organism: Aspergillus fumigatus

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

assay_conditions_summary: pH 7.5; buffer 50 mM MOPS

proof_lines: in 50 mM MOPS buffer, pH 7.5, with 1 mM MgCl2, 10 mM 2-mercaptoethanol, and 2.7 mM O-nitrophenyl-beta-D-galactopyranoside


enzyme_display_name: N-acetylneuraminate lyase

organism: Staphylococcus aureus (strain NCTC 8325 / PS 47)

substrate_name: ManNAc (for the aldol condensation of ManNAc and pyruvate)

source_db: uniprot

kcat_display: Not reported

ki_display: Not reported

kcat_over_km_display: Not reported

mutation_signature: Unknown

protein_accession_database: UniProt

source_license: CC BY 4.0

km_unit: mM

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

proof_lines: kcat is 250 min(-1) for the cleavage of Neu5Ac at pH 7.4, and is 260 min(-1) at pH 6.8 (PubMed:23418011). kcat is 22.1 sec(-1) with N-acetylneuraminate as substrate (PubMed:27943302). kcat is 510 min(-1) with N-acetylneuraminate as substrat

data_origin: experimental

enzyme: N-acetylneuraminate lyase

source: uniprot


substrate_name: erythrose (for the aldol condensation of erythrose and pyruvate)

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


enzyme_display_name: isocitrate lyase

organism: Mycobacterium tuberculosis

substrate_name: isocitrate

source_db: skid

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

sequence_source: multiple

proof_lines: kcat is 12.2 sec(-1) for isocitrate lyase activity with isocitrate as substrate(at pH 7 and 37 degrees Celsius). kcat is 8.5 sec(-1) for isocitrate lyase activity with succinate as substrate(at pH 7 and 37 degrees Celsius).

source_databases_merged: skid uniprot

enzyme: isocitrate lyase

substrate: isocitrate

source: skid


organism: Latilactobacillus sakei

substrate_name: N-acetylneuraminate

source_db: brenda

verification_status: verified

assay_conditions_summary: pH 7; buffer 20 mM phosphate; cofactor NADH

column_label: Table label: Table 2. Kinetic parameters of LsNAL, LaNAL and three mutants of LaNAL. Data column 1. Enzyme column header: LsNAL. Activity: Cleavage. Substrate: Neu5Ac. Cells read: K M (mM) 0.32±0.03, k cat (s -1 ) 0.9±0.01, k cat /K M (mM -1 s -1 ) 2.8. metric: kcat; raw value: 0.9; raw unit: s^-1; normalized value: 0.9 s^(-1); metric: Km; raw value: 0.32; raw unit: mM; normalized value: 0.32 mM; metric: kcat/Km; raw unit: s^-1 mM^-1; normalized value: 2.8125 s^-1 mM^-1; assay condition: Purified recombinant N-acetylneuraminate lyase; Neu5Ac cleavage was measured spectrophotometrically as the decrease in absorbance at 340 nm from NADH oxidation by lactate dehydrogenase. The standard reaction medium (1 mL) contained 150 uM NADH, 0.5 U LDH, 10 mM Neu5Ac and 1 ug of purified LaNAL or 17 ug of purified LsNAL in 20 mM phosphate buffer pH 7.0. Export row conditions: pH 7.

normalized_value_unit_evidence: Table 2 data column 1 (LsNAL | Cleavage | Neu5Ac): K M 0.32 mM = 0.32 mM, already the export's unit, no conversion needed; k cat 0.9 s^-1 = 0.9 s^(-1), already the export's unit; k cat /K M 2.8125 s^-1 mM^-1, the quotient of this column's own printed K M and k cat cells and the same unit the paper prints (mM^-1 s^-1 = s^-1 mM^-1). In the article asset the plus-minus sign renders as ±, the superscript minus one is flattened to −1, and the table is printed transposed (metrics as rows, enzyme/substrate as columns), so the SD suffix '±0.03' on the K M cell and '±0.01' on the k cat cell belong to the same column.

raw_value_unit_evidence: Table 2. Kinetic parameters of LsNAL, LaNAL and three mutants of LaNAL | Table 2 header cell rows (verbatim cell arrays) | Enzyme header row cells: LsNAL | LsNAL | LsNAL | LaNAL | LaNAL | LaNAL | ... ; Activities row cells: Cleavage | Synthesis | Synthesis | Cleavage | Synthesis | Synthesis | ... ; Substrate row cells: Neu5Ac | ManNAc | Pyr | Neu5Ac | ManNAc | Pyr | ... ; metric row labels: K M (mM), k cat (s -1 ), k cat /K M (mM -1 s -1 ) | data column 1 of Table 2 (enzyme LsNAL, activity Cleavage, substrate Neu5Ac) reads: K M (mM) cell 0.32±0.03; k cat (s -1 ) cell 0.9±0.01; k cat /K M (mM -1 s -1 ) cell 2.8. The paper's own units are mM for K M, s^-1 for k cat and mM^-1 s^-1 for k cat /K M.

row_label: LsNAL | Cleavage | Neu5Ac

substrate: N-acetylneuraminate

status: verified

source: brenda


substrate_name: pyruvate

assay_conditions_summary: pH 7; buffer 20 mM phosphate

column_label: Table label: Table 2. Kinetic parameters of LsNAL, LaNAL and three mutants of LaNAL. Data column 3. Enzyme column header: LsNAL. Activity: Synthesis. Substrate: Pyr. Cells read: K M (mM) 12.5±0.2, k cat (s -1 ) 3.9±0.1, k cat /K M (mM -1 s -1 ) 0.31. metric: kcat; raw value: 3.9; raw unit: s^-1; normalized value: 3.9 s^(-1); metric: Km; raw value: 12.5; raw unit: mM; normalized value: 12.5 mM; metric: kcat/Km; raw unit: s^-1 mM^-1; normalized value: 0.312 s^-1 mM^-1; assay condition: Purified recombinant N-acetylneuraminate lyase; the synthetic reaction (ManNAc + pyruvate) was followed by HPLC-ELSD-II. The standard reaction medium for LaNAL contained 500 mM ManNAc, 10 mM pyruvate and 2 ug purified LaNAL in 20 mM phosphate buffer pH 7.0, or 500 mM ManNAc, 30 mM pyruvate and 50 ug purified LsNAL in the same buffer in the case of LsNAL. Export row conditions: pH 7.

normalized_value_unit_evidence: Table 2 data column 3 (LsNAL | Synthesis | Pyr): K M 12.5 mM = 12.5 mM, already the export's unit, no conversion needed; k cat 3.9 s^-1 = 3.9 s^(-1), already the export's unit; k cat /K M 0.312 s^-1 mM^-1, the quotient of this column's own printed K M and k cat cells and the same unit the paper prints (mM^-1 s^-1 = s^-1 mM^-1). In the article asset the plus-minus sign renders as ±, the superscript minus one is flattened to −1, and the table is printed transposed (metrics as rows, enzyme/substrate as columns), so the SD suffix '±0.2' on the K M cell and '±0.1' on the k cat cell belong to the same column.

raw_value_unit_evidence: Table 2. Kinetic parameters of LsNAL, LaNAL and three mutants of LaNAL | Table 2 header cell rows (verbatim cell arrays) | Enzyme header row cells: LsNAL | LsNAL | LsNAL | LaNAL | LaNAL | LaNAL | ... ; Activities row cells: Cleavage | Synthesis | Synthesis | Cleavage | Synthesis | Synthesis | ... ; Substrate row cells: Neu5Ac | ManNAc | Pyr | Neu5Ac | ManNAc | Pyr | ... ; metric row labels: K M (mM), k cat (s -1 ), k cat /K M (mM -1 s -1 ) | data column 3 of Table 2 (enzyme LsNAL, activity Synthesis, substrate Pyr) reads: K M (mM) cell 12.5±0.2; k cat (s -1 ) cell 3.9±0.1; k cat /K M (mM -1 s -1 ) cell 0.31. The paper's own units are mM for K M, s^-1 for k cat and mM^-1 s^-1 for k cat /K M.

row_label: LsNAL | Synthesis | Pyr

substrate: pyruvate


substrate_name: N-acetyl-D-mannosamine

verification_status: corrected

column_label: Table 2 data column 2 | enzyme LsNAL | activity Synthesis | substrate ManNAc | K M (mM) 272±1 | k cat (s −1 ) 4.6±0.2 | k cat /K M (mM −1 s −1 ) 0.016

row_label: LsNAL | Synthesis | ManNAc

table_label: Table 2

substrate: N-acetyl-D-mannosamine

status: corrected


organism: Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)

proof_lines: kcat is 10.08 sec(-1) for the cleavage of Neu5Ac and 4.8 sec(-1) for the synthetic reaction.


verification_status: unverified

status: unverified


organism: Fusobacterium nucleatum subsp. nucleatum (strain ATCC 25586 / DSM 15643 / BCRC 10681 / CIP 101130 / JCM 8532 / KCTC 2640 / LMG 13131 / VPI 4355)


organism: Escherichia coli

substrate_name: N-Acetyl-D-neuraminate

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

assay_conditions_summary: pH 7

proof_lines: kcat is 7.7 sec(-1) with N-acetylneuraminate as substrate (PubMed:12711733). kcat is 0.47 sec(-1) for the aldol condensation of L-aspartate beta-semialdehyde and pyruvate (at pH 7.0) (PubMed:12711733). kcat is 0.27 sec(-1) for the aldol con

source_databases_merged: sabio_rk skid uniprot

substrate: N-Acetyl-D-neuraminate


organism: Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)

substrate_name: glyoxylate (at pH 7 and 37 degrees Celsius)


substrate_name: succinate (at pH 7 and 37 degrees Celsius)


organism: Zea mays


organism: Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)

substrate_name: DL-threo-2-methylisocitrate (MICA) (at pH 7.5)

proof_lines: kcat is 5.24 sec(-1) for isocitrate lyase activity with threo-DL-isocitrate as substrate (at pH 6). kcat is 1.25 sec(-1) for methylisocitrate lyase activity with DL-threo-2-methylisocitrate as substrate (at pH 7.5).


enzyme_display_name: hydroxymethylglutaryl-CoA lyase

organism: Homo sapiens

sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_mutation_ranked_match and applied mutation signature D204N with inferred residue-numbering offset +12 to reconstruct the assayed variant sequence.

mutation_type: substitution

assay_conditions_summary: pH 7.5; cofactor CoA

column_label: PMID 12746442 DOI 10.1074/jbc.M304276200 Results section; D204N mutant HL; apparent Km statement tied to Fig. 2 saturation kinetics with HMG-CoA.

normalized_value_unit_evidence: Km 6.6 mM.

raw_value_unit_evidence: The Results text states: apparent Km was 3.1 mM for wild type and 6.6 mM for mutant D204N; Fig. 2 shows saturation kinetics of wild type and D204N mutant HL with HMG-CoA.

row_label: D204N mutant human HMG-CoA lyase / HMG-CoA

table_label: Results text and Fig. 2. Saturation kinetics of wild type and D204N mutant HL

enzyme: hydroxymethylglutaryl-CoA lyase


organism: Mediterraneibacter gnavus (strain ATCC 29149 / DSM 114966 / JCM 6515 / VPI C7-9)


organism: Saccharolobus solfataricus


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

substrate_name: Unknown

km_display: Not reported

assay_conditions_summary: cofactor CoA

substrate: Unknown


organism: Staphylococcus aureus

proof_lines:
Raw SKiD Env: Temp=30°C, pH=7.4
Raw SKiD Env: Temp=30°C, pH=-----
Raw SKiD Env: Temp=30°C, pH=6.8


source_db: oed

kcat_over_km_origin: calculated

sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature N1G with inferred residue-numbering offset +3 to reconstruct the assayed variant sequence.

proof_lines:
E. coli D-Neu5Ac aldolase
directed evolution
L-KDO aldolase

source: oed


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature N2C with inferred residue-numbering offset +2 to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature N3A with inferred residue-numbering offset +1 to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature N4E to reconstruct the assayed variant sequence.


column_label: Table 1: Kinetics parameters of wild-type and evolved sialic acid aldolase (PNAS 2005, 102(26):9122-9126); enzyme row 'Wild type', substrate row 'D-sialic acid'; column 'Km, mM' = 2.6 (0.2); column 'kcat, s^-1' = 10.5 (1.8); column 'kcat/Km, mM^-1 s^-1' = 4.04

normalized_value_unit_evidence: Km: printed cell 2.6 mM is already the canonical unit, so no unit conversion applies and the value is 2.6 mM. kcat: printed cell 10.5 s^-1 is already the canonical unit, so no unit conversion applies and the value is 10.5 s^(-1). kcat/Km: printed cell 4.04 mM^-1 s^-1 is the canonical ratio unit written in the other order, so no unit conversion applies and the value is 4.04 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table 1, enzyme row 'Wild type', substrate row 'D-sialic acid': printed Km cell 2.6 (0.2) in the column head 'Km, mM'; printed kcat cell 10.5 (1.8) in the column head 'kcat, s^-1'; printed kcat/Km cell 4.04 in the column head 'kcat/Km, mM^-1 s^-1'. The parenthetical figures are the printed standard errors of the curve fitting.


substrate_name: N-Acetyl-L-neuraminate

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

substrate: N-Acetyl-L-neuraminate


substrate_name: Isocitrate

ki_unit: mM

proof_lines: kcat is 28.5 sec(-1) for isocitrate lyase activity with threo-D-isocitrate as substrate (at pH 7.3).

substrate: Isocitrate


organism: Colwellia maris

substrate_name: DL-isocitrate

proof_lines: 15°C, pH 6.8, Km increases with elevating temperature

substrate: DL-isocitrate


organism: Escherichia coli (strain K12)

substrate_name: threo-D-isocitrate (at pH 7.3)

substrate: threo-D-isocitrate (at pH 7.3)


substrate_name: threo D-(s)-isocitrate

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

proof_lines:
Icl enzyme, 37°C
Raw SKiD Env: Temp=-----, pH=6.8
Raw SKiD Env: Temp=30°C, pH=7.5

source_databases_merged: brenda skid uniprot

substrate: threo D-(s)-isocitrate


substrate_name: threo-DL-isocitrate (ICA) (at pH 6.8)

proof_lines: kcat is 1.38 sec(-1) for isocitrate lyase activity with threo-DL-isocitrate as substrate (at pH 6).

substrate: threo-DL-isocitrate (ICA) (at pH 6.8)


organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

substrate_name: threo-D(S)-isocitrate (at pH 7.0)

proof_lines: The Vmax with threo-D(S)-isocitrate as substrate is 5-fold higher than with threo-D(S)-2-methylisocitrate as substrate.

substrate: threo-D(S)-isocitrate (at pH 7.0)


organism: Sulfolobus acidocaldarius


column_label: Table 1: Kinetics parameters of wild-type and evolved sialic acid aldolase (PNAS 2005, 102(26):9122-9126); enzyme row 'Wild type', substrate row 'L-sialic acid'; column 'Km, mM' = 4.4 (3.2); column 'kcat, s^-1' = 0.0002 (.0001); column 'kcat/Km, mM^-1 s^-1' = 0.00005

normalized_value_unit_evidence: Km: printed cell 4.4 mM is already the canonical unit, so no unit conversion applies and the value is 4.4 mM. kcat: printed cell 0.0002 s^-1 is already the canonical unit, so no unit conversion applies and the value is 0.0002 s^(-1). kcat/Km: printed cell 0.00005 mM^-1 s^-1 is the canonical ratio unit written in the other order, so no unit conversion applies and the value is 0.00005 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table 1, enzyme row 'Wild type', substrate row 'L-sialic acid': printed Km cell 4.4 (3.2) in the column head 'Km, mM'; printed kcat cell 0.0002 (.0001) in the column head 'kcat, s^-1'; printed kcat/Km cell 0.00005 in the column head 'kcat/Km, mM^-1 s^-1'. The parenthetical figures are the printed standard errors of the curve fitting.


organism: Limosilactobacillus antri

sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:C8P490 and applied mutation signature G210S/Y213G to reconstruct the assayed variant sequence.

assay_conditions_summary: pH 7; 310.15 K; buffer 20 mM phosphate

column_label: Table 2 (Kinetic parameters of LsNAL, LaNAL and three mutants of LaNAL), enzyme column group LaNAL G210S/Y213G, activity Synthesis, substrate ManNAc; row 'KM (mM)' = 3200; row 'k cat (s-1)' = 15.3; row 'k cat /KM (mM-1s-1)' = 0.004.

normalized_value_unit_evidence: kcat: printed Table 2 cell 15.3 s^-1; the printed unit is already the export unit, no conversion, so the normalized value is 15.3 s^-1. KM: printed Table 2 cell 3200 mM; already the export unit, no conversion, so the normalized value is 3200.0 mM. kcat/KM: printed Table 2 cell 0.004 mM^-1 s^-1; mM^-1 s^-1 is the export unit s^(-1)*mM^(-1), no conversion, so the normalized value is 0.004 s^-1 mM^-1. This paper prints no min^-1, uM or M^-1 s^-1 kinetic cell in Table 2.

raw_value_unit_evidence: Table 2, LaNAL G210S/Y213G column group, Synthesis activity, substrate ManNAc: KM = 3200 mM; kcat = 15.3 s^-1; printed kcat/KM = 0.004 mM^-1 s^-1.

table_label: Table 2: Kinetic parameters of LsNAL, LaNAL and three mutants of LaNAL (PLoS ONE 2014, 9(5): e96976)


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:C8P490 and applied mutation signature P193Y to reconstruct the assayed variant sequence.

column_label: Table 2 (Kinetic parameters of LsNAL, LaNAL and three mutants of LaNAL), enzyme column group LaNAL P193Y, activity Synthesis, substrate ManNAc; row 'KM (mM)' = 915; row 'k cat (s-1)' = 2.4; row 'k cat /KM (mM-1s-1)' = 0.002.

normalized_value_unit_evidence: kcat: printed Table 2 cell 2.4 s^-1; the printed unit is already the export unit, no conversion, so the normalized value is 2.4 s^-1. KM: printed Table 2 cell 915 mM; already the export unit, no conversion, so the normalized value is 915.0 mM. kcat/KM: printed Table 2 cell 0.002 mM^-1 s^-1; mM^-1 s^-1 is the export unit s^(-1)*mM^(-1), no conversion, so the normalized value is 0.002 s^-1 mM^-1. This paper prints no min^-1, uM or M^-1 s^-1 kinetic cell in Table 2.

raw_value_unit_evidence: Table 2, LaNAL P193Y column group, Synthesis activity, substrate ManNAc: KM = 915 mM; kcat = 2.4 s^-1; printed kcat/KM = 0.002 mM^-1 s^-1.


column_label: Table 2 row LaNAL WT; synthesis; ManNAc; rows KM (mM), kcat (s^-1), kcat/KM (mM^-1 s^-1) under the LaNAL or LaNAL mutant column

raw_value_unit_evidence: LaNAL WT; synthesis; ManNAc: KM 333 +/- 2 mM; kcat 5.4 +/- 0.2 s^-1; kcat/KM 0.016 mM^-1 s^-1

row_label: LaNAL WT; synthesis; ManNAc

table_label: PMCID PMC4016182 Table 2


assay_conditions_summary: pH 7; 310.15 K; buffer 20 mM phosphate; cofactor NADH

column_label: Table 2 (Kinetic parameters of LsNAL, LaNAL and three mutants of LaNAL), enzyme column group LaNAL G210S/Y213G, activity Cleavage, substrate Neu5Ac; row 'KM (mM)' = 2.0; row 'k cat (s-1)' = 0.47; row 'k cat /KM (mM-1s-1)' = 0.23.

normalized_value_unit_evidence: kcat: printed Table 2 cell 0.47 s^-1; the printed unit is already the export unit, no conversion, so the normalized value is 0.47 s^-1. KM: printed Table 2 cell 2.0 mM; already the export unit, no conversion, so the normalized value is 2.0 mM. kcat/KM: printed Table 2 cell 0.23 mM^-1 s^-1; mM^-1 s^-1 is the export unit s^(-1)*mM^(-1), no conversion, so the normalized value is 0.23 s^-1 mM^-1. This paper prints no min^-1, uM or M^-1 s^-1 kinetic cell in Table 2.

raw_value_unit_evidence: Table 2, LaNAL G210S/Y213G column group, Cleavage activity, substrate Neu5Ac: KM = 2.0 mM; kcat = 0.47 s^-1; printed kcat/KM = 0.23 mM^-1 s^-1.


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:C8P490 and applied mutation signature G211S to reconstruct the assayed variant sequence.

column_label: Table 2 (Kinetic parameters of LsNAL, LaNAL and three mutants of LaNAL), enzyme column group LaNAL G211S, activity Cleavage, substrate Neu5Ac; row 'KM (mM)' = 1.2; row 'k cat (s-1)' = 0.032; row 'k cat /KM (mM-1s-1)' = 0.026.

normalized_value_unit_evidence: kcat: printed Table 2 cell 0.032 s^-1; the printed unit is already the export unit, no conversion, so the normalized value is 0.032 s^-1. KM: printed Table 2 cell 1.2 mM; already the export unit, no conversion, so the normalized value is 1.2 mM. kcat/KM: printed Table 2 cell 0.026 mM^-1 s^-1; mM^-1 s^-1 is the export unit s^(-1)*mM^(-1), no conversion, so the normalized value is 0.026 s^-1 mM^-1. This paper prints no min^-1, uM or M^-1 s^-1 kinetic cell in Table 2.

raw_value_unit_evidence: Table 2, LaNAL G211S column group, Cleavage activity, substrate Neu5Ac: KM = 1.2 mM; kcat = 0.032 s^-1; printed kcat/KM = 0.026 mM^-1 s^-1.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature P193Y to reconstruct the assayed variant sequence.


column_label: Table 2 row LaNAL WT; cleavage; Neu5Ac; rows KM (mM), kcat (s^-1), kcat/KM (mM^-1 s^-1) under the LaNAL or LaNAL mutant column

raw_value_unit_evidence: LaNAL WT; cleavage; Neu5Ac: KM 1.1 +/- 0.1 mM; kcat 1.9 +/- 0.2 s^-1; kcat/KM 1.7 mM^-1 s^-1

row_label: LaNAL WT; cleavage; Neu5Ac


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

column_label: Table 2 (Kinetic parameters of LsNAL, LaNAL and three mutants of LaNAL), enzyme column group LaNAL G210S/Y213G, activity Synthesis, substrate Pyr; row 'KM (mM)' = 4.3; row 'k cat (s-1)' = 3.0; row 'k cat /KM (mM-1s-1)' = 0.71.

normalized_value_unit_evidence: kcat: printed Table 2 cell 3.0 s^-1; the printed unit is already the export unit, no conversion, so the normalized value is 3.0 s^-1. KM: printed Table 2 cell 4.3 mM; already the export unit, no conversion, so the normalized value is 4.3 mM. kcat/KM: printed Table 2 cell 0.71 mM^-1 s^-1; mM^-1 s^-1 is the export unit s^(-1)*mM^(-1), no conversion, so the normalized value is 0.71 s^-1 mM^-1. This paper prints no min^-1, uM or M^-1 s^-1 kinetic cell in Table 2.

raw_value_unit_evidence: Table 2, LaNAL G210S/Y213G column group, Synthesis activity, substrate Pyr: KM = 4.3 mM; kcat = 3.0 s^-1; printed kcat/KM = 0.71 mM^-1 s^-1.


column_label: Table 2 row LaNAL WT; synthesis; Pyr; rows KM (mM), kcat (s^-1), kcat/KM (mM^-1 s^-1) under the LaNAL or LaNAL mutant column

raw_value_unit_evidence: LaNAL WT; synthesis; Pyr: KM 1.1 +/- 0.2 mM; kcat 5.6 +/- 0.1 s^-1; kcat/KM 5.1 mM^-1 s^-1

row_label: LaNAL WT; synthesis; Pyr


organism: Acinetobacter calcoaceticus

substrate_name: threo-D-isocitrate

sequence: MTYQTAIDAVRELKA

wild_type_sequence: MTYQTAIDAVRELKA

substrate: threo-D-isocitrate


organism: Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)


organism: Dianthus caryophyllus

substrate_name: (2R)-ethyl-(3S)-methyl malate

source_license: CC BY-NC-ND 4.0

substrate: (2R)-ethyl-(3S)-methyl malate


organism: Fomitopsis palustris


organism: Gloeothece citriformis PCC 7424


organism: Phycomyces blakesleeanus

substrate_name: Glyoxylate; Succinate

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

substrate: Glyoxylate; Succinate


organism: Pseudomonas aeruginosa

substrate_name: isocitrate

sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature E219A to reconstruct the assayed variant sequence.

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


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature N214D to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature Q211H to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature Q221K to reconstruct the assayed variant sequence.


organism: Neurospora crassa

substrate_name: glyoxylate

substrate: glyoxylate


substrate_name: succinate

substrate: succinate


substrate_name: threo-Ds-isocitrate

substrate: threo-Ds-isocitrate


organism: Staphylococcus carnosus

substrate_name: N-acetyl-D-mannosamine


substrate_name: N-acetylneuraminate

substrate: N-acetylneuraminate


substrate_name: pyruvate

substrate: pyruvate


proof_lines: Acinetobacter calcoaceticus isocitrate lyase


organism: Corynebacterium glutamicum

substrate: N-acetyl-D-mannosamine


organism: Haloferax volcanii

substrate_name: D-isocitrate

source_databases_merged: brenda uniprot

substrate: D-isocitrate


organism: Hyphomicrobium methylovorum


column_label: Abstract states the Km value for Ds-isocitrate was 0.51 mM.

raw_value_unit_evidence: Km raw_value=0.51 raw_unit=mM

row_label: Hyphomicrobium methylovorum GM2 isocitrate lyase with Ds-isocitrate

table_label: PubMed abstract PMID 9395332


substrate_name: D-Isocitrate

proof_lines:
isocitrate lyase
Mg2+-isocitrate complex
ordered Uni Bi mechanism

substrate: D-Isocitrate


proof_lines: isocitrate lyase on alpha-methylisocitrate


organism: Saccharomyces cerevisiae

substrate_name: Isocitrate

column_label: Abstract reports the Km value for threo-Ds-isocitrate was 1.4 mM.

raw_value_unit_evidence: Km raw_value=1.4 mM raw_unit=mM

row_label: Saccharomyces cerevisiae isocitrate lyase / threo-Ds-isocitrate

table_label: PubMed XML abstract PMID 3059712

substrate: Isocitrate


proof_lines:
isocitrate lyase
alpha-methylisocitrate


organism: Homo sapiens

sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P35914 and applied mutation signature D204A to reconstruct the assayed variant sequence.

assay_conditions_summary: pH 8.2; 303.15 K; cofactor CoA

column_label: TABLE II: Catalytic efficiencies of wild-type and mutant HMG-CoA lyases (J. Biol. Chem. 2003, 278(39):37092-37098); printed column heads Enzyme | Vmax (units/mg) | Km, HMG-CoA (uM) | kcat (s^-1) | kcat/Km (s^-1 uM^-1) | Ki, HG-CoA (uM). TABLE II, enzyme row D204A; column Vmax (units/mg) = 9.6 +/- 5.5; column Km, HMG-CoA (uM) = 166 +/- 31; column kcat (s^-1) = 5.5; column kcat/Km (s^-1 uM^-1) = 0.033; the Ki, HG-CoA column is blank on this line. captured primary segment: D204A | Vmax 9.6 +/- 5.5 units/mg | Km, HMG-CoA 166 +/- 31 uM | kcat 5.5 s^-1 | kcat/Km 0.033 s^-1 uM^-1

normalized_value_unit_evidence: Km: printed TABLE II Km, HMG-CoA cell 166 uM; 1 uM is 1/1000 mM, so 166 / 1000 = 0.166 mM. kcat: printed TABLE II kcat cell 5.5 s^-1; the printed unit is already s^-1 and no unit conversion applies. kcat/Km: printed TABLE II kcat/Km cell 0.033 s^-1 uM^-1; 1 s^-1 uM^-1 is 1000 s^-1 mM^-1, so 0.033 x 1000 = 33.0 s^-1 mM^-1. Quotient disclosure for this table line: 5.5 / 0.166 = 33.132530120481924 s^-1 mM^-1, against the printed catalytic-efficiency cell 33.0 s^-1 mM^-1.

raw_value_unit_evidence: TABLE II, enzyme line D204A: Km, HMG-CoA = 166 +/- 31 uM; kcat = 5.5 s^-1; printed kcat/Km = 0.033 s^-1 uM^-1; Vmax = 9.6 +/- 5.5 units/mg.

row_label: TABLE II, enzyme row D204A


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P35914 and applied mutation signature D280A to reconstruct the assayed variant sequence.

column_label: TABLE II: Catalytic efficiencies of wild-type and mutant HMG-CoA lyases (J. Biol. Chem. 2003, 278(39):37092-37098); printed column heads Enzyme | Vmax (units/mg) | Km, HMG-CoA (uM) | kcat (s^-1) | kcat/Km (s^-1 uM^-1) | Ki, HG-CoA (uM). TABLE II, enzyme row D280A; column Vmax (units/mg) = 195 +/- 10; column Km, HMG-CoA (uM) = 17 +/- 3; column kcat (s^-1) = 110.5; column kcat/Km (s^-1 uM^-1) = 6.39; the Ki, HG-CoA column is blank on this line. captured primary segment: D280A | Vmax 195 +/- 10 units/mg | Km, HMG-CoA 17 +/- 3 uM | kcat 110.5 s^-1 | kcat/Km 6.39 s^-1 uM^-1

normalized_value_unit_evidence: Km: printed TABLE II Km, HMG-CoA cell 17 uM; 1 uM is 1/1000 mM, so 17 / 1000 = 0.017 mM. kcat: printed TABLE II kcat cell 110.5 s^-1; the printed unit is already s^-1 and no unit conversion applies. kcat/Km: printed TABLE II kcat/Km cell 6.39 s^-1 uM^-1; 1 s^-1 uM^-1 is 1000 s^-1 mM^-1, so 6.39 x 1000 = 6390.0 s^-1 mM^-1. Quotient disclosure for this table line: 110.5 / 0.017 = 6499.999999999999 s^-1 mM^-1, against the printed catalytic-efficiency cell 6390.0 s^-1 mM^-1.

raw_value_unit_evidence: TABLE II, enzyme line D280A: Km, HMG-CoA = 17 +/- 3 uM; kcat = 110.5 s^-1; printed kcat/Km = 6.39 s^-1 uM^-1; Vmax = 195 +/- 10 units/mg.

row_label: TABLE II, enzyme row D280A


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P35914 and applied mutation signature D42E to reconstruct the assayed variant sequence.

column_label: TABLE II: Catalytic efficiencies of wild-type and mutant HMG-CoA lyases (J. Biol. Chem. 2003, 278(39):37092-37098); printed column heads Enzyme | Vmax (units/mg) | Km, HMG-CoA (uM) | kcat (s^-1) | kcat/Km (s^-1 uM^-1) | Ki, HG-CoA (uM). TABLE II, enzyme row D42E; column Vmax (units/mg) = 20 +/- 1; column Km, HMG-CoA (uM) = 32 +/- 6; column kcat (s^-1) = 11.3; column kcat/Km (s^-1 uM^-1) = 0.35; the Ki, HG-CoA column is blank on this line. captured primary segment: D42E | Vmax 20 +/- 1 units/mg | Km, HMG-CoA 32 +/- 6 uM | kcat 11.3 s^-1 | kcat/Km 0.35 s^-1 uM^-1

normalized_value_unit_evidence: Km: printed TABLE II Km, HMG-CoA cell 32 uM; 1 uM is 1/1000 mM, so 32 / 1000 = 0.032 mM. kcat: printed TABLE II kcat cell 11.3 s^-1; the printed unit is already s^-1 and no unit conversion applies. kcat/Km: printed TABLE II kcat/Km cell 0.35 s^-1 uM^-1; 1 s^-1 uM^-1 is 1000 s^-1 mM^-1, so 0.35 x 1000 = 350.0 s^-1 mM^-1. Quotient disclosure for this table line: 11.3 / 0.032 = 353.125 s^-1 mM^-1, against the printed catalytic-efficiency cell 350.0 s^-1 mM^-1.

raw_value_unit_evidence: TABLE II, enzyme line D42E: Km, HMG-CoA = 32 +/- 6 uM; kcat = 11.3 s^-1; printed kcat/Km = 0.35 s^-1 uM^-1; Vmax = 20 +/- 1 units/mg.

row_label: TABLE II, enzyme row D42E


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P35914 and applied mutation signature D42N to reconstruct the assayed variant sequence.

column_label: TABLE II: Catalytic efficiencies of wild-type and mutant HMG-CoA lyases (J. Biol. Chem. 2003, 278(39):37092-37098); printed column heads Enzyme | Vmax (units/mg) | Km, HMG-CoA (uM) | kcat (s^-1) | kcat/Km (s^-1 uM^-1) | Ki, HG-CoA (uM). TABLE II, enzyme row D42N; column Vmax (units/mg) = 0.33 +/- 0.17; column Km, HMG-CoA (uM) = 43 +/- 7; column kcat (s^-1) = 0.187; column kcat/Km (s^-1 uM^-1) = 0.0044; the Ki, HG-CoA column is blank on this line. captured primary segment: D42N | Vmax 0.33 +/- 0.17 units/mg | Km, HMG-CoA 43 +/- 7 uM | kcat 0.187 s^-1 | kcat/Km 0.0044 s^-1 uM^-1

normalized_value_unit_evidence: Km: printed TABLE II Km, HMG-CoA cell 43 uM; 1 uM is 1/1000 mM, so 43 / 1000 = 0.043 mM. kcat: printed TABLE II kcat cell 0.187 s^-1; the printed unit is already s^-1 and no unit conversion applies. kcat/Km: printed TABLE II kcat/Km cell 0.0044 s^-1 uM^-1; 1 s^-1 uM^-1 is 1000 s^-1 mM^-1, so 0.0044 x 1000 = 4.4 s^-1 mM^-1. Quotient disclosure for this table line: 0.187 / 0.043 = 4.348837209302326 s^-1 mM^-1, against the printed catalytic-efficiency cell 4.4 s^-1 mM^-1.

raw_value_unit_evidence: TABLE II, enzyme line D42N: Km, HMG-CoA = 43 +/- 7 uM; kcat = 0.187 s^-1; printed kcat/Km = 0.0044 s^-1 uM^-1; Vmax = 0.33 +/- 0.17 units/mg.

row_label: TABLE II, enzyme row D42N


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P35914 and applied mutation signature E279A to reconstruct the assayed variant sequence.

column_label: TABLE II: Catalytic efficiencies of wild-type and mutant HMG-CoA lyases (J. Biol. Chem. 2003, 278(39):37092-37098); printed column heads Enzyme | Vmax (units/mg) | Km, HMG-CoA (uM) | kcat (s^-1) | kcat/Km (s^-1 uM^-1) | Ki, HG-CoA (uM). TABLE II, enzyme row E279A; column Vmax (units/mg) = 163 +/- 9; column Km, HMG-CoA (uM) = 27 +/- 5; column kcat (s^-1) = 92.4; column kcat/Km (s^-1 uM^-1) = 3.38; the Ki, HG-CoA column is blank on this line. captured primary segment: E279A | Vmax 163 +/- 9 units/mg | Km, HMG-CoA 27 +/- 5 uM | kcat 92.4 s^-1 | kcat/Km 3.38 s^-1 uM^-1

normalized_value_unit_evidence: Km: printed TABLE II Km, HMG-CoA cell 27 uM; 1 uM is 1/1000 mM, so 27 / 1000 = 0.027 mM. kcat: printed TABLE II kcat cell 92.4 s^-1; the printed unit is already s^-1 and no unit conversion applies. kcat/Km: printed TABLE II kcat/Km cell 3.38 s^-1 uM^-1; 1 s^-1 uM^-1 is 1000 s^-1 mM^-1, so 3.38 x 1000 = 3380.0 s^-1 mM^-1. Quotient disclosure for this table line: 92.4 / 0.027 = 3422.2222222222226 s^-1 mM^-1, against the printed catalytic-efficiency cell 3380.0 s^-1 mM^-1.

raw_value_unit_evidence: TABLE II, enzyme line E279A: Km, HMG-CoA = 27 +/- 5 uM; kcat = 92.4 s^-1; printed kcat/Km = 3.38 s^-1 uM^-1; Vmax = 163 +/- 9 units/mg.

row_label: TABLE II, enzyme row E279A


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P35914 and applied mutation signature E37D to reconstruct the assayed variant sequence.

column_label: TABLE II: Catalytic efficiencies of wild-type and mutant HMG-CoA lyases (J. Biol. Chem. 2003, 278(39):37092-37098); printed column heads Enzyme | Vmax (units/mg) | Km, HMG-CoA (uM) | kcat (s^-1) | kcat/Km (s^-1 uM^-1) | Ki, HG-CoA (uM). TABLE II, enzyme row E37D; column Vmax (units/mg) = 152 +/- 6; column Km, HMG-CoA (uM) = 36 +/- 6; column kcat (s^-1) = 86.2; column kcat/Km (s^-1 uM^-1) = 2.39; the Ki, HG-CoA column is blank on this line. captured primary segment: E37D | Vmax 152 +/- 6 units/mg | Km, HMG-CoA 36 +/- 6 uM | kcat 86.2 s^-1 | kcat/Km 2.39 s^-1 uM^-1

normalized_value_unit_evidence: Km: printed TABLE II Km, HMG-CoA cell 36 uM; 1 uM is 1/1000 mM, so 36 / 1000 = 0.036 mM. kcat: printed TABLE II kcat cell 86.2 s^-1; the printed unit is already s^-1 and no unit conversion applies. kcat/Km: printed TABLE II kcat/Km cell 2.39 s^-1 uM^-1; 1 s^-1 uM^-1 is 1000 s^-1 mM^-1, so 2.39 x 1000 = 2390.0 s^-1 mM^-1. Quotient disclosure for this table line: 86.2 / 0.036 = 2394.444444444445 s^-1 mM^-1, against the printed catalytic-efficiency cell 2390.0 s^-1 mM^-1.

raw_value_unit_evidence: TABLE II, enzyme line E37D: Km, HMG-CoA = 36 +/- 6 uM; kcat = 86.2 s^-1; printed kcat/Km = 2.39 s^-1 uM^-1; Vmax = 152 +/- 6 units/mg.

row_label: TABLE II, enzyme row E37D


sequence_variant_note: Mutation signature E42A could not be applied safely because the resolved sequence does not match the expected reference residue(s).


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


substrate_name: magnesium ion

column_label: Official JBC full text Table III row/parameter Km Mg2+ (mM), wild-type column, gives 0.20 +/- 0.02.

raw_value_unit_evidence: Table III wild-type Km Mg2+ raw_value=0.20 +/- 0.02 raw_unit=mM

row_label: Wild-type human HMG-CoA lyase / Mg2+

table_label: Table III: Kinetic and cation binding parameters of wild-type and mutant HMG-CoA lyases

substrate: magnesium ion


organism: Clostridium perfringens (strain 13 / Type A)

substrate_name: Unknown

substrate: Unknown


organism: Escherichia coli

substrate_name: N-Acetyl-L-neuraminate

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

substrate: N-Acetyl-L-neuraminate


organism: Staphylococcus aureus (strain NCTC 8325 / PS 47)


organism: Sus scrofa


sequence_variant_note: Resolved canonical sequence from uniprotkb:P35914 and applied mutation signature R41Q to reconstruct the assayed variant sequence.

column_label: Primary Results prose on PDF page 5, Kinetic Characterization of Arginine-41 Mutants: row context R41Q; metric Km Mg; raw value 88; raw unit uM; normalized value 0.088 mM; metric kcat; raw/normalized value 0.0004 s^-1; derived same-prose ratio 0.004545454545454546 s^-1 mM^-1. Table 1 identifies the R41Q kinetic row and standard assay context.

raw_value_unit_evidence: Results prose: wild-type Km Mg = 200 uM; R41Q Km Mg = 88 uM; R41Q kcat = 0.0004 s^-1. Same-prose pair gives kcat/Km Mg = 0.0004 s^-1 / 0.088 mM = 0.004545454545454546 s^-1 mM^-1.

row_label: R41Q human HMG-CoA lyase; Km Mg and kcat

table_label: Kinetic Characterization of Arginine-41 Mutants prose adjacent to Table 1


organism: Sulfolobus acidocaldarius

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

column_label: Table 1 lists KM (uM) = 720 +/- 150 for isocitrate under the Isocitrate lyase column.

raw_value_unit_evidence: Km raw_value=720 +/- 150 uM raw_unit=microM

row_label: KM (uM) row, Isocitrate lyase column, substrate isocitrate

table_label: ScienceDirect full text Table 1: Characterization of isocitrate lyase and malate synthase from S. acidocaldarius

substrate: isocitrate


column_label: Abstract reports the lyase exhibits a Km of 3.2 mM for Neu5Ac and a Vmax of 27.5 U mg(-1).

raw_value_unit_evidence: Km raw_value=3.2 mM raw_unit=mM

row_label: Clostridium perfringens N-acetylneuraminate lyase / Neu5Ac

table_label: PubMed XML abstract PMID 11432751


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

assay_conditions_summary: 310.15 K; cofactor CoA

proof_lines: Abstract-level context: mutant HMG-CoA lyases were kinetically characterized and Km values were reported as comparable to wild-type.


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

substrate_name: HMG-CoA (at pH 6.7 and 37 degrees Celsius)


organism: Aspergillus nidulans


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


substrate_name: N-acetylneuraminic acid

substrate: N-acetylneuraminic acid


proof_lines:
E192S mutant protein, pH 7.5, 25°C
pH 7.5, 25°C, mutant enzyme E192S


proof_lines:
E192N mutant protein, pH 7.7.5, 25°C
pH 7.5, 25°C, mutant enzyme E192N
E192N mutant protein , pH 7.5, 25°C


substrate_name: N-acetyl-L-neuraminic acid

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

substrate: N-acetyl-L-neuraminic acid


proof_lines: pH 7.5, 25°C, mutant enzyme Y98H/F115L/V251I


proof_lines: pH 7.5, 25°C, mutant enzyme Y98H/F115L/V251I/V265I


substrate_name: L-3-deoxy-manno-2-octulosonic acid

proof_lines:
pH 7.5, 25°C, wild-type enzyme
wild type (E192), pH 7.5, 25°C

substrate: L-3-deoxy-manno-2-octulosonic acid


substrate_name: N-acetyl-D-neuraminic acid

substrate: N-acetyl-D-neuraminic acid


substrate_name: D-3-deoxy-manno-2-octulosonic acid

substrate: D-3-deoxy-manno-2-octulosonic acid


proof_lines:
pH 7.5, 25°C, Y98H/F115L
pH 7.5, 25°C, mutant enzyme Y98H/F115L


assay_conditions_summary: pH 7.6; 303.15 K; buffer sodium phosphate

proof_lines: mutant enzyme L199N/I229D, in sodium phosphate buffer (100 mM, pH 7.6), at 30°C


proof_lines: mutant enzyme L199N/I229N, in sodium phosphate buffer (100 mM, pH 7.6), at 30°C


proof_lines: mutant enzyme L171N/I229N, in sodium phosphate buffer (100 mM, pH 7.6), at 30°C


proof_lines: mutant enzyme I229D, in sodium phosphate buffer (100 mM, pH 7.6), at 30°C


proof_lines: mutant enzyme L171R, in sodium phosphate buffer (100 mM, pH 7.6), at 30°C


proof_lines: mutant enzyme I229N, in sodium phosphate buffer (100 mM, pH 7.6), at 30°C


proof_lines: mutant enzyme I229R, in sodium phosphate buffer (100 mM, pH 7.6), at 30°C


proof_lines: mutant enzyme L199N, in sodium phosphate buffer (100 mM, pH 7.6), at 30°C


proof_lines: mutant enzyme L199N/I229R, in sodium phosphate buffer (100 mM, pH 7.6), at 30°C


proof_lines: mutant enzyme L199R/I229N, in sodium phosphate buffer (100 mM, pH 7.6), at 30°C


organism: Clostridium perfringens


proof_lines: pH 7.2, 50 mM phosphate buffer, wild-type

proof_lines: pH 7.2, 250 mM phosphate buffer, wild-type


proof_lines:
pH 7.5, 25°C, mutant enzyme E192V
E192V mutant protein, pH 7.5, 25°C


proof_lines:
pH 7.5, 25°C, mutant enzyme E192N
E192N mutant protein, pH 7.7.5, 25°C


assay_conditions_summary: pH 7.5; 298.15 K; buffer sodium phosphate

proof_lines: wild type enzyme, in sodium phosphate buffer (100 mM, pH 7.6), at 30°C


substrate_name: N-Formylneuraminic acid

substrate: N-Formylneuraminic acid


substrate_name: N-Succinylneuraminic acid

substrate: N-Succinylneuraminic acid


substrate_name: N-glycolylneuraminic acid

substrate: N-glycolylneuraminic acid


substrate_name: N-Acetyl-7-O-acetylneuraminic acid

substrate: N-Acetyl-7-O-acetylneuraminic acid


substrate_name: N-acetyl-4-O-acetylneuraminic acid

substrate: N-acetyl-4-O-acetylneuraminic acid


enzyme_display_name: citrate (pro-3S)-lyase

organism: Lacrimispora sphenoides

substrate_name: citrate

proof_lines:
citrate lyase
C. sphenoides
L-glutamate

enzyme: citrate (pro-3S)-lyase

substrate: citrate


organism: Mycobacterium tuberculosis

substrate_name: threo-DL-Isocitrate

sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_ranked_match and applied mutation signature E423D/E424D to reconstruct the assayed variant sequence.

proof_lines: mutant enzyme E423D/E424D, at pH 7.5 and 30°C

substrate: threo-DL-Isocitrate


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_ranked_match and applied mutation signature E423D to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_ranked_match and applied mutation signature E424D to reconstruct the assayed variant sequence.


organism: Escherichia coli K-12

substrate_name: pyruvate

substrate: pyruvate


substrate_name: N-acetyl-D-mannosamine

substrate: N-acetyl-D-mannosamine


substrate_name: N-acetylneuraminate

substrate: N-acetylneuraminate


organism: Pseudomonas aeruginosa

substrate_name: isocitrate

proof_lines: recombinant His-tagged mutant N214D, pH 7.8, 30°C


proof_lines: recombinant His-tagged mutant Q221K, pH 7.8, 30°C


proof_lines: recombinant His-tagged mutant Q211H, pH 7.8, 30°C


proof_lines: recombinant His-tagged mutant E219A, pH 7.8, 30°C


proof_lines: recombinant His-tagged wild-type enzyme, pH 7.8, 30°C


organism: Pasteurella multocida


substrate_name: glyoxylate

proof_lines: recombinant detagged enzyme, pH 7.0, 37°C

substrate: glyoxylate


substrate_name: succinate

substrate: succinate


substrate: isocitrate


organism: Colwellia psychrerythraea


organism: Pyricularia oryzae


organism: Staphylococcus aureus

proof_lines: purified recombinant mutant K165C, pH 7.4, 30°C


proof_lines: purified recombinant mutant K165-gamma-thialysine, pH 6.8, 30°C

proof_lines: purified recombinant mutant K165-gamma-thialysine, pH 7.4, 30°C


proof_lines: purified recombinant wild-type enzyme, pH 7.4, 30°C

proof_lines: purified recombinant wild-type enzyme, pH 6.8, 30°C


organism: Staphylococcus carnosus

proof_lines: recombinant His-taggged enzyme, pH 7.0, 37°C


substrate_name: N-acetylneuraminic acid

substrate: N-acetylneuraminic acid


organism: Mycoplasma sp.


organism: Escherichia coli


substrate_name: threo-Ds-isocitrate

substrate: threo-Ds-isocitrate


substrate_name: DL-isocitrate

assay_conditions_summary: pH 6.8; buffer 100 mM potassium phosphate

proof_lines: in 100 mM potassium phosphate buffer (pH 7.1), 10 mM MgCl2, 12 mM cysteine

substrate: DL-isocitrate


organism: Homo sapiens


substrate_name: Unknown

substrate: Unknown


organism: Bos taurus


organism: Lactiplantibacillus plantarum


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

proof_lines: cross-linked enzyme aggregates, pH 7.5, 37°C


organism: Lupinus sp.


organism: Haemophilus influenzae


assay_conditions_summary: 303.15 K; cofactor CoA

proof_lines: K48Q mutant protein, pH not specified in the publication, 30°C


proof_lines: K48N mutant protein, pH not specified in the publication, 30°C


organism: Ricinus communis

proof_lines:
pH 6.5
phosphate, pH 7.0
phosphate, pH 6.8


substrate_name: hydroxymethylglutaryl-CoA

assay_conditions_summary: pH 8.2; 310.15 K; cofactor CoA

proof_lines: HMGCLL1 mutant G2A and wild-type HMGCL, pH 8.2, 37°C

substrate: hydroxymethylglutaryl-CoA


organism: Yarrowia lipolytica


organism: Anas sp.


organism: Candida tropicalis


organism: Pseudomonas sp. 'mevalonii'


organism: Bacillus sp. (in: firmicutes)

proof_lines: 0.4 M KCl, 25 mM imidazole buffer, pH 6.8


organism: Cucumis sativus


substrate_name: N-acetyl-neuraminic acid

assay_conditions_summary: pH 7; buffer 0.1 M phosphate

substrate: N-acetyl-neuraminic acid


organism: Clostridium perfringens


organism: Faecalispora sporosphaeroides


proof_lines:
Hepes, pH 7.4
Hepes, pH 7.4, 60 mM Cl-


organism: Glycine max


organism: Staphylococcus aureus

proof_lines: at 30°C, pH not specified in the publication


organism: Helianthus annuus

assay_conditions_summary: pH 6

proof_lines:
phosphate, pH 6.0
phosphate, pH 7.5


organism: Acinetobacter calcoaceticus


organism: Homo sapiens

mutation_signature: deletion mutant Mut15

mutation_type: deletion


organism: Escherichia coli

substrate_name: N-glycolylneuraminic acid

substrate: N-glycolylneuraminic acid


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


organism: Klebsiella pneumoniae


organism: Lactiplantibacillus plantarum


assay_conditions_summary: pH 7.5; 310.15 K; cofactor CoA


organism: Paecilomyces variotii


organism: Mycobacterium tuberculosis

proof_lines: AceA enzyme, Tricine buffer, 37°C, pH 7.5


organism: Rubrivivax gelatinosus

proof_lines:
with 2 mM Mg2+
with 5 mM Mg2+


organism: Vogesella indigofera


organism: Zea mays

substrate_name: Isocitrate

substrate: Isocitrate


organism: Lupinus sp.

assay_conditions_summary: pH 6.8; buffer conditions (imidazole

proof_lines: Tris, triethanolamine or imidazole buffer


organism: Anas platyrhynchos


organism: Raphanus sativus


organism: Pseudomonas indigofera


organism: Geobacillus stearothermophilus


organism: Sus scrofa


organism: Rhodopseudomonas sp.


enzyme_display_name: 4-Hydroxy-2-oxoglutarate aldolase

organism: Rattus norvegicus

enzyme: 4-Hydroxy-2-oxoglutarate aldolase


substrate_name: Pyruvic acid ethyl ester

smiles: CCOC(=O)C(=O)C

substrate: Pyruvic acid ethyl ester


substrate_name: pyruvic acid methyl ester

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

substrate: pyruvic acid methyl ester


substrate_name: Pyruvaldehyde

smiles: CC(=O)C=O

substrate: Pyruvaldehyde


substrate_name: acetaldehyde

smiles: CC=O

substrate: acetaldehyde


enzyme_display_name: L-erythro-3-hydroxyaspartate aldolase

organism: Paracoccus denitrificans

enzyme: L-erythro-3-hydroxyaspartate aldolase


enzyme_display_name: 4-hydroxy-2-oxoglutarate aldolase

organism: Homo sapiens

sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature N78T to reconstruct the assayed variant sequence.

proof_lines: pH and temperature not specified in the publication, mutant enzyme N78T

enzyme: 4-hydroxy-2-oxoglutarate aldolase


proof_lines: pH and temperature not specified in the publication, wild-type enzyme


substrate_name: oxaloacetate

proof_lines:
condensation with glyoxylate
competitive

substrate: oxaloacetate


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature S77A to reconstruct the assayed variant sequence.

proof_lines: pH and temperature not specified in the publication, mutant enzyme S77A


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature S198A with inferred residue-numbering offset -11 to reconstruct the assayed variant sequence.

proof_lines: pH and temperature not specified in the publication, mutant enzyme S198A


organism: Bos taurus

assay_conditions_summary: pH 8.3; cofactor NADH

column_label: Table IV row DL-KHG; columns Km and Vmax.

raw_value_unit_evidence: Table IV row DL-KHG: Km 26 uM; Vmax 10.7 umol pyruvate/min/mg protein.

row_label: DL-KHG

table_label: Table IV Kinetic values for the aldolase and beta-decarboxylase activities of bovine kidney 2-keto-4-hydroxyglutarate aldolase


column_label: Table IV row L-KHG; columns Km and Vmax.

raw_value_unit_evidence: Table IV row L-KHG: Km 24 uM; Vmax 12.1 umol pyruvate/min/mg protein.

row_label: L-KHG


substrate_name: Oxaloacetate

column_label: Table IV row Oxalacetate; columns Km and Vmax.

raw_value_unit_evidence: Table IV row Oxalacetate: Km 164 uM; Vmax 1.27 umol pyruvate/min/mg protein.

row_label: Oxalacetate

substrate: Oxaloacetate


column_label: Abstract/Fig. 5 discussion; substrate glyoxylate; apparent Km = 0.43 mM.

raw_value_unit_evidence: Abstract reports apparent Km values at pH 7.5 for pyruvate, glyoxylate and gamma-hydroxy-alpha-ketoglutarate were 10 mM, 0.43 mM and 1.33 mM respectively.

row_label: Glyoxylate

table_label: Abstract and Fig. 5 discussion: apparent Km values for rat liver gamma-hydroxy-alpha-ketoglutarate synthase

substrate: glyoxylate


substrate_name: pyruvate

column_label: Abstract/Fig. 5 discussion; substrate pyruvate; apparent Km = 10 mM.

row_label: Pyruvate

substrate: pyruvate


organism: Pseudomonas straminea

proof_lines: Cloning, sequencing, and expression of the gene encoding 4-hydroxy-4-methyl-2-oxoglutarate aldolase from Pseudomonas ochraceae NGJ1


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:Q86XE5 and applied mutation signature S77T to reconstruct the assayed variant sequence.

assay_conditions_summary: pH 8.5; 310.15 K; cofactor NADH

column_label: Table 2 (Kinetic parameters.), body row 'S77T'; column 'k cat (sec-1)' = 0.8; column 'K M (uM)' = 58; column 'k cat /K M (M-1 sec-1) x 10^3' = 14; column 'Relative k cat' and column 'Relative k cat /K M' print unitless ratios against the WT row.

normalized_value_unit_evidence: kcat: printed Table 2 cell 0.8 in a column headed sec-1; sec-1 is the canonical s^-1, so no conversion is applied and the value is 0.8 s^(-1). Km: printed Table 2 cell 58 in a column headed uM; 58 / 1000 = 0.058 mM. kcat/Km: printed Table 2 cell 14 in a column headed (M-1 sec-1) x 10^3, that is 14000 M^-1 sec^-1; 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 14000 / 1000 = 14.0 s^-1 mM^-1, while the exported ratio is 13.793103448275863.

raw_value_unit_evidence: Table 2, body row 'S77T': k cat = 0.8 sec-1; K M = 58 uM; printed k cat /K M = 14 in a column headed (M-1 sec-1) x 10^3, that is 14 x 10^3 M^-1 sec^-1.

row_label: Table 2, body row S77T

table_label: Table 2: Kinetic parameters. (PLoS ONE 2011, 6(10): e26021)


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:Q86XE5 and applied mutation signature S77V to reconstruct the assayed variant sequence.

column_label: Table 2 (Kinetic parameters.), body row 'S77V'; column 'k cat (sec-1)' = 1.2; column 'K M (uM)' = 82; column 'k cat /K M (M-1 sec-1) x 10^3' = 15; column 'Relative k cat' and column 'Relative k cat /K M' print unitless ratios against the WT row.

normalized_value_unit_evidence: kcat: printed Table 2 cell 1.2 in a column headed sec-1; sec-1 is the canonical s^-1, so no conversion is applied and the value is 1.2 s^(-1). Km: printed Table 2 cell 82 in a column headed uM; 82 / 1000 = 0.082 mM. kcat/Km: printed Table 2 cell 15 in a column headed (M-1 sec-1) x 10^3, that is 15000 M^-1 sec^-1; 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 15000 / 1000 = 15.0 s^-1 mM^-1, while the exported ratio is 14.634146341463413.

raw_value_unit_evidence: Table 2, body row 'S77V': k cat = 1.2 sec-1; K M = 82 uM; printed k cat /K M = 15 in a column headed (M-1 sec-1) x 10^3, that is 15 x 10^3 M^-1 sec^-1.

row_label: Table 2, body row S77V


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature Y140F to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:Q86XE5 and applied mutation signature N78Q to reconstruct the assayed variant sequence.

column_label: Table 2 (Kinetic parameters.), body row 'N78Q'; column 'k cat (sec-1)' = 6.2; column 'K M (uM)' = 281; column 'k cat /K M (M-1 sec-1) x 10^3' = 22; column 'Relative k cat' and column 'Relative k cat /K M' print unitless ratios against the WT row.

normalized_value_unit_evidence: kcat: printed Table 2 cell 6.2 in a column headed sec-1; sec-1 is the canonical s^-1, so no conversion is applied and the value is 6.2 s^(-1). Km: printed Table 2 cell 281 in a column headed uM; 281 / 1000 = 0.281 mM. kcat/Km: printed Table 2 cell 22 in a column headed (M-1 sec-1) x 10^3, that is 22000 M^-1 sec^-1; 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 22000 / 1000 = 22.0 s^-1 mM^-1, while the exported ratio is 22.06405693950178.

raw_value_unit_evidence: Table 2, body row 'N78Q': k cat = 6.2 sec-1; K M = 281 uM; printed k cat /K M = 22 in a column headed (M-1 sec-1) x 10^3, that is 22 x 10^3 M^-1 sec^-1.

row_label: Table 2, body row N78Q


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:Q86XE5 and applied mutation signature N78A to reconstruct the assayed variant sequence.

column_label: Table 2 (Kinetic parameters.), body row 'N78A'; column 'k cat (sec-1)' = 7.6; column 'K M (uM)' = 66; column 'k cat /K M (M-1 sec-1) x 10^3' = 115; column 'Relative k cat' and column 'Relative k cat /K M' print unitless ratios against the WT row.

normalized_value_unit_evidence: kcat: printed Table 2 cell 7.6 in a column headed sec-1; sec-1 is the canonical s^-1, so no conversion is applied and the value is 7.6 s^(-1). Km: printed Table 2 cell 66 in a column headed uM; 66 / 1000 = 0.066 mM. kcat/Km: printed Table 2 cell 115 in a column headed (M-1 sec-1) x 10^3, that is 115000 M^-1 sec^-1; 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 115000 / 1000 = 115.0 s^-1 mM^-1, while the exported ratio is 115.15151515151514.

raw_value_unit_evidence: Table 2, body row 'N78A': k cat = 7.6 sec-1; K M = 66 uM; printed k cat /K M = 115 in a column headed (M-1 sec-1) x 10^3, that is 115 x 10^3 M^-1 sec^-1.

row_label: Table 2, body row N78A


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:Q86XE5 and applied mutation signature S198T to reconstruct the assayed variant sequence.

column_label: Table 2 (Kinetic parameters.), body row 'S198T'; column 'k cat (sec-1)' = 7.8; column 'K M (uM)' = 77; column 'k cat /K M (M-1 sec-1) x 10^3' = 101; column 'Relative k cat' and column 'Relative k cat /K M' print unitless ratios against the WT row.

normalized_value_unit_evidence: kcat: printed Table 2 cell 7.8 in a column headed sec-1; sec-1 is the canonical s^-1, so no conversion is applied and the value is 7.8 s^(-1). Km: printed Table 2 cell 77 in a column headed uM; 77 / 1000 = 0.077 mM. kcat/Km: printed Table 2 cell 101 in a column headed (M-1 sec-1) x 10^3, that is 101000 M^-1 sec^-1; 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 101000 / 1000 = 101.0 s^-1 mM^-1, while the exported ratio is 101.2987012987013.

raw_value_unit_evidence: Table 2, body row 'S198T': k cat = 7.8 sec-1; K M = 77 uM; printed k cat /K M = 101 in a column headed (M-1 sec-1) x 10^3, that is 101 x 10^3 M^-1 sec^-1.

row_label: Table 2, body row S198T


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

column_label: Table IV row DL-KHG; Km column.


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

column_label: Abstract/Fig. 5 discussion; substrate gamma-hydroxy-alpha-ketoglutarate; apparent Km = 1.33 mM.

row_label: Gamma-hydroxy-alpha-ketoglutarate


enzyme_display_name: UniProt P9WFX2

substrate_name: chorismate

enzyme: UniProt P9WFX2

substrate: chorismate


enzyme_display_name: UniProt P00900

organism: Serratia marcescens

enzyme: UniProt P00900


enzyme_display_name: 2-methylisocitrate lyase, mitochondrial

organism: Yarrowia lipolytica (strain CLIB 122 / E 150)

enzyme: 2-methylisocitrate lyase, mitochondrial


substrate_name: magnesium chloride (MgCl(2))

substrate: magnesium chloride (MgCl(2))


substrate_name: cysteine

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

substrate: cysteine


enzyme_display_name: UniProt Q2L887

organism: Aspergillus niger

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

enzyme: UniProt Q2L887


enzyme_display_name: anthranilate synthase

organism: Ailanthus altissimus

substrate_name: Gln

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

enzyme: anthranilate synthase

substrate: Gln


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


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:Q86XE5 and applied mutation signature N78T to reconstruct the assayed variant sequence.

column_label: Table 2. Kinetic parameters; row N78T; columns kcat (sec^-1), KM (uM), kcat/KM (M^-1 sec^-1) x 10^3.

normalized_value_unit_evidence: kcat paper=4.0 s^-1; Km paper=0.016 mM; kcat/Km paper=250 s^-1 mM^-1

table_label: Table 2. Kinetic parameters


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:Q86XE5 and applied mutation signature S198A to reconstruct the assayed variant sequence.

column_label: Table 2 (Kinetic parameters.), body row 'S198A'; column 'k cat (sec-1)' = 2.4; column 'K M (uM)' = 44; column 'k cat /K M (M-1 sec-1) x 10^3' = 55; column 'Relative k cat' and column 'Relative k cat /K M' print unitless ratios against the WT row.

normalized_value_unit_evidence: kcat: printed Table 2 cell 2.4 in a column headed sec-1; sec-1 is the canonical s^-1, so no conversion is applied and the value is 2.4 s^(-1). Km: printed Table 2 cell 44 in a column headed uM; 44 / 1000 = 0.044 mM. kcat/Km: printed Table 2 cell 55 in a column headed (M-1 sec-1) x 10^3, that is 55000 M^-1 sec^-1; 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 55000 / 1000 = 55.0 s^-1 mM^-1, while the exported ratio is 54.54545454545455.

raw_value_unit_evidence: Table 2, body row 'S198A': k cat = 2.4 sec-1; K M = 44 uM; printed k cat /K M = 55 in a column headed (M-1 sec-1) x 10^3, that is 55 x 10^3 M^-1 sec^-1.

row_label: Table 2, body row S198A


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:Q86XE5 and applied mutation signature S77A to reconstruct the assayed variant sequence.

column_label: Table 2 (Kinetic parameters.), body row 'S77A'; column 'k cat (sec-1)' = 2.5; column 'K M (uM)' = 84; column 'k cat /K M (M-1 sec-1) x 10^3' = 30; column 'Relative k cat' and column 'Relative k cat /K M' print unitless ratios against the WT row.

normalized_value_unit_evidence: kcat: printed Table 2 cell 2.5 in a column headed sec-1; sec-1 is the canonical s^-1, so no conversion is applied and the value is 2.5 s^(-1). Km: printed Table 2 cell 84 in a column headed uM; 84 / 1000 = 0.084 mM. kcat/Km: printed Table 2 cell 30 in a column headed (M-1 sec-1) x 10^3, that is 30000 M^-1 sec^-1; 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 30000 / 1000 = 30.0 s^-1 mM^-1, while the exported ratio is 29.76190476190476.

raw_value_unit_evidence: Table 2, body row 'S77A': k cat = 2.5 sec-1; K M = 84 uM; printed k cat /K M = 30 in a column headed (M-1 sec-1) x 10^3, that is 30 x 10^3 M^-1 sec^-1.

row_label: Table 2, body row S77A


column_label: Table 2. Kinetic parameters; row WT; columns kcat (sec^-1), KM (uM), kcat/KM (M^-1 sec^-1) x 10^3.

normalized_value_unit_evidence: kcat paper=6.1 s^-1; Km paper=0.011 mM; kcat/Km paper=555 s^-1 mM^-1

row_label: WT


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:Q86XE5 and applied mutation signature Y140F to reconstruct the assayed variant sequence.

column_label: Table 2. Kinetic parameters; row Y140F; columns kcat (sec^-1), KM (uM), kcat/KM (M^-1 sec^-1) x 10^3.

normalized_value_unit_evidence: kcat paper=5.2 s^-1; Km paper=0.008 mM; kcat/Km paper=650 s^-1 mM^-1


organism: Ogataea henricii

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

proof_lines: Gln-dependent enzyme that is composed of 2 NH4+-dependent subunits and of 2 amidotransferase subunits (I2II2)


enzyme_display_name: 2,3-dimethylmalate lyase

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

proof_lines:
mutant P240T
mutant enzyme P240T, at pH 7.5 and 25°C

enzyme: 2,3-dimethylmalate lyase


proof_lines:
mutant C124A
mutant enzyme C124A, at pH 7.5 and 25°C


proof_lines: wild type enzyme, in 50 mM K+-HEPES (pH 7.5 and 25°C)


proof_lines:
mutant P240S
mutant enzyme P240S, at pH 7.5 and 25°C


assay_conditions_summary: buffer direct optical method

proof_lines: direct optical method, K+-Hepes as buffer

proof_lines: pH and temperature not specified in the publication

proof_lines: direct optical method, imidazole as buffer


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


proof_lines: mutant enzyme P240T, in 50 mM K+-HEPES (pH 7.5 and 25°C)


proof_lines: mutant enzyme P240S, in 50 mM K+-HEPES (pH 7.5 and 25°C)


proof_lines:
smaller than 0.00001 s-1
larger than 5 mM
Ki above 5 mM


substrate_name: (R)-malate

proof_lines: kcat less than 0.00001 sec-1, pH and temperature not specified in the publication

substrate: (R)-malate


substrate_name: Phosphonopyruvate

proof_lines:
smaller than 0.00001 s-1
in 50 mM K+-HEPES (pH 7.5 and 25°C)

substrate: Phosphonopyruvate


proof_lines: mutant enzyme Y44F, in 50 mM K+-HEPES (pH 7.5 and 25°C)


proof_lines: mutant enzyme C124S, in 50 mM K+-HEPES (pH 7.5 and 25°C)


proof_lines: mutant enzyme D59S, in 50 mM K+-HEPES (pH 7.5 and 25°C)


proof_lines: mutant enzyme C124A, in 50 mM K+-HEPES (pH 7.5 and 25°C)


proof_lines: mutant enzyme D59A, in 50 mM K+-HEPES (pH 7.5 and 25°C)


proof_lines:
mutant C124S
mutant enzyme C124S, at pH 7.5 and 25°C


enzyme_display_name: (S)-citramalyl-CoA lyase

substrate_name: (3S)-citramalyl-CoA (for citramalyl-CoA lyase activity)

assay_conditions_summary: cofactor CoA

proof_lines: kcat is 0.12 sec(-1) for malate synthase reaction (PubMed:24334609). kcat is 0.09 sec(-1) for beta-methylmalate synthase reaction (PubMed:24334609). kcat is 0.135 sec(-1) for beta-methylmalate synthase reaction (PubMed:29056341). kcat is 0.

enzyme: (S)-citramalyl-CoA lyase


substrate_name: propionyl-CoA (for beta-methylmalate synthase)


substrate_name: acetyl-CoA (for malate synthase)

substrate: acetyl-CoA (for malate synthase)


organism: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)


substrate_name: anthranilate (with the dimeric form and for the phosphoribosyltransferase activity at pH 7.5)


substrate_name: phosphoribosylpyrophosphate (with the monomeric and dimeric forms and for the phosphoribosyltransferase activity at pH 7.5)


substrate_name: magnesium ion (with the monomeric and dimeric forms and for the phosphoribosyltransferase activity at pH 7.5)


substrate_name: glyoxylate (with acetyl-CoA as cosubstrate)


substrate_name: (S)-malyl-CoA (for malyl-CoA thioesterase activity)


enzyme_display_name: methylisocitrate lyase

organism: Escherichia coli (strain K12)

substrate_name: magnesium

smiles: [Mg]

assay_conditions_summary: pH 7

proof_lines: kcat is 12 sec(-1) for methylisocitrate lyase with threo-2-methylisocitrate as substrate (mixture of (2R,3S)- and (2S,3R)-2-methylisocitrate at pH 7 and 30 degrees Celsius).

enzyme: methylisocitrate lyase

substrate: magnesium


organism: Oryza sativa

sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_mutation_ranked_match and applied mutation signature Y367A to reconstruct the assayed variant sequence.

proof_lines: pH 8.3, 32°C, Y367A mutant anthranilate synthase alpha-subunit OASA2


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_mutation_ranked_match and applied mutation signature S126F to reconstruct the assayed variant sequence.

proof_lines: pH 8.3, 32°C, S126F mutant anthranilate synthase alpha-subunit OASA2


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_mutation_ranked_match and applied mutation signature A369L to reconstruct the assayed variant sequence.

proof_lines: pH 8.3, 32°C, A369L mutant anthranilate synthase alpha-subunit OASA2


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_mutation_ranked_match and applied mutation signature A369L/L530D to reconstruct the assayed variant sequence.

proof_lines: pH 8.3, 32°C, A369L/L530D mutant anthranilate synthase alpha-subunit OASA2


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_mutation_ranked_match and applied mutation signature S126F/L530D to reconstruct the assayed variant sequence.

proof_lines: pH 8.3, 32°C, S126F/L530D mutant anthranilate synthase alpha-subunit OASA2


organism: Arabidopsis thaliana

substrate_name: L-Glutamine; Chorismate

substrate: L-Glutamine; Chorismate


organism: Escherichia coli

substrate_name: Chorismate; L-Glutamine

substrate: Chorismate; L-Glutamine


substrate_name: Chorismate

substrate: Chorismate


organism: Pseudomonas putida


organism: Saccharomyces cerevisiae


organism: Salmonella typhimurium


organism: [Bacillus] caldotenax

substrate_name: chorismate

assay_conditions_summary: pH 9

column_label: Primary-paper prose in the wild-type ASI kinetic-parameter segment: kcat was 2.3 x 10^4 min^-1; the same sentence identifies chorismate Km and the preceding sentence fixes pH 9 and 37 C.

normalized_value_unit_evidence: 23000 min^-1 / 60 = 383.3333333333333 s^-1; target 383.0 s^-1 is accepted as whole-s^-1 rounding while preserving the unrounded conversion.

raw_value_unit_evidence: The paper reports kcat = 2.3 x 10^4 min^-1.

row_label: Wild-type B. caldotenax anthranilate synthase I; chorismate assay

table_label: Results and Discussion: Enzymatic Properties of B. caldotenax ASI (prose kinetic-parameter statement)


column_label: Primary-paper prose in the wild-type ASI kinetic-parameter segment: the Km values for NH4Cl and chorismate were 46 mM and 38 micromolar, respectively; the preceding sentence fixes pH 9 and 37 C.

raw_value_unit_evidence: The paper reports chorismate Km = 38 micromolar.


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature R429H with inferred residue-numbering offset -13 to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature R358H/R416H to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature R321H to reconstruct the assayed variant sequence.


organism: Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)

substrate_name: DL-threo-2-methylisocitrate (MICA) (at pH 7.5)

proof_lines: kcat is 5.24 sec(-1) for isocitrate lyase activity with threo-DL-isocitrate as substrate (at pH 6). kcat is 1.25 sec(-1) for methylisocitrate lyase activity with DL-threo-2-methylisocitrate as substrate (at pH 7.5).


organism: Oryza sativa subsp. japonica

substrate_name: chorismate (for recombinant ASA1 and ASB1 proteins synthesized with the wheat germ cell-free system)

proof_lines: kcat is 34.7 sec(-1) with chorismate as substrate (for recombinant ASA1 and ASB1 proteins synthesized with the wheat germ cell-free system).


substrate_name: chorismate (for recombinant ASA2 and ASB1 proteins synthesized with the wheat germ cell-free system)

proof_lines: kcat is 14.6 sec(-1) with chorismate as substrate (for recombinant ASA2 and ASB1 proteins synthesized with the wheat germ cell-free system).


proof_lines: kcat is 34.7 sec(-1) with chorismate as substrate (for recombinant ASA1 and ASB1 proteins synthesized with the wheat germ cell-free system). kcat is 14.6 sec(-1) with chorismate as substrate (for recombinant ASA2 and ASB1 proteins synthesiz

substrate: chorismate (for recombinant ASA1 and ASB1 proteins synthesized with the wheat germ cell-free system)


organism: Homo sapiens

substrate_name: Unknown

substrate: Unknown


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


enzyme_display_name: UniProt P0A853

substrate_name: L-tryptophan

enzyme: UniProt P0A853

substrate: L-tryptophan


substrate_name: S-ethyl-L-cysteine

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

substrate: S-ethyl-L-cysteine


enzyme_display_name: tyrosine phenol-lyase

organism: Symbiobacterium sp.

substrate_name: L-tyrosine

enzyme: tyrosine phenol-lyase

substrate: L-tyrosine


substrate_name: S-(o-nitrophenyl)-L-cysteine

substrate: S-(o-nitrophenyl)-L-cysteine


organism: Symbiobacterium thermophilum

substrate_name: S-methyl-L-Cys

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

substrate: S-methyl-L-Cys


organism: Pantoea agglomerans


substrate_name: S-methyl-L-cysteine

substrate: S-methyl-L-cysteine


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


substrate_name: beta-chloro-L-alanine

substrate: beta-chloro-L-alanine


substrate_name: L-Ser

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

substrate: L-Ser


enzyme_display_name: UniProt P31013

organism: Citrobacter freundii

substrate_name: S-Benzyl-L-cysteine

enzyme: UniProt P31013

substrate: S-Benzyl-L-cysteine


substrate_name: L-Tyr

proof_lines:
Raw SKiD Env: Temp=-----, pH=-----
Raw SKiD Env: Temp=25°C, pH=8
Raw SKiD Env: Temp=30°C, pH=8

substrate: L-Tyr


proof_lines:
Raw SKiD Env: Temp=25°C, pH=8
Raw SKiD Env: Temp=30°C, pH=8


proof_lines:
Raw SKiD Env: Temp=30°C, pH=8
Raw SKiD Env: Temp=25°C, pH=8


enzyme_display_name: UniProt Q8ZNC4

organism: Salmonella enterica subsp. enterica serovar Typhimurium

substrate_name: D-Lysine

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

proof_lines:
Raw SKiD Env: Temp=37°C, pH=7
Raw SKiD Env: Temp=25°C, pH=7

enzyme: UniProt Q8ZNC4

substrate: D-Lysine


substrate_name: D-ornithine

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

substrate: D-ornithine


substrate_name: NH3; Chorismate

substrate: NH3; Chorismate


organism: Catharanthus roseus

substrate_name: L-Glutamine; Chorismate

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

substrate: L-Glutamine; Chorismate


organism: Aspergillus niger

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


substrate_name: chorismate

substrate: chorismate


substrate_name: Gln

substrate: Gln


assay_conditions_summary: pH 7.5; 298.15 K; buffer imidazole or K+-Hepes

column_label: Table 1: Steady-state kinetic and competitive inhibition constants determined for A. niger DMML; 2R-Methylmalate row; 2R-Methylmalate row: kcat 2.64 +/- 0.09 s^-1; Km 2.2 +/- 0.2 mM; kcat/Km 1 × 10^3 M^-1 s^-1.

normalized_value_unit_evidence: Km already mM; kcat already s^-1; kcat/Km 1 × 10^3 M^-1 s^-1 normalized to 1 s^-1 mM^-1.

row_label: 2R-Methylmalate row


column_label: Table 1: Steady-state kinetic and competitive inhibition constants determined for A. niger DMML; 2R-Propyl-3S-methylmalate row; 2R-Propyl-3S-methylmalate row: kcat 0.79 +/- 0.01 s^-1; Km 2.7 +/- 0.1 mM; kcat/Km 3 × 10^2 M^-1 s^-1.

normalized_value_unit_evidence: Km already mM; kcat already s^-1; kcat/Km 3 × 10^2 M^-1 s^-1 normalized to 0.3 s^-1 mM^-1.

row_label: 2R-Propyl-3S-methylmalate row


organism: Chloroflexus aurantiacus

substrate_name: (S)-malyl-CoA (for L-malyl-CoA lyase activity)

assay_conditions_summary: pH 7.1; cofactor CoA

column_label: Table 2 properties table; Apparent Km values (mM); L-malyl-CoA entry 0.061 +/- 0.01.

normalized_value_unit_evidence: Paper reports L-malyl-CoA Km 0.061 mM; exported row is 0.01 mM.

raw_value_unit_evidence: Apparent Km values (mM): 0.061 +/- 0.01 (L-malyl-CoA)

row_label: Apparent Km values row for L-malyl-CoA

table_label: Table 2: Properties of recombinant L-malyl-CoA lyase/beta-methylmalyl-CoA lyase


substrate_name: (2R,3S)-beta-methylmalyl-CoA (for beta-methylmalyl-CoA lyase activity)

column_label: Table 2 properties table; Apparent Km values (mM); beta-methylmalyl-CoA entry 0.089 +/- 0.02.

normalized_value_unit_evidence: Paper reports beta-methylmalyl-CoA Km 0.089 mM.

raw_value_unit_evidence: Apparent Km values (mM): 0.089 +/- 0.02 (beta-methylmalyl-CoA)

row_label: Apparent Km values row for beta-methylmalyl-CoA


substrate_name: acetyl-CoA (for L-malyl-CoA lyase activity)

column_label: Table 2 properties table; Apparent Km values (mM); acetyl-CoA entry 0.36 +/- 0.15.

normalized_value_unit_evidence: Paper reports acetyl-CoA Km 0.36 mM.

raw_value_unit_evidence: Apparent Km values (mM): 0.36 +/- 0.15 (acetyl-CoA)

row_label: Apparent Km values row for acetyl-CoA


substrate_name: propionyl-CoA (for beta-methylmalyl-CoA lyase activity)

column_label: Table 2 properties table; Apparent Km values (mM); propionyl-CoA entry 1.2 +/- 0.6.

normalized_value_unit_evidence: Paper reports propionyl-CoA Km 1.2 mM.

raw_value_unit_evidence: Apparent Km values (mM): 1.2 +/- 0.6 (propionyl-CoA)

row_label: Apparent Km values row for propionyl-CoA


substrate_name: glyoxylate (for beta-methylmalyl-CoA and L-malyl-CoA lyase activities)

column_label: Table 2 properties table; Apparent Km values (mM); glyoxylate entry 2.0 +/- 0.5.

normalized_value_unit_evidence: Paper reports glyoxylate Km 2.0 mM.

raw_value_unit_evidence: Apparent Km values (mM): 2.0 +/- 0.5 (glyoxylate)

row_label: Apparent Km values row for glyoxylate


organism: Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.)

substrate_name: glyoxylate (for L-malyl-CoA formation)

column_label: PMC HTML Table 1 Mcl1 column reports 3.1 mM for glyoxylate in the acetyl-CoA + glyoxylate condensation; the same table separately lists 4.1 mM glyoxylate for the propionyl-CoA condition.

raw_value_unit_evidence: Km raw_value=3.1 raw_unit=mM

row_label: 3.1 (glyoxylate), acetyl-CoA + glyoxylate condition

table_label: Table 1. Molecular and catalytic properties of recombinant Mcl1 and Mcl2 from R. sphaeroides

substrate: glyoxylate (for L-malyl-CoA formation)


substrate_name: acetyl-CoA (for L-malyl-CoA formation)

column_label: Primary Results prose adjacent to Table 1 gives an apparent Km of 0.07 mM for acetyl-CoA in the acetyl-CoA + glyoxylate condensation reaction.

raw_value_unit_evidence: Km raw_value=0.07 raw_unit=mM

row_label: acetyl-CoA in acetyl-CoA + glyoxylate condensation to (3S)-malyl-CoA

table_label: Results prose adjacent to Table 1, Heterologous production of Mcl1 from R. sphaeroides

substrate: acetyl-CoA (for L-malyl-CoA formation)


substrate_name: propionyl-CoA (for beta-methylmalyl-CoA formation)

column_label: PMC HTML Table 1 Mcl1 column reports apparent Km values including 0.2 mM for propionyl-CoA in the propionyl-CoA + glyoxylate to beta-methylmalyl-CoA reaction.

raw_value_unit_evidence: Km raw_value=0.2 raw_unit=mM

row_label: 0.2 (propionyl-CoA)


column_label: PMC HTML Table 1 Mcl1 column reports apparent Km values including 0.02 mM for (3S)-malyl-CoA.

raw_value_unit_evidence: Km raw_value=0.02 raw_unit=mM


substrate_name: beta-methylmalyl-CoA

column_label: PMC HTML Table 1 Mcl1 column reports apparent Km values including 0.01 mM for beta-methylmalyl-CoA.

raw_value_unit_evidence: Km raw_value=0.01 raw_unit=mM

row_label: 0.01 (beta-methylmalyl-CoA)

substrate: beta-methylmalyl-CoA


organism: Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)

substrate_name: Unknown

substrate: Unknown


organism: Escherichia coli (strain K12)

substrate_name: threo-2-methylisocitrate (a mixture of (2R,3S)- and (2S,3R)-2-methylisocitrate in presence of 2 mM magnesium at pH 7 and 30 degrees Celsius)


substrate_name: threo-D-isocitrate (at pH 6.8 and 37 degrees Celsius)


organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

substrate_name: threo-D(S)-isocitrate (at pH 7.0)

proof_lines: The Vmax with threo-D(S)-isocitrate as substrate is 5-fold higher than with threo-D(S)-2-methylisocitrate as substrate.

substrate: threo-D(S)-isocitrate (at pH 7.0)


proof_lines: kcat is 74 sec(-1) for 2-methylisocitrate lyase with 2-methylisocitrate as substrate.


enzyme_display_name: UniProt Q54764

organism: Synechococcus elongatus

substrate_name: n-Heptanal

smiles: CCCCCCC=O

enzyme: UniProt Q54764

substrate: n-Heptanal


enzyme_display_name: UniProt Q55688

organism: Synechocystis sp. PCC 6803

substrate_name: n-hexadecanal

smiles: CCCCCCCCCCCCCCCC=O

enzyme: UniProt Q55688

substrate: n-hexadecanal


column_label: Table 1: Steady-state kinetic and competitive inhibition constants determined for A. niger DMML; 2R,3S- and 2S,3R-2-methylisocitrate row; 2R,3S- and 2S,3R-2-methylisocitrate row: kcat 0.13 +/- 0.01 s^-1; Km 12 +/- 3 mM; kcat/Km 1 × 10^1 M^-1 s^-1.

normalized_value_unit_evidence: Km already mM; kcat already s^-1; kcat/Km 1 × 10^1 M^-1 s^-1 normalized to 0.01 s^-1 mM^-1.

row_label: 2R,3S- and 2S,3R-2-methylisocitrate row


sequence_variant_note: Resolved canonical sequence from accession_anchored:Q2L887 and applied mutation signature C124A to reconstruct the assayed variant sequence.

column_label: PDF page 10, Table 3, row C124A under DMM: kcat=(1.78 +/- 0.05) x 10^-4 s^-1; Km=36 +/- 3 microM; kcat/Km=5 x 10^0 M^-1 s^-1. Table caption gives 50 mM K+-Hepes pH 7.5, 25 C, and 5 mM MgCl2.

normalized_value_unit_evidence: kcat=0.000178 s^-1; Km=0.036 mM; explicit paper kcat/Km=0.005 s^-1 mM^-1 after converting 5 M^-1 s^-1 by dividing by 1000.

row_label: C124A; DMM

table_label: Table 3: Steady-state kinetic constants determined for the A. niger DMML site-directed mutants


sequence_variant_note: Resolved canonical sequence from accession_anchored:Q2L887 and applied mutation signature C124S to reconstruct the assayed variant sequence.

column_label: PDF page 10, Table 3, row C124S under DMM: kcat=(1.21 +/- 0.05) x 10^-4 s^-1; Km=3600 +/- 300 microM; kcat/Km=3 x 10^-2 M^-1 s^-1. Table caption gives 50 mM K+-Hepes pH 7.5, 25 C, and 5 mM MgCl2.

normalized_value_unit_evidence: kcat=0.000121 s^-1; Km=3.6 mM; explicit paper kcat/Km=0.00003 s^-1 mM^-1 after converting 3 x 10^-2 M^-1 s^-1 by dividing by 1000.

row_label: C124S; DMM


sequence_variant_note: Resolved canonical sequence from accession_anchored:Q2L887 and applied mutation signature D59A to reconstruct the assayed variant sequence.

column_label: PDF page 10, Table 3, row D59A under DMM: kcat=(4.27 +/- 0.09) x 10^-4 s^-1; Km=7400 +/- 400 microM; kcat/Km=6 x 10^-2 M^-1 s^-1. Table caption gives 50 mM K+-Hepes pH 7.5, 25 C, and 5 mM MgCl2.

normalized_value_unit_evidence: kcat=0.000427 s^-1; Km=7.4 mM; explicit paper kcat/Km=0.00006 s^-1 mM^-1 after converting 6 x 10^-2 M^-1 s^-1 by dividing by 1000.

row_label: D59A; DMM


sequence_variant_note: Resolved canonical sequence from accession_anchored:Q2L887 and applied mutation signature D59S to reconstruct the assayed variant sequence.

column_label: PDF page 10, Table 3, row D59S under DMM: kcat=(1.4 +/- 0.1) x 10^-4 s^-1; Km=6000 +/- 1000 microM; kcat/Km=2 x 10^-2 M^-1 s^-1. Table caption gives 50 mM K+-Hepes pH 7.5, 25 C, and 5 mM MgCl2.

normalized_value_unit_evidence: kcat=0.00014 s^-1; Km=6.0 mM; explicit paper kcat/Km=0.00002 s^-1 mM^-1 after converting 2 x 10^-2 M^-1 s^-1 by dividing by 1000.

row_label: D59S; DMM


sequence_variant_note: Resolved canonical sequence from accession_anchored:Q2L887 and applied mutation signature P240S to reconstruct the assayed variant sequence.

column_label: PDF page 10, Table 3, row P240S footnote b under DMM: kcat=11.7 +/- 0.6 s^-1; Km=5900 +/- 700 microM; kcat/Km=2 x 10^3 M^-1 s^-1. Footnote b explains the soluble His6-tagged construct and matched His6-WT control.

normalized_value_unit_evidence: kcat=11.7 s^-1; Km=5.9 mM; explicit paper kcat/Km=2.0 s^-1 mM^-1 after converting 2 x 10^3 M^-1 s^-1 by dividing by 1000.

row_label: P240S footnote b; DMM


sequence_variant_note: Resolved canonical sequence from accession_anchored:Q2L887 and applied mutation signature P240T to reconstruct the assayed variant sequence.

column_label: PDF page 10, Table 3, row P240T under DMM: kcat=2.8 +/- 0.2 s^-1; Km=4100 +/- 800 microM; kcat/Km=7 x 10^2 M^-1 s^-1. Table caption gives 50 mM K+-Hepes pH 7.5, 25 C, and 5 mM MgCl2.

normalized_value_unit_evidence: kcat=2.8 s^-1; Km=4.1 mM; explicit paper kcat/Km=0.7 s^-1 mM^-1 after converting 7 x 10^2 M^-1 s^-1 by dividing by 1000.

row_label: P240T; DMM


column_label: Table 1: Steady-state kinetic and competitive inhibition constants determined for A. niger DMML; 2R,3S-Dimethylmalate row; 2R,3S-Dimethylmalate row: kcat 19.2 +/- 0.5 s^-1; Km 0.22 +/- 0.02 mM; kcat/Km 9 × 10^4 M^-1 s^-1.

normalized_value_unit_evidence: Km already mM; kcat already s^-1; kcat/Km 9 × 10^4 M^-1 s^-1 normalized to 90 s^-1 mM^-1.

row_label: 2R,3S-Dimethylmalate row


column_label: Table 1: Steady-state kinetic and competitive inhibition constants determined for A. niger DMML; 2R-Ethyl-3S-methylmalate row; 2R-Ethyl-3S-methylmalate row: kcat 63 +/- 2 s^-1; Km 1.17 +/- 0.09 mM; kcat/Km 5 × 10^4 M^-1 s^-1.

normalized_value_unit_evidence: Km already mM; kcat already s^-1; kcat/Km 5 × 10^4 M^-1 s^-1 normalized to 50 s^-1 mM^-1.

row_label: 2R-Ethyl-3S-methylmalate row


organism: Escherichia coli

substrate_name: L-Tyr

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


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


substrate_name: L-Asp

substrate: L-Asp


substrate_name: L-Glu

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

substrate: L-Glu


enzyme_display_name: tryptophanase

organism: Porphyromonas gingivalis

substrate_name: L-Trp

assay_conditions_summary: pH 7.5; 310.15 K; buffer 200 mM sodium phosphate

proof_lines: purified recombinant tryptophanase in 200 mM sodium phosphate buffer (pH 7.5), at 37°C

proof_lines: purified recombinant tryptophanase in 200 mM potassium phosphate buffer (pH 7.5), at 37°C

enzyme: tryptophanase

substrate: L-Trp


substrate_name: S-methyl-L-cysteine

assay_conditions_summary: pH 7.5; 310.15 K; buffer 200 mM potassium phosphate

substrate: S-methyl-L-cysteine


substrate_name: S-ethyl-L-cysteine

substrate: S-ethyl-L-cysteine


enzyme_display_name: 3-hydroxybenzoate synthase

organism: Lentzea aerocolonigenes

substrate_name: chorismate

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

enzyme: 3-hydroxybenzoate synthase


organism: Prevotella intermedia


substrate_name: L-tryptophan

substrate: L-tryptophan


enzyme_display_name: 4-hydroxy-2-oxohexanoate aldolase

organism: Burkholderia xenovorans

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

enzyme: 4-hydroxy-2-oxohexanoate aldolase


organism: Aeromonas phenologenes

substrate: L-Tyr


organism: Streptomyces conglobatus


enzyme_display_name: UniProt A0A0H2UN41

organism: Streptococcus pneumoniae

substrate_name: D-ribulose 5-phosphate

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

enzyme: UniProt A0A0H2UN41

substrate: D-ribulose 5-phosphate


organism: Xylella fastidiosa

substrate: chorismate


enzyme_display_name: (4S)-4-hydroxy-2-oxoglutarate aldolase

organism: Azotobacter vinelandii

enzyme: (4S)-4-hydroxy-2-oxoglutarate aldolase


organism: Paraburkholderia xenovorans

sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature L87W/Y290F to reconstruct the assayed variant sequence.

assay_conditions_summary: pH 8

proof_lines: L87W/Y290F variant of BphI, steady-state kinetic parameter, pH 8.0, 25°C

proof_lines: L87W/Y290F variant of BphI, app. Km-value, steady-state kinetic parameter, pH 8.0, 25°C

proof_lines: L87W/Y290F variant of BphI, app. kcat/Km-value, steady-state kinetic parameter, pH 8.0, 25°C


substrate_name: oxaloacetate

sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P51015 and applied mutation signature L87N to reconstruct the assayed variant sequence.

assay_conditions_summary: pH 8; 298.15 K; buffer 100 mM HEPES

column_label: Table 2: Steady-State Kinetic Parameters of BphI and Its Variants for Oxaloacetate Decarboxylation (J. Am. Chem. Soc. 2012, 134(1), 507-513); enzyme row 'L87N'; column block 'oxaloacetate decarboxylation'; column 'Km,app (mM)' = 0.21; column 'kcat (10^-1 s^-1)' = 0.5; column 'kcat/Km,app (M^-1 s^-1)' = 254.

normalized_value_unit_evidence: Km: printed Table 2 cell 0.21 mM; already in mM, so the canonical value is 0.21 mM; the catalog value is 0.21 mM. kcat: printed Table 2 cell 0.5 x 10^-1 s^-1 under the column head kcat (10^-1 s^-1); already in s^-1 after the printed power of ten is applied, giving 0.05 s^(-1); the catalog value is 0.05 s^(-1). kcat/Km: printed Table 2 cell 254 M^-1 s^-1 under the column head kcat/Km,app (M^-1 s^-1); 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 254.0 / 1000 = 0.254 s^-1 mM^-1.

raw_value_unit_evidence: Table 2, enzyme row 'L87N', column block 'oxaloacetate decarboxylation': Km,app = 0.21 mM; kcat = 0.5 (column head kcat (10^-1 s^-1)); printed kcat/Km,app = 254 M^-1 s^-1.

substrate: oxaloacetate


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P51015 and applied mutation signature L87N/Y290F to reconstruct the assayed variant sequence.

column_label: Table 2: Steady-State Kinetic Parameters of BphI and Its Variants for Oxaloacetate Decarboxylation (J. Am. Chem. Soc. 2012, 134(1), 507-513); enzyme row 'L87N;Y290F'; column block 'oxaloacetate decarboxylation'; column 'Km,app (mM)' = 0.84; column 'kcat (10^-1 s^-1)' = 0.8; column 'kcat/Km,app (M^-1 s^-1)' = 98.

normalized_value_unit_evidence: Km: printed Table 2 cell 0.84 mM; already in mM, so the canonical value is 0.84 mM; the catalog value is 0.84 mM. kcat: printed Table 2 cell 0.8 x 10^-1 s^-1 under the column head kcat (10^-1 s^-1); already in s^-1 after the printed power of ten is applied, giving 0.08 s^(-1); the catalog value is 0.08 s^(-1). kcat/Km: printed Table 2 cell 98 M^-1 s^-1 under the column head kcat/Km,app (M^-1 s^-1); 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 98.0 / 1000 = 0.098 s^-1 mM^-1.

raw_value_unit_evidence: Table 2, enzyme row 'L87N;Y290F', column block 'oxaloacetate decarboxylation': Km,app = 0.84 mM; kcat = 0.8 (column head kcat (10^-1 s^-1)); printed kcat/Km,app = 98 M^-1 s^-1.


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature L87N/Y290F to reconstruct the assayed variant sequence.

proof_lines: L87N/Y290F variant of BphI, steady-state kinetic parameter, pH 8.0, 25°C

proof_lines: L87N/Y290F variant of BphI, app. Km-value, steady-state kinetic parameter, pH 8.0, 25°C

proof_lines: L87N/Y290F variant of BphI, app. kcat/Km-value, steady-state kinetic parameter, pH 8.0, 25°C


substrate_name: propionaldehyde

smiles: CCC=O

proof_lines: L87N/Y290F variant of BphI, app. kcat-value, steady-state kinetic parameter, pH 8.0, 25°C

substrate: propionaldehyde


substrate_name: pyruvate

substrate: pyruvate


proof_lines: L87W/Y290F variant of BphI, app. kcat-value, steady-state kinetic parameter, pH 8.0, 25°C


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P51015 and applied mutation signature L87W/Y290F to reconstruct the assayed variant sequence.

column_label: Table 5: Steady-State Kinetic Parameters for the Utilization of Pyruvate in the Aldol Addition Reaction (J. Am. Chem. Soc. 2012, 134(1), 507-513); enzyme row 'L87W;Y290F'; column block 'pyruvate'; column 'Km,app (mM)' = 38.2; column 'kcat,app (s^-1)' = 0.16; column '(kcat/Km)app (M^-1 s^-1)' = 4.3.

normalized_value_unit_evidence: Km: printed Table 5 cell 38.2 mM; already in mM, so the canonical value is 38.2 mM; the catalog value is 38.2 mM. kcat: printed Table 5 cell 0.16 s^-1 under the column head kcat,app (s^-1); already in s^-1 after the printed power of ten is applied, giving 0.16 s^(-1); the catalog value is 0.16 s^(-1). kcat/Km: printed Table 5 cell 4.3 M^-1 s^-1 under the column head (kcat/Km)app (M^-1 s^-1); 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 4.3 / 1000 = 0.0043 s^-1 mM^-1.

raw_value_unit_evidence: Table 5, enzyme row 'L87W;Y290F', column block 'pyruvate': Km,app = 38.2 mM; kcat,app = 0.16 s^-1; printed (kcat/Km)app = 4.3 M^-1 s^-1.


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature Y290F to reconstruct the assayed variant sequence.

proof_lines: Y290F variant of BphI, app. kcat-value, steady-state kinetic parameter, pH 8.0, 25°C

proof_lines: Y290F variant of BphI, app. Km-value, steady-state kinetic parameter, pH 8.0, 25°C

proof_lines: Y290F variant of BphI, app. kcat/Km-value, steady-state kinetic parameter, pH 8.0, 25°C


substrate_name: Butyraldehyde

smiles: CCCC=O

substrate: Butyraldehyde


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P51015 and applied mutation signature Y290F to reconstruct the assayed variant sequence.

column_label: Table 5: Steady-State Kinetic Parameters for the Utilization of Pyruvate in the Aldol Addition Reaction (J. Am. Chem. Soc. 2012, 134(1), 507-513); enzyme row 'Y290F'; column block 'pyruvate'; column 'Km,app (mM)' = 20.0; column 'kcat,app (s^-1)' = 0.19; column '(kcat/Km)app (M^-1 s^-1)' = 8.4.

normalized_value_unit_evidence: Km: printed Table 5 cell 20.0 mM; already in mM, so the canonical value is 20.0 mM; the catalog value is 20.0 mM. kcat: printed Table 5 cell 0.19 s^-1 under the column head kcat,app (s^-1); already in s^-1 after the printed power of ten is applied, giving 0.19 s^(-1); the catalog value is 0.19 s^(-1). kcat/Km: printed Table 5 cell 8.4 M^-1 s^-1 under the column head (kcat/Km)app (M^-1 s^-1); 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 8.4 / 1000 = 0.0084 s^-1 mM^-1.

raw_value_unit_evidence: Table 5, enzyme row 'Y290F', column block 'pyruvate': Km,app = 20.0 mM; kcat,app = 0.19 s^-1; printed (kcat/Km)app = 8.4 M^-1 s^-1.


substrate_name: acetaldehyde

smiles: CC=O

substrate: acetaldehyde


column_label: Table 2: Steady-State Kinetic Parameters of BphI and Its Variants for Oxaloacetate Decarboxylation (J. Am. Chem. Soc. 2012, 134(1), 507-513); enzyme row 'Y290F'; column block 'oxaloacetate decarboxylation'; column 'Km,app (mM)' = 0.92; column 'kcat (10^-1 s^-1)' = 2.7; column 'kcat/Km,app (M^-1 s^-1)' = 530.

normalized_value_unit_evidence: Km: printed Table 2 cell 0.92 mM; already in mM, so the canonical value is 0.92 mM; the catalog value is 0.92 mM. kcat: printed Table 2 cell 2.7 x 10^-1 s^-1 under the column head kcat (10^-1 s^-1); already in s^-1 after the printed power of ten is applied, giving 0.27 s^(-1); the catalog value is 0.27 s^(-1). kcat/Km: printed Table 2 cell 530 M^-1 s^-1 under the column head kcat/Km,app (M^-1 s^-1); 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 530.0 / 1000 = 0.53 s^-1 mM^-1.

raw_value_unit_evidence: Table 2, enzyme row 'Y290F', column block 'oxaloacetate decarboxylation': Km,app = 0.92 mM; kcat = 2.7 (column head kcat (10^-1 s^-1)); printed kcat/Km,app = 530 M^-1 s^-1.


column_label: Table 6: Steady-State Kinetic Parameters for the Utilization of Various Aldehydes of the BphI Wild Type and Variants in the Aldol Addition Reaction (J. Am. Chem. Soc. 2012, 134(1), 507-513); enzyme row 'L87N;Y290F'; column block 'acetaldehyde, two carbons'; column 'Km,app (mM)' = 70.7; column 'kcat,app (s^-1)' = 0.30; column 'kcat/Km,app (M^-1 s^-1)' = 4.3.

normalized_value_unit_evidence: Km: printed Table 6 cell 70.7 mM; already in mM, so the canonical value is 70.7 mM; the catalog value is 70.7 mM. kcat: printed Table 6 cell 0.30 s^-1 under the column head kcat,app (s^-1); already in s^-1 after the printed power of ten is applied, giving 0.3 s^(-1); the catalog value is 0.3 s^(-1). kcat/Km: printed Table 6 cell 4.3 M^-1 s^-1 under the column head kcat/Km,app (M^-1 s^-1); 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 4.3 / 1000 = 0.0043 s^-1 mM^-1.

raw_value_unit_evidence: Table 6, enzyme row 'L87N;Y290F', column block 'acetaldehyde, two carbons': Km,app = 70.7 mM; kcat,app = 0.30 s^-1; printed kcat/Km,app = 4.3 M^-1 s^-1.


column_label: Table 2: Steady-State Kinetic Parameters of BphI and Its Variants for Oxaloacetate Decarboxylation (J. Am. Chem. Soc. 2012, 134(1), 507-513); enzyme row 'L87W;Y290F'; column block 'oxaloacetate decarboxylation'; column 'Km,app (mM)' = 6.2; column 'kcat (10^-1 s^-1)' = 4; column 'kcat/Km,app (M^-1 s^-1)' = 64.

normalized_value_unit_evidence: Km: printed Table 2 cell 6.2 mM; already in mM, so the canonical value is 6.2 mM; the catalog value is 6.2 mM. kcat: printed Table 2 cell 4 x 10^-1 s^-1 under the column head kcat (10^-1 s^-1); already in s^-1 after the printed power of ten is applied, giving 0.4 s^(-1); the catalog value is 0.4 s^(-1). kcat/Km: printed Table 2 cell 64 M^-1 s^-1 under the column head kcat/Km,app (M^-1 s^-1); 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 64.0 / 1000 = 0.064 s^-1 mM^-1.

raw_value_unit_evidence: Table 2, enzyme row 'L87W;Y290F', column block 'oxaloacetate decarboxylation': Km,app = 6.2 mM; kcat = 4 (column head kcat (10^-1 s^-1)); printed kcat/Km,app = 64 M^-1 s^-1.


column_label: Table 6: Steady-State Kinetic Parameters for the Utilization of Various Aldehydes of the BphI Wild Type and Variants in the Aldol Addition Reaction (J. Am. Chem. Soc. 2012, 134(1), 507-513); enzyme row 'L87W;Y290F'; column block 'acetaldehyde, two carbons'; column 'Km,app (mM)' = 86.3; column 'kcat,app (s^-1)' = 0.59; column 'kcat/Km,app (M^-1 s^-1)' = 6.9.

normalized_value_unit_evidence: Km: printed Table 6 cell 86.3 mM; already in mM, so the canonical value is 86.3 mM; the catalog value is 86.3 mM. kcat: printed Table 6 cell 0.59 s^-1 under the column head kcat,app (s^-1); already in s^-1 after the printed power of ten is applied, giving 0.59 s^(-1); the catalog value is 0.59 s^(-1). kcat/Km: printed Table 6 cell 6.9 M^-1 s^-1 under the column head kcat/Km,app (M^-1 s^-1); 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 6.9 / 1000 = 0.0069 s^-1 mM^-1.

raw_value_unit_evidence: Table 6, enzyme row 'L87W;Y290F', column block 'acetaldehyde, two carbons': Km,app = 86.3 mM; kcat,app = 0.59 s^-1; printed kcat/Km,app = 6.9 M^-1 s^-1.


column_label: Table 2: Steady-State Kinetic Parameters of BphI and Its Variants for Oxaloacetate Decarboxylation (J. Am. Chem. Soc. 2012, 134(1), 507-513); enzyme row 'wild-type BphI'; column block 'oxaloacetate decarboxylation'; column 'Km,app (mM)' = 7.4; column 'kcat (10^-1 s^-1)' = 163; column 'kcat/Km,app (M^-1 s^-1)' = 2200.

normalized_value_unit_evidence: Km: printed Table 2 cell 7.4 mM; already in mM, so the canonical value is 7.4 mM; the catalog value is 7.4 mM. kcat: printed Table 2 cell 163 x 10^-1 s^-1 under the column head kcat (10^-1 s^-1); already in s^-1 after the printed power of ten is applied, giving 16.3 s^(-1); the catalog value is 16.3 s^(-1). kcat/Km: printed Table 2 cell 2200 M^-1 s^-1 under the column head kcat/Km,app (M^-1 s^-1); 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 2200.0 / 1000 = 2.2 s^-1 mM^-1.

raw_value_unit_evidence: Table 2, enzyme row 'wild-type BphI', column block 'oxaloacetate decarboxylation': Km,app = 7.4 mM; kcat = 163 (column head kcat (10^-1 s^-1)); printed kcat/Km,app = 2200 M^-1 s^-1.


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P51015 and applied mutation signature H20S to reconstruct the assayed variant sequence.

assay_conditions_summary: pH 8; 298.15 K; buffer 100 mM HEPES; cofactor NADH

column_label: Table 5 (Biochemistry 2011, 50, 3559-3569): steady-state kinetic parameters for the aldol cleavage of (4S)-HOPA; the transcribed cells come from the 'Km (uM)', 'kcat (x 10^-2 s^-1)' and 'kcat/Km (x 10^2 M^-1 s^-1)' of construct 'H20S' at column '(4S)-HOPA': Km = 228 uM, kcat = 8.9 x 10^-2 s^-1, kcat/Km = 3.4 x 10^2 M^-1 s^-1.

normalized_value_unit_evidence: Km: printed Table 5 cell 228 uM; 228 / 1000 = 0.228 mM; the exported value is 0.228 mM. kcat: printed Table 5 cell 8.9 under the column head kcat (x 10^-2 s^-1); 8.9 x 10^-2 = 0.08900000000000001 s^-1; the exported value is 0.089 s^(-1). kcat/Km: printed Table 5 cell 3.4 x 10^2 M^-1 s^-1; 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 340.0 / 1000 = 0.34 s^-1 mM^-1, which this pass carries as the paper value of the catalytic efficiency.

raw_value_unit_evidence: Table 5, construct 'H20S', (4S)-HOPA: Km = 228 uM; kcat = 8.9 x 10^-2 s^-1; printed kcat/Km = 3.4 x 10^2 M^-1 s^-1.

row_label: Table 5, row 'H20S', (4S)-HOPA block


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

proof_lines: H20A variant of BphI, steady-state kinetic parameter, pH 8.0, 25°C


proof_lines: Y290F variant of BphI, steady-state kinetic parameter, pH 8.0, 25°C


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature Y290S to reconstruct the assayed variant sequence.

proof_lines: Y290S variant of BphI, steady-state kinetic parameter, pH 8.0, 25°C


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P51015 and applied mutation signature L87A to reconstruct the assayed variant sequence.

assay_conditions_summary: pH 8; 298.15 K; buffer varying concentrations of aldehydes in 100 mM HEPES

column_label: Table 2 (Biochemistry 2011, 50, 3559-3569): aldehyde specificities of BphI in the aldol addition reaction; the transcribed cells come from the 'Km,app (mM)', 'kcat,app (s^-1)' and '(kcat/Km)app (M^-1 s^-1)' of construct 'L87A' at column 'butryaldehyde (four carbons)': Km = 323 mM, kcat = 0.260 s^-1, kcat/Km = 0.790 M^-1 s^-1.

normalized_value_unit_evidence: Km: printed Table 2 cell 323 mM; already in mM, so no unit conversion applies; the exported value is 323.0 mM. kcat: printed Table 2 cell 0.260 s^-1; already in s^-1, so no unit conversion applies; the exported value is 0.26 s^(-1). kcat/Km: printed Table 2 cell 0.790 M^-1 s^-1; 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 0.79 / 1000 = 0.00079 s^-1 mM^-1, which this pass carries as the paper value of the catalytic efficiency.

raw_value_unit_evidence: Table 2, construct 'L87A', butryaldehyde (four carbons): Km = 323 mM; kcat = 0.260 s^-1; printed kcat/Km = 0.790 M^-1 s^-1.

row_label: Table 2, kinetic-parameter cells of construct 'L87A', column 'butryaldehyde (four carbons)'


column_label: Table 2 (Biochemistry 2011, 50, 3559-3569): aldehyde specificities of BphI in the aldol addition reaction; the transcribed cells come from the 'Km,app (mM)', 'kcat,app (s^-1)' and '(kcat/Km)app (M^-1 s^-1)' of construct 'L87A' at column 'propionaldehyde (three carbons)': Km = 16.8 mM, kcat = 0.290 s^-1, kcat/Km = 17.5 M^-1 s^-1.

normalized_value_unit_evidence: Km: printed Table 2 cell 16.8 mM; already in mM, so no unit conversion applies; the exported value is 16.8 mM. kcat: printed Table 2 cell 0.290 s^-1; already in s^-1, so no unit conversion applies; the exported value is 0.29 s^(-1). kcat/Km: printed Table 2 cell 17.5 M^-1 s^-1; 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 17.5 / 1000 = 0.0175 s^-1 mM^-1, which this pass carries as the paper value of the catalytic efficiency.

raw_value_unit_evidence: Table 2, construct 'L87A', propionaldehyde (three carbons): Km = 16.8 mM; kcat = 0.290 s^-1; printed kcat/Km = 17.5 M^-1 s^-1.

row_label: Table 2, kinetic-parameter cells of construct 'L87A', column 'propionaldehyde (three carbons)'


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature L87A/L89A to reconstruct the assayed variant sequence.

proof_lines: L87A/L89A variant of BphI, app. kcat-value, pH 8.0, 25°C

proof_lines: L87A/L89A variant of BphI, app. Km-value, pH 8.0, 25°C

proof_lines: L87A/L89A variant of BphI, app. kcat/Km-value, pH 8.0, 25°C


assay_conditions_summary: pH 8; 298.15 K; buffer varying concentrations of pyruvate in 100 mM HEPES

column_label: Table 1 (Biochemistry 2011, 50, 3559-3569): steady-state kinetic parameters for the utilization of pyruvate in the aldol addition reaction; the transcribed cells come from the 'Km,app (mM)', 'kcat,app (s^-1)' and '(kcat/Km)app (M^-1 s^-1)' of construct 'L87A' at column 'varied substrate pyruvate': Km = 20.2 mM, kcat = 0.32 s^-1, kcat/Km = 15.9 M^-1 s^-1.

normalized_value_unit_evidence: Km: printed Table 1 cell 20.2 mM; already in mM, so no unit conversion applies; the exported value is 20.2 mM. kcat: printed Table 1 cell 0.32 s^-1; already in s^-1, so no unit conversion applies; the exported value is 0.32 s^(-1). kcat/Km: printed Table 1 cell 15.9 M^-1 s^-1; 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 15.9 / 1000 = 0.0159 s^-1 mM^-1, which this pass carries as the paper value of the catalytic efficiency.

raw_value_unit_evidence: Table 1, construct 'L87A', varied substrate pyruvate: Km = 20.2 mM; kcat = 0.32 s^-1; printed kcat/Km = 15.9 M^-1 s^-1.

row_label: Table 1, kinetic-parameter cells of construct 'L87A', column 'varied substrate pyruvate'