 is s^-1, µM is uM.

raw_value_unit_evidence: Results sentence on p 9412 (Figure 6C context): the steady-state kinetic constants for acetyl phosphate read kcat = 16.6 +/- 0.3 s^-1 and Km = 800 +/- 30 uM. In the OCR text the sentence spans the two right-column lines `the steady-state kinetic constants (kcat ) 16.6 ( 0.3 s-1 and` and `Km ) 800 ( 30 µM) for acetyl phosphate were derived from`, interleaved with the left-column line `illustrated by the kinetic plot measured with R-G16P (Figure`.

substrate: Acetyl phosphate


substrate_name: alpha-D-Glucose 1,6-bisphosphate

normalized_value_unit_evidence: kcat: Table 2 wild-type cell 17.1 ( 0.6 is 17.1 +/- 0.6 s^-1 = 17.1 s^(-1) exactly as stored; the Figure 6A prose prints the same turnover as 17 s^-1 at its own two-figure precision. Km: printed `a Km of 20 µM ... for the activator R-G16P` is 20 uM = 0.02 mM (1 uM = 0.001 mM), exactly as stored. kcat/Km: the paper prints no efficiency ratio for R-G16P; the export value is the quotient 17.1 s^-1 / 0.02 mM = 855.0 s^-1 mM^-1. OCR quirks: R- renders the Greek alpha (R-G16P is alpha-D-glucose 1,6-bisphosphate, defined in the abbreviations footnote), ( renders +/-, s-1 is s^-1, µM is uM; the prose segment interleaves the right-column line `a separate set of initial velocity data measured over a range` between the two left-column fragments.

raw_value_unit_evidence: Two mutually consistent printed locations for the same wild-type R-G16P-activated measurement context. (1) Results prose, Figure 6A bi-bi ping-pong fit: `Data fitting defined a kcat of 17 s-1 and a Km of 20 µM` ... `for the activator R-G16P.` - Km for the activator R-G16P = 20 uM and kcat = 17 s^-1. (2) Table 2: Kinetic Constants for Wild-Type and Mutant beta-PGMs (in the presence of 50 uM R-G16P as the activator), header `enzyme Km-Mg2+ (µM) Km-G1P (µM) kcat (s-1)`, row `wild type 270 ( 20 14.6 ( 0.5 17.1 ( 0.6` - the wild-type kcat cell reads 17.1 +/- 0.6 s^-1. The exported kcat is the Table 2 cell 17.1 s^-1; the prose kcat 17 s^-1 is the same turnover number printed at two significant figures.

row_label: wild type

table_label: Table 2: Kinetic Constants for Wild-Type and Mutant β-PGMs (in the presence of 50 µM R-G16P as the activator)

substrate: alpha-D-Glucose 1,6-bisphosphate


normalized_value_unit_evidence: Km: Table 2 wild-type Km-Mg2+ cell 270 ( 20 is 270 +/- 20 uM = 0.27 mM (1 uM = 0.001 mM), exactly as stored. kcat: Table 2 wild-type kcat cell 17.1 ( 0.6 is 17.1 +/- 0.6 s^-1 = 17.1 s^(-1), exactly as stored. kcat/Km: the paper prints no efficiency ratio for Mg2+ activation; the export value is the quotient of this row's own printed cells, 17.1 s^-1 / 0.27 mM = 63.333333333333336 s^-1 mM^-1. OCR quirks: ( renders +/-, s-1 is s^-1, µM is uM.

raw_value_unit_evidence: Table 2: Kinetic Constants for Wild-Type and Mutant beta-PGMs (in the presence of 50 uM R-G16P as the activator) | header row: `enzyme Km-Mg2+ (µM) Km-G1P (µM) kcat (s-1)` | row: `wild type 270 ( 20 14.6 ( 0.5 17.1 ( 0.6` | wild-type cells read: Km-Mg2+ = 270 +/- 20 uM; Km-G1P = 14.6 +/- 0.5 uM; kcat = 17.1 +/- 0.6 s^-1. Corroborating Results prose (Figure 5): `apparent Km for Mg2+ of 270 ( 20 µM` - an apparent Km for Mg2+ of 270 +/- 20 uM.


organism: Lactococcus lactis subsp. lactis (strain IL1403)

substrate_name: alpha-D-glucose 1,6-bisphosphate (at pH 7 and 25 degrees Celsius)


substrate_name: magnesium (at pH 7 and 25 degrees Celsius)

smiles: [Mg]


substrate_name: acetyl-phosphate (at pH 7 and 25 degrees Celsius)


organism: Pseudomonas aeruginosa

substrate_name: D-Mannose 1-phosphate

proof_lines: kcat is 3000 min(-1) for glucose 1-phosphate and 1350 min(-1) for mannose 1-phosphate.

substrate: D-Mannose 1-phosphate


substrate_name: Glycerate 1,3-bisphosphate

substrate: Glycerate 1,3-bisphosphate


organism: Homo sapiens

substrate_name: alpha-D-Ribose 1-phosphate

substrate: alpha-D-Ribose 1-phosphate


organism: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

substrate_name: glucose 1-phosphate

substrate: glucose 1-phosphate


column_label: Table 1. Apparent kinetic constants for YcjM (pH 6.5), YcjT (pH 7.5), and YcjU (pH 8.0) at 30 C; row YcjU / beta-D-glucose-1-P; fixed substrate none; columns kcat column raw 21 +/- 1 normalized 21 s^-1; Km column raw 0.018 +/- 0.001 normalized 0.018 mM; kcat/Km column raw (1.1 +/- 0.1) x 10^6 M^-1 s^-1 normalized from same-row kcat and Km as 1166.6666666666667 s^-1*mM^-1; export values for required/current metrics match these normalized values.

normalized_value_unit_evidence: kcat normalized_value=21 normalized_unit=s^-1; Km normalized_value=0.018 normalized_unit=mM; kcat/Km normalized_value=1166.6666666666667 normalized_unit=s^-1*mM^-1 from same-row kcat and Km; printed efficiency=(1.1 +/- 0.1) x 10^6 M^-1 s^-1

raw_value_unit_evidence: kcat raw_value=21 +/- 1 raw_unit=s^-1; Km raw_value=0.018 +/- 0.001 raw_unit=mM; kcat/Km raw_value=(1.1 +/- 0.1) x 10^6 M^-1 s^-1 raw_unit=M^-1 s^-1


substrate_name: D-Glucose 6-phosphate

column_label: Table 1. Apparent kinetic constants for YcjM (pH 6.5), YcjT (pH 7.5), and YcjU (pH 8.0) at 30 C; row YcjU / D-glucose-6-P; fixed substrate none; columns kcat column raw 0.5 +/- 0.1 normalized 0.5 s^-1; Km column raw 1.19 +/- 0.04 normalized 1.19 mM; kcat/Km column raw (4.2 +/- 0.1) x 10^2 M^-1 s^-1 normalized from same-row kcat and Km as 0.42016806722689076 s^-1*mM^-1; export values for required/current metrics match these normalized values.

normalized_value_unit_evidence: kcat normalized_value=0.5 normalized_unit=s^-1; Km normalized_value=1.1900000000000002 normalized_unit=mM; kcat/Km normalized_value=0.4201680672268907 normalized_unit=s^-1*mM^-1 from same-row kcat and Km; printed efficiency=(4.2 +/- 0.1) x 10^2 M^-1 s^-1

raw_value_unit_evidence: kcat raw_value=0.5 +/- 0.1 raw_unit=s^-1; Km raw_value=1.19 +/- 0.04 raw_unit=mM; kcat/Km raw_value=(4.2 +/- 0.1) x 10^2 M^-1 s^-1 raw_unit=M^-1 s^-1

substrate: D-Glucose 6-phosphate


substrate_name: beta-D-Allose 1-phosphate

substrate: beta-D-Allose 1-phosphate


substrate_name: beta-D-glucose 1-phosphate

substrate: beta-D-glucose 1-phosphate


substrate_name: beta-D-glucose 6-phosphate

normalized_value_unit_evidence: kcat normalized_value=0.5 normalized_unit=s^-1; Km normalized_value=1.19 normalized_unit=mM; kcat/Km normalized_value=0.42016806722689076 normalized_unit=s^-1*mM^-1 from same-row kcat and Km; printed efficiency=(4.2 +/- 0.1) x 10^2 M^-1 s^-1

row_label: YcjU / D-glucose-6-P; fixed substrate none

table_label: Table 1. Apparent kinetic constants for YcjM (pH 6.5), YcjT (pH 7.5), and YcjU (pH 8.0) at 30 C

substrate: beta-D-glucose 6-phosphate


organism: Escherichia coli (strain K12)

substrate_name: ribose 1-phosphate

substrate: ribose 1-phosphate


organism: Thermotoga maritima

substrate_name: alpha-D-ribose 5-phosphate

proof_lines:
at pH 7.5 and 60°C
at pH 7.5 and 90°C

substrate: alpha-D-ribose 5-phosphate


organism: Gallus gallus


substrate_name: beta-D-Glucose 1,6-bisphosphate

substrate: beta-D-Glucose 1,6-bisphosphate


substrate_name: D-glucose 1-phosphate

substrate: D-glucose 1-phosphate


sequence_variant_note: Mutation context is present, but no sequence was resolved for this record.


proof_lines:
R247A mutant
mutant R247A


sequence_variant_note: No sequence was resolved for this record, so variant-aware sequence handling could not be applied.


substrate_name: D-Ribose 1-phosphate

substrate: D-Ribose 1-phosphate


substrate_name: alpha-D-glucose 1-phosphate

substrate: alpha-D-glucose 1-phosphate


substrate_name: Unknown

proof_lines:
at pH 7.0 and 25°C
Ki about 0.2 mM, at pH 7.0 and 25°C

substrate: Unknown


substrate_name: Ribose 5-phosphate

smiles: C(C(C(C(C=O)O)O)O)OP(=O)(O)O

substrate: Ribose 5-phosphate


substrate_name: phosphoenolpyruvate

column_label: Abstract states PEP mutase catalyzed conversion of PEP to P-pyr at pH 7.5 and 25 degrees C has Km = 0.77 +/- 0.05 mM.

raw_value_unit_evidence: Km raw_value=0.77 +/- 0.05 raw_unit=mM

row_label: Tetrahymena pyriformis PEP mutase with phosphoenolpyruvate

table_label: PubMed abstract PMID 8605214

substrate: phosphoenolpyruvate


proof_lines: mutant enzyme E325A, at 25°C in 50 mM MOPS (pH 7.4) with 1 mM dithiothreitol, 1.5 mM MgSO4


proof_lines: mutant enzyme Y17A, at 25°C in 50 mM MOPS (pH 7.4) with 1 mM dithiothreitol, 1.5 mM MgSO4


proof_lines: mutant enzyme R262A/P368G, at 25°C in 50 mM MOPS (pH 7.4) with 1 mM dithiothreitol, 1.5 mM MgSO4


proof_lines: mutant enzyme R262A, at 25°C in 50 mM MOPS (pH 7.4) with 1 mM dithiothreitol, 1.5 mM MgSO4


proof_lines: mutant enzyme P368A, at 25°C in 50 mM MOPS (pH 7.4) with 1 mM dithiothreitol, 1.5 mM MgSO4


proof_lines: mutant enzyme P368G, at 25°C in 50 mM MOPS (pH 7.4) with 1 mM dithiothreitol, 1.5 mM MgSO4


proof_lines: mutant enzyme S369A, at 25°C in 50 mM MOPS (pH 7.4) with 1 mM dithiothreitol, 1.5 mM MgSO4


proof_lines: wild type enzyme, at 25°C in 50 mM MOPS (pH 7.4) with 1 mM dithiothreitol, 1.5 mM MgSO4


organism: Escherichia coli


proof_lines:
single-mutation S100T
single mutation S100T


substrate_name: D-glucosamine 6-phosphate

substrate: D-glucosamine 6-phosphate


substrate_name: D-glucosamine 1-phosphate

substrate: D-glucosamine 1-phosphate


substrate_name: D-glucosamine 1,6-diphosphate

substrate: D-glucosamine 1,6-diphosphate


substrate_name: D-Glucose 1,6-bisphosphate

substrate: D-Glucose 1,6-bisphosphate


organism: Lactococcus lactis subsp. lactis


substrate_name: beta-D-Glucose 1-phosphate

substrate: beta-D-Glucose 1-phosphate


organism: Mus musculus

substrate_name: glucose-1,6-bisphosphate in the presence of 1 uM IMP


organism: Aspergillus fumigatus


substrate_name: alpha-D-mannose 1-phosphate

substrate: alpha-D-mannose 1-phosphate


substrate_name: beta-D-glucose 6-phosphate


substrate_name: beta-D-glucose 1-phosphate

substrate: beta-D-glucose 1-phosphate


organism: Arabidopsis thaliana

proof_lines:
mutant enzyme G7R/R37Q, at 18°C
mutant enzyme G7R/R37Q, at 28°C


proof_lines:
mutant enzyme R37Q, at 18°C
mutant enzyme R37Q, at 28°C


proof_lines:
wild type enzyme, at 18°C
wild type enzyme, at 28°C


proof_lines:
mutant enzyme G7R, at 18°C
mutant enzyme G7R, at 28°C


enzyme_display_name: selenocysteine lyase

organism: Citrobacter freundii

substrate_name: L-selenocysteine

smiles: C(C(C(=O)O)N)[SeH]

enzyme: selenocysteine lyase

substrate: L-selenocysteine


substrate_name: beta-chloro-L-alanine

smiles: C(C(C(=O)O)N)Cl

substrate: beta-chloro-L-alanine


organism: Zea mays

substrate_name: D-Glucose 1-phosphate

proof_lines: 25°C, pH 7.6, substrate inhibition at high concentrations

substrate: D-Glucose 1-phosphate


substrate_name: alpha-D-Glucose 1,6-bisphosphate

substrate: alpha-D-Glucose 1,6-bisphosphate


substrate_name: D-Mannose 1-phosphate

substrate: D-Mannose 1-phosphate


proof_lines: wild-type, heterodimer, room temperature


proof_lines:
mutant enzyme R159A, at pH 7.5 and 25°C
mutant R159A, 25°C, pH 7.5


proof_lines:
mutant enzyme H190A, at pH 7.5 and 25°C
mutant H190A, 25°C, pH 7.5


proof_lines:
mutant enzyme N122D, at pH 7.5 and 25°C
mutant N122D, 25°C, pH 7.5


proof_lines:
wild type enzyme, at pH 7.5 and 25°C
wild-type, pH 7.5, 25°C


substrate_name: poly(A)poly(U)

proof_lines:
ADA mutant
PE3 variant, pH 5.5, 25°C
PE3I2 variant, pH 5.5, 25°C

substrate: poly(A)poly(U)


organism: Lactococcus lactis


enzyme_display_name: prostaglandin-E synthase

substrate_name: prostaglandin H2

enzyme: prostaglandin-E synthase

substrate: prostaglandin H2


enzyme_display_name: dichloromethane dehalogenase

organism: Hyphomicrobium sp.

substrate_name: Diiodomethane

smiles: C(I)I

enzyme: dichloromethane dehalogenase

substrate: Diiodomethane


substrate_name: Dibromomethane

smiles: C(Br)Br

substrate: Dibromomethane


organism: Malus domestica

substrate_name: S-methyl-L-methionine

smiles: C[S+](C)CCC(C(=O)O)N

substrate: S-methyl-L-methionine


substrate_name: L-alanine

smiles: CC(C(=O)O)N

substrate: L-alanine


substrate_name: L-Vinylglycine

smiles: C=CC(C(=O)O)N

proof_lines:
inactivation
deamination
alpha-ketobutyrate production

substrate: L-Vinylglycine


enzyme_display_name: leukotriene-C4 synthase

substrate_name: leukotriene A4

proof_lines: pH 7.8, temperature not specified in the publication, recombinant enzyme

enzyme: leukotriene-C4 synthase

substrate: leukotriene A4


substrate_name: glutathione

smiles: C(CC(=O)NC(CS)C(=O)NCC(=O)O)C(C(=O)O)N

substrate: glutathione


substrate_name: Unknown

substrate: Unknown


enzyme_display_name: UniProt Q86N96

organism: Leishmania mexicana

enzyme: UniProt Q86N96


enzyme_display_name: L-lysine 2,3-aminomutase

organism: Bacillus subtilis (strain 168)

substrate_name: L-lysine

smiles: C(CCN)CC(C(=O)O)N

enzyme: L-lysine 2,3-aminomutase

substrate: L-lysine


enzyme_display_name: UniProt E3PY96

organism: Acetoanaerobium sticklandii

substrate_name: D-ornithine

smiles: C(CC(C(=O)O)N)CN

enzyme: UniProt E3PY96

substrate: D-ornithine


enzyme_display_name: methionine gamma-lyase

substrate_name: L-cystathionine

smiles: C(CSCC(C(=O)O)N)C(C(=O)O)N

enzyme: methionine gamma-lyase

substrate: L-cystathionine


substrate_name: L-cysteine

smiles: C(C(C(=O)O)N)S

substrate: L-cysteine


substrate_name: L-methionine

smiles: CSCCC(C(=O)O)N

substrate: L-methionine


enzyme_display_name: cysteine-S-conjugate beta-lyase

organism: Pseudomonas sp. 'cruciviae'

substrate_name: pyridoxal phosphate

enzyme: cysteine-S-conjugate beta-lyase

substrate: pyridoxal phosphate


substrate_name: S-methyl-L-cysteine

smiles: CSCC(C(=O)O)N

substrate: S-methyl-L-cysteine


substrate_name: S-methyl-L-cysteine sulfoxide

smiles: CS(=O)CC(C(=O)O)N

substrate: S-methyl-L-cysteine sulfoxide


organism: Pseudomonas putida

substrate_name: Se-methyl-L-selenocysteine

smiles: C[Se]CC(C(=O)O)N

substrate: Se-methyl-L-selenocysteine


substrate_name: O-methyl-L-serine

smiles: COCC(C(=O)O)N

substrate: O-methyl-L-serine


organism: Rattus norvegicus

proof_lines: mitochondria cytoplasm


substrate_name: beta-chloroalanine

substrate: beta-chloroalanine


substrate_name: protoporphyrin IX

assay_conditions_summary: pH 8

proof_lines: mutant enzyme F283L, at pH 8.0, temperature not specified in the publication

substrate: protoporphyrin IX


proof_lines: mutant enzyme H287L, at pH 8.0, temperature not specified in the publication


organism: Sus scrofa

substrate_name: Glycerate 3-phosphate

proof_lines:
MB-type and BB-type isozymes
MM-type isozyme

substrate: Glycerate 3-phosphate


enzyme_display_name: lysine 5,6-aminomutase

organism: Porphyromonas gingivalis

substrate_name: (S)-lysine

proof_lines: pH and temperature not specified in the publication

enzyme: lysine 5,6-aminomutase

substrate: (S)-lysine


substrate_name: (S)-beta-lysine

smiles: C(CC(CC(=O)O)N)CN

substrate: (S)-beta-lysine


organism: Plasmodium falciparum


organism: Zymomonas mobilis


substrate_name: L-homoserine

smiles: C(CO)C(C(=O)O)N

substrate: L-homoserine


substrate_name: DL-homocysteine

substrate: DL-homocysteine


organism: Tetrahymena pyriformis

substrate_name: Phosphonopyruvate

substrate: Phosphonopyruvate


enzyme_display_name: D-ornithine 4,5-aminomutase

substrate_name: D-ornithine

sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_mutation_ranked_match and applied mutation signature H225A with inferred residue-numbering offset -3 to reconstruct the assayed variant sequence.

enzyme: D-ornithine 4,5-aminomutase

substrate: D-ornithine


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_mutation_ranked_match and applied mutation signature H225Q with inferred residue-numbering offset -3 to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:E3PY95 and applied mutation signature E81A to reconstruct the assayed variant sequence.

assay_conditions_summary: pH 8.5; 298.15 K; buffer and pH stated in its Fig

column_label: Table 1: Summary of steady-state kinetic parameters for OAM and its active site variants with substrate D-ornithine and inhibitor 2,4-diaminobutyrate (BBA - Proteins and Proteomics 2017, 1865:1077-1084); Enzyme row 'E81A': column 'kcat (s-1)' = 0.013; column 'Km (uM)' = 780; column 'kcat/Km x 103 (s-1 M-1)' = 0.016; column 'Ki (DABA) (uM)' = ND. The efficiency column is printed in units of 10^3 s-1 M-1, which is the same size as 1 s-1 mM-1.

normalized_value_unit_evidence: kcat: printed Table 1 cell 0.013 s-1; the printed unit is already s^(-1), no unit conversion applies; the paper value is 0.013 s^(-1); the exported value is 0.013 s^(-1). Km: printed Table 1 cell 780 uM; 780 / 1000 = 0.78 mM; the exported value is 0.78 mM. kcat/Km: printed Table 1 cell 0.016 in units of 10^3 s-1 M-1, that is 16 s-1 M-1; 1 s-1 M-1 is 0.001 s-1 mM-1, so the printed cell becomes 0.016 s^(-1)*mM^(-1), and the full-precision quotient of the same two printed component cells is 0.013 / 0.78 = 0.016666666666666666 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table 1, Enzyme row 'E81A': kcat = 0.013 s-1; Km = 780 uM; printed kcat/Km = 0.016 in the column's units of 10^3 s-1 M-1.

row_label: Table 1, Enzyme row 'E81A', the printed kcat, Km and kcat/Km cells of that row


sequence_variant_note: Resolved sequence already matches the mutant residue(s), so it is treated as a source-provided variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:E3PY95 and applied mutation signature Y160F to reconstruct the assayed variant sequence.

assay_conditions_summary: pH 8.5; buffer and pH stated in its Fig

column_label: Table 1: Summary of steady-state kinetic parameters for OAM and its active site variants with substrate D-ornithine and inhibitor 2,4-diaminobutyrate (BBA - Proteins and Proteomics 2017, 1865:1077-1084); Enzyme row 'Y160F': column 'kcat (s-1)' = 0.027; column 'Km (uM)' = 140; column 'kcat/Km x 103 (s-1 M-1)' = 0.19; column 'Ki (DABA) (uM)' = 2000 uM. The efficiency column is printed in units of 10^3 s-1 M-1, which is the same size as 1 s-1 mM-1.

normalized_value_unit_evidence: kcat: printed Table 1 cell 0.027 s-1; the printed unit is already s^(-1), no unit conversion applies; the paper value is 0.027 s^(-1); the exported value is 0.027 s^(-1). Km: printed Table 1 cell 140 uM; 140 / 1000 = 0.14 mM; the exported value is 0.14 mM. kcat/Km: printed Table 1 cell 0.19 in units of 10^3 s-1 M-1, that is 190 s-1 M-1; 1 s-1 M-1 is 0.001 s-1 mM-1, so the printed cell becomes 0.19 s^(-1)*mM^(-1), and the full-precision quotient of the same two printed component cells is 0.027 / 0.14 = 0.19285714285714284 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table 1, Enzyme row 'Y160F': kcat = 0.027 s-1; Km = 140 uM; printed kcat/Km = 0.19 in the column's units of 10^3 s-1 M-1.

row_label: Table 1, Enzyme row 'Y160F', the printed kcat, Km and kcat/Km cells of that row


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:E3PY95 and applied mutation signature S162A to reconstruct the assayed variant sequence.

column_label: Table 1: Summary of steady-state kinetic parameters for OAM and its active site variants with substrate D-ornithine and inhibitor 2,4-diaminobutyrate (BBA - Proteins and Proteomics 2017, 1865:1077-1084); Enzyme row 'S162A': column 'kcat (s-1)' = 0.37; column 'Km (uM)' = 29; column 'kcat/Km x 103 (s-1 M-1)' = 13; column 'Ki (DABA) (uM)' = 270 uM. The efficiency column is printed in units of 10^3 s-1 M-1, which is the same size as 1 s-1 mM-1.

normalized_value_unit_evidence: kcat: printed Table 1 cell 0.37 s-1; the printed unit is already s^(-1), no unit conversion applies; the paper value is 0.37 s^(-1); the exported value is 0.37 s^(-1). Km: printed Table 1 cell 29 uM; 29 / 1000 = 0.029 mM; the exported value is 0.029 mM. kcat/Km: printed Table 1 cell 13 in units of 10^3 s-1 M-1, that is 13000 s-1 M-1; 1 s-1 M-1 is 0.001 s-1 mM-1, so the printed cell becomes 13.0 s^(-1)*mM^(-1), and the full-precision quotient of the same two printed component cells is 0.37 / 0.029 = 12.75862068965517 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table 1, Enzyme row 'S162A': kcat = 0.37 s-1; Km = 29 uM; printed kcat/Km = 13 in the column's units of 10^3 s-1 M-1.

row_label: Table 1, Enzyme row 'S162A', the printed kcat, Km and kcat/Km cells of that row


organism: Acetoanaerobium sticklandii (strain ATCC 12662 / DSM 519 / JCM 1433 / CCUG 9281 / NCIMB 10654 / HF)

sequence_variant_note: Sequence is treated as wild-type because the source explicitly marked the record as wild-type.

column_label: Primary paper abstract/results list apparent Km values in substrate order D-ornithine, AdoCbl, PLP and Figure 4A is the D-ornithine panel.

normalized_value_unit_evidence: 44.5 uM normalizes to 0.0445 mM.

raw_value_unit_evidence: D-ornithine apparent Km 44.5 +/- 2.8 uM.

row_label: D-ornithine

table_label: Abstract and Results: Kinetic Analysis; Figure 4A


substrate_name: adenosylcobalamin

column_label: Primary paper abstract/results give apparent Km values and Figure 4B is the AdoCbl panel.

normalized_value_unit_evidence: 0.43 uM normalizes to 0.00043 mM.

raw_value_unit_evidence: AdoCbl apparent Km 0.43 +/- 0.04 uM.

row_label: 5'-deoxyadenosylcobalamin (AdoCbl)

table_label: Abstract and Results: Kinetic Analysis; Figure 4B

substrate: adenosylcobalamin


column_label: Primary paper abstract/results list apparent Km values in substrate order D-ornithine, AdoCbl, PLP and Figure 4C is the PLP panel.

normalized_value_unit_evidence: 1.5 uM normalizes to 0.0015 mM.

raw_value_unit_evidence: PLP apparent Km 1.5 +/- 0.1 uM.

row_label: pyridoxal 5'-phosphate (PLP)

table_label: Abstract and Results: Kinetic Analysis; Figure 4C


organism: Clostridium sticklandii

substrate_name: D-Lysine

substrate: D-Lysine


sequence_variant_note: Resolved sequence already matches the mutant residue(s) after applying an inferred residue-numbering offset -10, so it is treated as a source-provided variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature E338A with inferred residue-numbering offset -3 to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature E338D with inferred residue-numbering offset -3 to reconstruct the assayed variant sequence.


substrate_name: DL-Ornithine

smiles: NCCCC(N)C(=O)O

substrate: DL-Ornithine


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:E3PY95 and applied mutation signature I424E with inferred residue-numbering offset -3 to reconstruct the assayed variant sequence.

assay_conditions_summary: pH 8.5; 298.15 K; cofactor NADH

column_label: Table 2 (The steady-state kinetic parameters for wild-type OAM and variant forms); Table 2, classification 'Group A', enzyme row 'I424E'; column 'kcat' = 0.76; column 'Km' = 185; column 'kcat/Km' = 4.12, the table printing a single unit row x 10^3 M^-1 s^-1 above that column.

normalized_value_unit_evidence: kcat: printed cell 0.76 s^-1; no unit conversion applies, so the canonical value is 0.76 s^(-1). Km: printed cell 185 uM; 185 / 1000 = 0.185 mM. kcat/Km: printed cell 4.12 x 10^3 M^-1 s^-1; 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 4.12 x 10^3 / 1000 = 4.12 s^-1 mM^-1. The quotient of the two printed component cells is 0.76 / 0.185 = 4.108108108108108 s^-1 mM^-1, which lies outside the rounding interval of the printed efficiency cell, so the printed efficiency cell is the paper's own fitted primary value and 4.12 s^(-1)*mM^(-1) is proposed for kcat_over_km.

raw_value_unit_evidence: Table 2, classification 'Group A', enzyme row 'I424E': printed kcat cell 0.76; printed Km cell 185; printed kcat/Km cell 4.12 carrying the table's own unit row x 10^3 M^-1 s^-1. Section 6 of the local extract resolves the kcat column as s^-1 and the Km column as uM from that printed unit row and from the arithmetic of all ten numeric rows of Tables 1 and 2.

table_label: Table 2: the steady-state kinetic parameters measured with D-ornithine (J. Biol. Chem. 2014, 289(49):34161-34174)


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:E3PY95 and applied mutation signature D627A with inferred residue-numbering offset -3 to reconstruct the assayed variant sequence.

column_label: Table 2 (The steady-state kinetic parameters for wild-type OAM and variant forms); Table 2, classification 'Group A', enzyme row 'D627A'; column 'kcat' = 2.89; column 'Km' = 193; column 'kcat/Km' = 15.0, the table printing a single unit row x 10^3 M^-1 s^-1 above that column.

normalized_value_unit_evidence: kcat: printed cell 2.89 s^-1; no unit conversion applies, so the canonical value is 2.89 s^(-1). Km: printed cell 193 uM; 193 / 1000 = 0.193 mM. kcat/Km: printed cell 15.0 x 10^3 M^-1 s^-1; 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 15.0 x 10^3 / 1000 = 15.0 s^-1 mM^-1. The exported kcat/Km 14.974093264248705 s^(-1)*mM^(-1) is the exact quotient 2.89 / 0.193 of the two printed component cells of this same table line, and the printed efficiency cell is that quotient rendered at the table's own precision, so the exported ratio is kept as printed evidence of it.

raw_value_unit_evidence: Table 2, classification 'Group A', enzyme row 'D627A': printed kcat cell 2.89; printed Km cell 193; printed kcat/Km cell 15.0 carrying the table's own unit row x 10^3 M^-1 s^-1. Section 6 of the local extract resolves the kcat column as s^-1 and the Km column as uM from that printed unit row and from the arithmetic of all ten numeric rows of Tables 1 and 2.


organism: Schizosaccharomyces pombe

proof_lines:
phosphatase activity
mutase activity


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature E93D to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature R14Q to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature R120Q to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature R121Q to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature R120Q/R121Q to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature R94Q with inferred residue-numbering offset +14 to reconstruct the assayed variant sequence.


organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

substrate_name: 2,3-bisphosphoglycerate (for mutase reaction)

proof_lines: kcat is 490 sec(-1) for the mutase reaction, 0.0074 sec(-1) for the synthase reaction and 0.0087 sec(-1) for the phosphatase reaction with 3-phosphoglycerate as substrate.


organism: Schistosoma mansoni

proof_lines: at pH 7.8, temperature not specified in the publication


organism: Escherichia coli (strain K12)

substrate_name: 2-PGA (at pH 7 and 30 degrees Celsius)

smiles: CCCC(CCC(=O)O)C(=O)O

column_label: ScienceDirect Table 1 row Km 2-PGA, dPGM column, reports 190 +/- 35 microM.

raw_value_unit_evidence: Table 1 dPGM Km 2-PGA=190 +/- 35 microM.

row_label: E. coli dPGM / 2-PGA

table_label: ScienceDirect Table 1

substrate: 2-PGA (at pH 7 and 30 degrees Celsius)


proof_lines: kcat is 22 sec(-1) for mutase with 3-PGA as substrate (at pH 7 and 30 degrees Celsius). kcat is 10 sec(-1) for mutase with 2-PGA as substrate (at pH 7 and 30 degrees Celsius).


organism: Saccharomyces cerevisiae

sequence_variant_note: Source notes indicate a mutant or variant enzyme, but no machine-applicable substitution signature was available.


substrate_name: Unknown

sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_mutation_ranked_match and applied mutation signature H225Q with inferred residue-numbering offset -3 to reconstruct the assayed variant sequence.

substrate: Unknown


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_mutation_ranked_match and applied mutation signature Y160F with inferred residue-numbering offset -3 to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_mutation_ranked_match and applied mutation signature S162A with inferred residue-numbering offset -3 to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_mutation_ranked_match and applied mutation signature Y187F with inferred residue-numbering offset +4 to reconstruct the assayed variant sequence.


organism: Lactococcus lactis subsp. lactis

sequence_variant_note: Sequence identity was resolved, but no explicit wild-type or mutant call was captured.

assay_conditions_summary: pH 7.2; buffer triethanol-HCl

proof_lines: in triethanol-HCl buffer (125 mM, pH 7.2, 5 mM MgCl2, 10 mM KCl), 0.1 mM 2,3-bisphosphoglyceric acid, temperature not specified in the publication


organism: Gallus gallus

substrate_name: 2,3-Bisphospho-D-glycerate; H2O

sequence_variant_note: Sequence is treated as wild-type because the source explicitly marked the record as wild-type.

substrate: 2,3-Bisphospho-D-glycerate; H2O


organism: Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)


enzyme_display_name: lysine 2,3-aminomutase

organism: Clostridium subterminale

enzyme: lysine 2,3-aminomutase


organism: Acetoanaerobium sticklandii

sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_mutation_ranked_match and applied mutation signature H225A with inferred residue-numbering offset -3 to reconstruct the assayed variant sequence.


smiles: O=C(O)C(COP(=O)(O)O)OP(=O)(O)O


sequence_variant_note: Resolved sequence already matches the mutant residue(s), so it is treated as a source-provided variant sequence.

smiles: O=C(O)C(O)COP(=O)(O)O


organism: Escherichia coli

assay_conditions_summary: pH 7; cofactor NADH

column_label: Primary article Section 3.3, Table 1, iPGM column; rows Km 3-PGA, kcat forward, and Forward kcat/Km.

normalized_value_unit_evidence: Km 0.21 mM; kcat 22 s^-1; explicit printed kcat/Km 100 s^-1 mM^-1.

raw_value_unit_evidence: Table 1 iPGM column: Km 3-PGA 210 +/- 39 uM; kcat forward 22 +/- 1 s^-1; forward kcat/Km 1.0 x 10^5 M^-1 s^-1.

row_label: iPGM; forward reaction; 3-PGA substrate

table_label: Table 1. Kinetic constants for E. coli dPGM and iPGM and S. cerevisiae PGM


substrate_name: L-lysine

substrate: L-lysine


substrate_name: adenosylmethionine

substrate: adenosylmethionine


smiles: C(CSCC(C(=O)O)N)N

column_label: Abstract reports Km for 4-thialysine is 1.4 +/- 0.1 mM under the same assay conditions.

raw_value_unit_evidence: Km raw_value=1.4 +/- 0.1 mM raw_unit=mM

row_label: Clostridium subterminale lysine 2,3-aminomutase / 4-thialysine

table_label: PubMed XML abstract PMID 11370852


organism: Rattus norvegicus


organism: Thermoplasma acidophilum


organism: Saccharolobus solfataricus

proof_lines: 65°C, pH not specified in the publication

proof_lines: 70°C, pH not specified in the publication

proof_lines: 80°C, pH not specified in the publication


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_mutation_ranked_match and applied mutation signature Y187A with inferred residue-numbering offset +4 to reconstruct the assayed variant sequence.

proof_lines: pH 8.5, 20°C, recombinant beta-subunit mutant Y187A


proof_lines: pH 8.5, 20°C, recombinant beta-subunit mutant Y187F

proof_lines: pH 8.5, 25°C, recombinant beta-subunit mutant Y187F


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:E3PY95 and applied mutation signature S162A to reconstruct the assayed variant sequence.

table_label: Table 1: Summary of steady-state kinetic parameters for OAM and its active site variants with substrate D-ornithine and inhibitor 2,4-diaminobutyrate (BBA - Proteins and Proteomics 2017, 1865:1077-1084)


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:E3PY95 and applied mutation signature Y160F to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:E3PY95 and applied mutation signature Y187F to reconstruct the assayed variant sequence.

column_label: Table 1: Summary of steady-state kinetic parameters for OAM and its active site variants with substrate D-ornithine and inhibitor 2,4-diaminobutyrate (BBA - Proteins and Proteomics 2017, 1865:1077-1084); Enzyme row 'Y187F': column 'kcat (s-1)' = 0.12; column 'Km (uM)' = 31; column 'kcat/Km x 103 (s-1 M-1)' = 3.9; column 'Ki (DABA) (uM)' = 32 uM. The efficiency column is printed in units of 10^3 s-1 M-1, which is the same size as 1 s-1 mM-1.

normalized_value_unit_evidence: kcat: printed Table 1 cell 0.12 s-1; the printed unit is already s^(-1), no unit conversion applies; the paper value is 0.12 s^(-1); the exported value is 0.12 s^(-1). Km: printed Table 1 cell 31 uM; 31 / 1000 = 0.031 mM; the exported value is 0.031 mM. kcat/Km: printed Table 1 cell 3.9 in units of 10^3 s-1 M-1, that is 3900 s-1 M-1; 1 s-1 M-1 is 0.001 s-1 mM-1, so the printed cell becomes 3.9 s^(-1)*mM^(-1), and the full-precision quotient of the same two printed component cells is 0.12 / 0.031 = 3.8709677419354835 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table 1, Enzyme row 'Y187F': kcat = 0.12 s-1; Km = 31 uM; printed kcat/Km = 3.9 in the column's units of 10^3 s-1 M-1.

row_label: Table 1, Enzyme row 'Y187F', the printed kcat, Km and kcat/Km cells of that row


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_mutation_ranked_match and applied mutation signature S11G with inferred residue-numbering offset +1 to reconstruct the assayed variant sequence.


organism: Archaeoglobus fulgidus

column_label: Primary PDF results prose, text lines 310-312: 3PGA Vmax 3.3 +/- 0.2 U/mg and Km 0.8 +/- 0.1 mM.

raw_value_unit_evidence: Results prose: Vmax 3.3 +/- 0.2 U mg^-1 and Km 0.8 +/- 0.1 mM for 3PGA.

row_label: A. fulgidus AF1751; 3PGA to 2PGA direction

table_label: Rate-dependence results prose


column_label: Primary PDF results prose, text lines 310-313: 2PGA Vmax 0.8 +/- 0.01 U/mg and Km 0.2 +/- 0.01 mM.

raw_value_unit_evidence: Results prose: Vmax 0.8 +/- 0.01 U mg^-1 and Km 0.2 +/- 0.01 mM for 2PGA.

row_label: A. fulgidus AF1751; 2PGA to 3PGA direction


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:E3PY95 and applied mutation signature G339W with inferred residue-numbering offset -3 to reconstruct the assayed variant sequence.

column_label: Table 2 (The steady-state kinetic parameters for wild-type OAM and variant forms); Table 2, classification 'Group B', enzyme row 'G339W'; column 'kcat' = 0.20; column 'Km' = 190; column 'kcat/Km' = 1.05, the table printing a single unit row x 10^3 M^-1 s^-1 above that column.

normalized_value_unit_evidence: kcat: printed cell 0.20 s^-1; no unit conversion applies, so the canonical value is 0.2 s^(-1). Km: printed cell 190 uM; 190 / 1000 = 0.19 mM. kcat/Km: printed cell 1.05 x 10^3 M^-1 s^-1; 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 1.05 x 10^3 / 1000 = 1.05 s^-1 mM^-1. The exported kcat/Km 1.0526315789473684 s^(-1)*mM^(-1) is the exact quotient 0.2 / 0.19 of the two printed component cells of this same table line, and the printed efficiency cell is that quotient rendered at the table's own precision, so the exported ratio is kept as printed evidence of it.

raw_value_unit_evidence: Table 2, classification 'Group B', enzyme row 'G339W': printed kcat cell 0.20; printed Km cell 190; printed kcat/Km cell 1.05 carrying the table's own unit row x 10^3 M^-1 s^-1. Section 6 of the local extract resolves the kcat column as s^-1 and the Km column as uM from that printed unit row and from the arithmetic of all ten numeric rows of Tables 1 and 2.


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:E3PY95 and applied mutation signature C700S with inferred residue-numbering offset -3 to reconstruct the assayed variant sequence.

column_label: Table 1 (The steady-state kinetic parameters for wild-type OAM and C700S variant before and after MTSL nitroxide spin labeling); Table 1, enzyme row 'C700S unlabeled' (cysteine residues labeled with MTSL: NA); column 'kcat' = 2.88; column 'Km' = 186; column 'kcat/Km' = 15.5, the table printing a single unit row x 10^3 M^-1 s^-1 above that column.

normalized_value_unit_evidence: kcat: printed cell 2.88 s^-1; no unit conversion applies, so the canonical value is 2.88 s^(-1). Km: printed cell 186 uM; 186 / 1000 = 0.186 mM. kcat/Km: printed cell 15.5 x 10^3 M^-1 s^-1; 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 15.5 x 10^3 / 1000 = 15.5 s^-1 mM^-1. The exported kcat/Km 15.483870967741934 s^(-1)*mM^(-1) is the exact quotient 2.88 / 0.186 of the two printed component cells of this same table line, and the printed efficiency cell is that quotient rendered at the table's own precision, so the exported ratio is kept as printed evidence of it.

raw_value_unit_evidence: Table 1, enzyme row 'C700S unlabeled' (cysteine residues labeled with MTSL: NA): printed kcat cell 2.88; printed Km cell 186; printed kcat/Km cell 15.5 carrying the table's own unit row x 10^3 M^-1 s^-1. Section 6 of the local extract resolves the kcat column as s^-1 and the Km column as uM from that printed unit row and from the arithmetic of all ten numeric rows of Tables 1 and 2.

table_label: Table 1: the steady-state kinetic parameters measured with D-ornithine (J. Biol. Chem. 2014, 289(49):34161-34174)


source_license: CC BY 4.0; CC BY-NC-ND 4.0

proof_lines:
pH 7.0, 50°C
Raw SKiD Env: Temp=50°C, pH=7

source_databases_merged: brenda skid


organism: Brugia malayi


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_mutation_ranked_match and applied mutation signature S11A with inferred residue-numbering offset +1 to reconstruct the assayed variant sequence.


column_label: Primary article Section 3.3, Table 1, iPGM column; rows Km 2-PGA, kcat reverse, and Reverse kcat/Km.

normalized_value_unit_evidence: Km 0.097 mM; kcat 10 s^-1; explicit printed kcat/Km 100 s^-1 mM^-1.

raw_value_unit_evidence: Table 1 iPGM column: Km 2-PGA 97 +/- 14 uM; kcat reverse 10 +/- 0.5 s^-1; reverse kcat/Km 1.0 x 10^5 M^-1 s^-1.

row_label: iPGM; reverse reaction; 2-PGA substrate


assay_conditions_summary: pH 7; 303.15 K; cofactor NADH


organism: Triticum aestivum


organism: Homo sapiens

substrate_name: 2,3-Bisphosphoglycerate; H2O

substrate: 2,3-Bisphosphoglycerate; H2O


substrate_name: H2O; 2,3-Bisphospho-D-glycerate

substrate: H2O; 2,3-Bisphospho-D-glycerate


organism: Geobacillus stearothermophilus


organism: Trypanosoma brucei brucei (strain 927/4 GUTat10.1)

substrate_name: 3-phosphoglycerate (at pH 7.4, 37 degrees Celsius and in the presence of Mn(2+) and Co(2+))


substrate_name: 3-phosphoglycerate (at pH 7.4 and 25 degrees Celsius)


substrate_name: 2-phosphoglycerate (at pH 7.4 and 25 degrees Celsius)


organism: Zea mays


organism: Trypanosoma brucei


organism: Acetoanaerobium sticklandii (strain ATCC 12662 / DSM 519 / JCM 1433 / CCUG 9281 / NCIMB 10654 / HF)

substrate_name: adenosylcobalamin (for recombinant alpha and beta subunits expressed together in E.coli to overcome presence of corrinoids in native system)

column_label: Metric label Km; row adenosylcobalamin; value 6.6 microM

raw_value_unit_evidence: adenosylcobalamin 6.6 microM

row_label: Km values for adenosylcobalamin and pyridoxal 5'-phosphate

table_label: Abstract


substrate_name: adenosylcobalamin (for recombinant alpha and beta subunits expressed together in E.coli to overcome the presence of corrinoids in native system)


enzyme_display_name: UniProt Q68G84

organism: Taxus chinensis

substrate_name: L-beta-phenylalanine

enzyme: UniProt Q68G84

substrate: L-beta-phenylalanine


enzyme_display_name: phenylalanine aminomutase (D-beta-phenylalanine forming)

organism: Pantoea agglomerans


enzyme: phenylalanine aminomutase (D-beta-phenylalanine forming)


substrate_name: L-Phenylalanine

substrate: L-Phenylalanine


organism: Amycolatopsis methanolica

substrate_name: Glycerate 3-phosphate

substrate: Glycerate 3-phosphate


organism: Wolbachia sp.

proof_lines: recombinant His-tagged enzyme, pH 7.5, 30°C


organism: Wolbachia endosymbiont of Dirofilaria immitis

proof_lines: in 30 mM Tris-HCl, 5 mM MgSO4, 20 mM KCl, pH 7.5, at 30°C


organism: Acetoanaerobium sticklandii

substrate_name: D-ornithine


organism: Escherichia coli

proof_lines: kcat is 330 sec(-1) for mutase with 3-PGA as substrate (at pH 7 and 30 degrees Celsius). kcat is 220 sec(-1) for mutase with 2-PGA as substrate (at pH 7 and 30 degrees Celsius).


enzyme_display_name: phenylalanine aminomutase (L-beta-phenylalanine forming)

substrate_name: trans-cinnamic acid

sequence_variant_note: No sequence was resolved for this record, so variant-aware sequence handling could not be applied.

substrate: trans-cinnamic acid


sequence_variant_note: Mutation context is present, but no sequence was resolved for this record.

enzyme: phenylalanine aminomutase (L-beta-phenylalanine forming)


enzyme_display_name: tyrosine 2,3-aminomutase

organism: Oryza sativa

substrate_name: L-tyrosine

proof_lines: alpha-tyrosine, pH 8.0, 29°C, recombinant mutant N446K

enzyme: tyrosine 2,3-aminomutase

substrate: L-tyrosine


substrate_name: L-phenylalanine

proof_lines: alpha-phenylalanine, pH 8.0, 29°C, recombinant mutant Y125C

substrate: L-phenylalanine


proof_lines: alpha-phenylalanine, pH 8.0, 29°C, recombinant mutant Y125C/N446K


proof_lines: alpha-tyrosine, pH 8.0, 29°C, recombinant mutant Y125C


proof_lines: alpha-phenylalanine, pH 8.0, 29°C, recombinant mutant N446K


proof_lines: alpha-phenylalanine, pH 8.0, 29°C, recombinant wild-type enzyme


proof_lines: alpha-tyrosine, pH 8.0, 29°C, recombinant wild-type enzyme


sequence_variant_note: Source notes indicate a mutant or variant enzyme, but no machine-applicable substitution signature was available.


normalized_value_unit_evidence: kcat: printed cell 0.20 s^-1; no unit conversion applies, so the canonical value is 0.2 s^(-1). Km: printed cell 190 uM; 190 / 1000 = 0.19 mM. kcat/Km: printed cell 1.05 x 10^3 M^-1 s^-1; 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 1.05 x 10^3 / 1000 = 1.05 s^-1 mM^-1. All three printed primary cells of this G339W line are proposed for this row: kcat 0.2 s^(-1), Km 0.19 mM and kcat/Km 1.05 s^(-1)*mM^(-1).

row_label: Table 2, classification 'Group B', enzyme row 'G339W'

substrate: D-ornithine


normalized_value_unit_evidence: kcat: printed cell 2.88 s^-1; no unit conversion applies, so the canonical value is 2.88 s^(-1). Km: printed cell 186 uM; 186 / 1000 = 0.186 mM. kcat/Km: printed cell 15.5 x 10^3 M^-1 s^-1; 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 15.5 x 10^3 / 1000 = 15.5 s^-1 mM^-1. All three printed primary cells of this C700S line are proposed for this row: kcat 2.88 s^(-1), Km 0.186 mM and kcat/Km 15.5 s^(-1)*mM^(-1).

row_label: Table 1, enzyme row 'C700S unlabeled' (cysteine residues labeled with MTSL: NA)


organism: Cupriavidus crocatus

proof_lines: pH and temperature not specified in the publication


enzyme_display_name: isochorismate synthase

organism: Arabidopsis thaliana

substrate_name: chorismate

enzyme: isochorismate synthase

substrate: chorismate


organism: Galium mollugo

substrate_name: isochorismate

substrate: isochorismate


substrate_name: Chorismate

proof_lines: kcat is 290 min(-1) for mutase activity with chorismate. kcat is 173 min(-1) for mutase activity with chorismate (at pH 7.8 and 37 degrees Celsius). kcat is 108 min(-1) for mutase activity with isochorismate (at pH 7.8 and 37 degrees Celsiu

substrate: Chorismate


substrate_name: Isochorismate

substrate: Isochorismate


proof_lines:
pH 8.0, 31°C, recombinant enzyme
Raw SKiD Env: Temp=31°C, pH=8


proof_lines: pH not specified in the publication, temperature not specified in the publication

proof_lines: 25°C, pH not specified in the publication


organism: Taxus canadensis

proof_lines: kcat is 0.053 sec(-1) for L-phenylalanine.

source_databases_merged: skid uniprot


organism: Escherichia coli (strain K12)

substrate_name: isochorismate (at pH 7.5 and 37 degrees Celsius)

proof_lines: kcat is 213 min(-1) for mutase activity with chorismate. kcat is 176 min(-1) for mutase activity with chorismate in the presence of 30 mM of beta-mercaptoethanol (BME). kcat is 144.9 min(-1) for mutase activity with chorismate (at pH 7.5 an


substrate_name: magnesium

smiles: [Mg]

substrate: magnesium


organism: Chondromyces crocatus

substrate_name: L-Tyrosine

substrate: L-Tyrosine


proof_lines: mutant CmdF_MIYMLV, product (R)-beta-tyrosine

proof_lines: mutant CmdF_MIYMLV, product para-hydroxycinnamic acid


proof_lines: wild-type enzme, product para-hydroxycinnamic acid

proof_lines: wild-type enzme, product (R)-beta-tyrosine


substrate_name: DL-Ornithine

substrate: DL-Ornithine


sequence_variant_note: Mutation signature Y187F could not be applied safely because the resolved sequence does not match the expected reference residue(s).


organism: Streptomyces maritimus


substrate_name: D-beta-phenylalanine

substrate: D-beta-phenylalanine


substrate_name: D-alpha-phenylalanine

substrate: D-alpha-phenylalanine


organism: Streptomyces globisporus


substrate_name: Unknown

substrate: Unknown


organism: Gallus gallus


organism: Thermoplasma acidophilum (strain ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)

column_label: Primary PDF results prose, text lines 199-203 and Figure 1 caption lines 280-285: apparent Km 17 +/- 0.7 uM.

normalized_value_unit_evidence: Km 17 uM = 0.017 mM (uncertainty 0.0007 mM).

raw_value_unit_evidence: Results prose/Figure 1: apparent Km 17 +/- 0.7 uM for 2,3-bisphosphoglycerate; apparent Vmax 14 +/- 0.3 U mg^-1.

row_label: T. acidophilum TA1347; 2,3-bisphosphoglycerate cofactor dependence

table_label: Figure 1 and cofactor-dependence results prose


organism: Catharanthus roseus

column_label: Abstract states: The Km values for chorismate were 558 and 319 microM for isoforms I and II, respectively.

raw_value_unit_evidence: Km raw_value=319 raw_unit=microM

row_label: Catharanthus roseus isochorismate synthase isoform II with chorismate

table_label: PubMed abstract PMID 9952467


substrate_name: Mg(2+) (in the presence of 2 mM chorismate)


organism: Pantoea agglomerans


organism: Sus scrofa

sequence: IVYELDQALKPTKPMRFLGDEETVRKAMEAVAAQGKAK


organism: Streptomyces coelicolor


organism: Zymomonas mobilis


organism: Geobacillus stearothermophilus


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature L104A to reconstruct the assayed variant sequence.


column_label: Table 3; row substrate 2 3'-methyl-alpha-phenylalanine; enzyme TcPAM (wild_type); columns K_M (M)x10^3, beta-kcat (s^-1), beta-kcat/K_M (M^-1 s^-1); cells 0.397 (+/-0.03), 0.022 (+/-0.002), 55 (+/-7).

normalized_value_unit_evidence: K_M 0.397 mM; beta-kcat 0.022 s^-1; beta-kcat/K_M 55 M^-1 s^-1 = 0.055 s^-1*mM^-1; exported kcat/K_M 0.0554156 is consistent with beta-kcat/K_M after table rounding or kcat/K_M recomputation from beta-kcat and K_M.

raw_value_unit_evidence: Table 3 row substrate 2 3'-methyl-alpha-phenylalanine; enzyme TcPAM (wild_type): K_M 0.397 (+/-0.03) mM; beta-kcat 0.022 (+/-0.002) s^-1; beta-kcat/K_M 55 (+/-7) M^-1 s^-1. Sibling columns: cin-kcat 0.017 (+/-0.002) s^-1; total kcat/K_M 98 (+/-20) M^-1 s^-1.

table_label: PMID 21361343 Table 3, TcPAM/PAMeLA_104 kinetic parameters


column_label: Table 3; row substrate 3 4'-methyl-alpha-phenylalanine; enzyme TcPAM (wild_type); columns K_M (M)x10^3, beta-kcat (s^-1), beta-kcat/K_M (M^-1 s^-1); cells 0.091 (+/-0.005), 0.030 (+/-0.002), 330 (+/-20).

normalized_value_unit_evidence: K_M 0.091 mM; beta-kcat 0.030 s^-1; beta-kcat/K_M 330 M^-1 s^-1 = 0.33 s^-1*mM^-1; exported kcat/K_M 0.32967 is consistent with beta-kcat/K_M after table rounding or kcat/K_M recomputation from beta-kcat and K_M.

raw_value_unit_evidence: Table 3 row substrate 3 4'-methyl-alpha-phenylalanine; enzyme TcPAM (wild_type): K_M 0.091 (+/-0.005) mM; beta-kcat 0.030 (+/-0.002) s^-1; beta-kcat/K_M 330 (+/-20) M^-1 s^-1. Sibling columns: cin-kcat 0.005 (+/-0.002) s^-1; total kcat/K_M 380 (+/-20) M^-1 s^-1.


substrate_name: styryl-alpha-alanine

substrate: styryl-alpha-alanine


substrate_name: L-Phenylalanine

substrate: L-Phenylalanine