organism: Photobacterium damselae subsp. piscicida


enzyme_display_name: glutamate decarboxylase

organism: Oryza sativa

substrate_name: L-glutamate

source_db: brenda

kcat_display: Not reported

ki_display: Not reported

kcat_over_km_display: Not reported

mutation_signature: Unknown

source_license: CC BY 4.0

km_unit: mM

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

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

proof_lines:
partially purified enzyme, pH 5.6, 40°C
pH 5.6, 40°C

enzyme: glutamate decarboxylase

substrate: L-glutamate

source: brenda


organism: Neurospora crassa

substrate_name: L-Glu

verification_status: unverified

substrate: L-Glu

status: unverified


organism: Priestia aryabhattai


enzyme_display_name: malonyl-CoA decarboxylase

organism: Rattus norvegicus

substrate_name: malonyl-CoA

assay_conditions_summary: pH 8.5; 333.15 K; buffer 100 mM potassium phosphate; cofactor CoA

proof_lines: gastrocnemius after 5 min of contraction

proof_lines: in 100 mM potassium phosphate buffer (pH 8.5) and 1 mM thiophenol, at 60°C

enzyme: malonyl-CoA decarboxylase

substrate: malonyl-CoA


enzyme_display_name: aspartate 1-decarboxylase

organism: Pyrococcus furiosus

substrate_name: L-aspartate

enzyme: aspartate 1-decarboxylase

substrate: L-aspartate


organism: Rhizobium leguminosarum

assay_conditions_summary: cofactor CoA


substrate_name: L-Glutamate

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

ki_unit: mM

proof_lines: isoform GAD67, treated with trypsin, which also increases vmax value by 31%

proof_lines: isoform GAD65, treated with trypsin, which also increases vmax value by 33%

substrate: L-Glutamate


organism: Saccharomyces cerevisiae


organism: Solanum tuberosum


organism: Sus scrofa

proof_lines:
enzyme form alpha
enzyme form beta
gamma-form


organism: Streptococcus thermophilus


organism: Tribolium castaneum

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

mutation_type: substitution


organism: Vicia faba


organism: Vigna unguiculata


organism: Corynebacterium jeikeium

km_display: Not reported

protein_accession_database: UniProt

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

assay_conditions_summary: pH 7

data_origin: experimental


enzyme_display_name: UniProt P32377

source_db: skid

source_license: CC BY-NC-ND 4.0

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

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

enzyme: UniProt P32377

source: skid


enzyme_display_name: UniProt Q9FD73

organism: Staphylococcus epidermidis

enzyme: UniProt Q9FD73


substrate_name: ATP

substrate: ATP


proof_lines:
Raw SKiD Env: Temp=-----, pH=-----
Raw SKiD Env: Temp=30°C, pH=7


enzyme_display_name: UDP-glucuronate decarboxylase

organism: Papiliotrema laurentii

substrate_name: UDPglucuronate

enzyme: UDP-glucuronate decarboxylase

substrate: UDPglucuronate


enzyme_display_name: UniProt P06132

organism: Homo sapiens

substrate_name: uroporphyrinogen-III

enzyme: UniProt P06132

substrate: uroporphyrinogen-III


substrate_name: uroporphyrinogen-I

substrate: uroporphyrinogen-I


enzyme_display_name: ribulose-bisphosphate carboxylase

organism: Paracoccus denitrificans

enzyme: ribulose-bisphosphate carboxylase


substrate_name: D-ribulose 1,5-bisphosphate

substrate: D-ribulose 1,5-bisphosphate


enzyme_display_name: UniProt O93627

organism: Thermococcus kodakarensis

enzyme: UniProt O93627


enzyme_display_name: UniProt P04718

organism: Rhodospirillum rubrum

smiles: O=O

enzyme: UniProt P04718


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


enzyme_display_name: UniProt O28635

organism: Archaeoglobus fulgidus

proof_lines:
Raw SKiD Env: Temp=83°C, pH=-----
Raw SKiD Env: Temp=83°C, pH=8.3

enzyme: UniProt O28635


enzyme_display_name: Ribulose bisphosphate carboxylase large chain

organism: Hydrogenophaga pseudoflava

substrate_name: ribulose 1,5-bisphosphate

source_db: uniprot

substrate: ribulose 1,5-bisphosphate

source: uniprot


smiles: [Co]

enzyme: Ribulose bisphosphate carboxylase large chain


organism: Xanthobacter flavus

source_db: oed

smiles: O=C=O

source: oed


substrate_name: D-Ribulose 1,5-bisphosphate; H2O; CO2

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

substrate: D-Ribulose 1,5-bisphosphate; H2O; CO2


organism: Zea mays

substrate_name: H2O; CO2; D-Ribulose 1,5-bisphosphate

substrate: H2O; CO2; D-Ribulose 1,5-bisphosphate


organism: Bradyrhizobium diazoefficiens


substrate_name: CO2; H2O; D-Ribulose 1,5-bisphosphate

substrate: CO2; H2O; D-Ribulose 1,5-bisphosphate


organism: Nicotiana tabacum

substrate_name: CO2; D-Ribulose 1,5-bisphosphate; H2O

substrate: CO2; D-Ribulose 1,5-bisphosphate; H2O


substrate_name: D-Ribulose 1,5-bisphosphate; CO2; H2O

substrate: D-Ribulose 1,5-bisphosphate; CO2; H2O


substrate_name: H2O; D-Ribulose 1,5-bisphosphate; CO2

substrate: H2O; D-Ribulose 1,5-bisphosphate; CO2


organism: Rhodobacter sphaeroides


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature L341M to reconstruct the assayed variant sequence.


enzyme_display_name: diphosphomevalonate decarboxylase

organism: Cymbopogon citratus

enzyme: diphosphomevalonate decarboxylase


substrate_name: GTP

substrate: GTP


substrate_name: CTP

substrate: CTP


assay_conditions_summary: cofactor ATP


organism: Thiomicrospira thyasirae


organism: Equus caballus


organism: Synechococcus sp.

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


substrate_name: D-Ribulose 1,5-bisphosphate

kcat_over_km_origin: calculated

substrate: D-Ribulose 1,5-bisphosphate


organism: Synechococcus elongatus


organism: Gossypium hirsutum


substrate_name: phosphoenolpyruvate

substrate: phosphoenolpyruvate


organism: Rattus norvegicus


substrate_name: phosphopantothenoyl-L-Cys

substrate: phosphopantothenoyl-L-Cys


organism: Acinetobacter sp.


organism: Aphanothece halophytica


organism: Lolium giganteum

proof_lines: 20°C, pH not specified in the publication

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

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


organism: Selenomonas ruminantium

substrate_name: ADP

assay_conditions_summary: cofactor ADP

substrate: ADP


organism: Helianthus tuberosus

substrate_name: UDPglucuronate

substrate: UDPglucuronate


organism: Lemna minor


organism: Oryctolagus cuniculus


organism: Flavobacterium johnsoniae


organism: Sus scrofa


enzyme_display_name: uroporphyrinogen decarboxylase

organism: Homo sapiens

substrate_name: 5-COOH-porphyrinogen III

proof_lines:
isoenzyme I
isoenzyme II
enzyme from healthy individuals

enzyme: uroporphyrinogen decarboxylase

substrate: 5-COOH-porphyrinogen III


organism: Neohelice granulata


organism: Parachlorella kessleri

substrate_name: uroporphyrinogen III

substrate: uroporphyrinogen III


organism: Sorghum bicolor


organism: Eucalyptus moorei

substrate_name: D-ribulose 1,5-bisphosphate

proof_lines: in 100 mM Bicine-NaOH pH 8.0, 20 mM MgCl2, at 25°C

substrate: D-ribulose 1,5-bisphosphate


organism: Aphanocapsa alpicola


organism: Eucalyptus neglecta


organism: Panicum milioides


organism: Plectonema boryanum


organism: Helianthus maximus


organism: Anaerolinea thermophila

sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature R71A to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature R26V to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature N20K/H194M to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature N20K to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature H194M to reconstruct the assayed variant sequence.


substrate_name: ATP

assay_conditions_summary: pH 7.5; 303.15 K; cofactor ATP

substrate: ATP


organism: Synechocystis sp.

verification_status: corrected

sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P54205 and applied mutation signature H298A with inferred residue-numbering offset -5 to reconstruct the assayed variant sequence.

column_label: Table 2 (Kinetic properties of Rubisco mutants), strain row 'H298A'; column 'Site' = 5P; column 'Kcat (min-1)' = 43; column 'Km(RuBP) (uM)' = 267; column 'apparent Km (CO2) (uM)' = NM; column 'Ki(Pi) (mM)' = 6.3. Table 2 prints no kcat/Km column.

normalized_value_unit_evidence: kcat: printed Table 2 cell 43 under the column head Kcat (min-1); one min^-1 is 1/60 s^-1, so 43 / 60 = 0.7166666666666667 s^(-1). km: printed Table 2 cell 267 under the column head Km(RuBP) (uM); one uM is 1/1000 mM, so 267 / 1000 = 0.267 mM. kcat/Km: Table 2 has no kcat/Km column, so nothing is converted for the ratio; the canonical catalytic efficiency is the quotient of those two converted cells of the same strain row, 0.7166666666666667 / 0.267 = 2.6841448189762795 s^(-1)*mM^(-1), typed derived_same_measurement against them.

raw_value_unit_evidence: Table 2, strain row H298A, site 5P: Kcat = 43 min^-1; Km(RuBP) = 267 uM. Table 2 prints no kcat/Km column, and this article prints no catalytic-efficiency cell for this measurement.

row_label: Table 2, strain row H298A, site 5P

table_label: Table 2: Kinetic properties of Rubisco mutants (Journal of Bacteriology 2005, 187(12):4222-4228)

status: corrected


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P54205 and applied mutation signature H327Q with inferred residue-numbering offset -5 to reconstruct the assayed variant sequence.

column_label: Table 2 (Kinetic properties of Rubisco mutants), strain row 'H327Q'; column 'Site' = 5P; column 'Kcat (min-1)' = 92; column 'Km(RuBP) (uM)' = 490; column 'apparent Km (CO2) (uM)' = 175; column 'Ki(Pi) (mM)' = 0.67. Table 2 prints no kcat/Km column.

normalized_value_unit_evidence: kcat: printed Table 2 cell 92 under the column head Kcat (min-1); one min^-1 is 1/60 s^-1, so 92 / 60 = 1.5333333333333334 s^(-1). km: printed Table 2 cell 490 under the column head Km(RuBP) (uM); one uM is 1/1000 mM, so 490 / 1000 = 0.49 mM. kcat/Km: Table 2 has no kcat/Km column, so nothing is converted for the ratio; the canonical catalytic efficiency is the quotient of those two converted cells of the same strain row, 1.5333333333333334 / 0.49 = 3.1292517006802725 s^(-1)*mM^(-1), typed derived_same_measurement against them.

raw_value_unit_evidence: Table 2, strain row H327Q, site 5P: Kcat = 92 min^-1; Km(RuBP) = 490 uM. Table 2 prints no kcat/Km column, and this article prints no catalytic-efficiency cell for this measurement.

row_label: Table 2, strain row H327Q, site 5P


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature K305A with inferred residue-numbering offset +6 to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P54205 and applied mutation signature R134A with inferred residue-numbering offset -5 to reconstruct the assayed variant sequence.

column_label: Table 2 (Kinetic properties of Rubisco mutants), strain row 'R134A'; column 'Site' = Latch; column 'Kcat (min-1)' = 178; column 'Km(RuBP) (uM)' = 212; column 'apparent Km (CO2) (uM)' = 161; column 'Ki(Pi) (mM)' = 6.0. Table 2 prints no kcat/Km column.

normalized_value_unit_evidence: kcat: printed Table 2 cell 178 under the column head Kcat (min-1); one min^-1 is 1/60 s^-1, so 178 / 60 = 2.966666666666667 s^(-1). km: printed Table 2 cell 212 under the column head Km(RuBP) (uM); one uM is 1/1000 mM, so 212 / 1000 = 0.212 mM. kcat/Km: Table 2 has no kcat/Km column, so nothing is converted for the ratio; the canonical catalytic efficiency is the quotient of those two converted cells of the same strain row, 2.966666666666667 / 0.212 = 13.9937106918239 s^(-1)*mM^(-1), typed derived_same_measurement against them.

raw_value_unit_evidence: Table 2, strain row R134A, site Latch: Kcat = 178 min^-1; Km(RuBP) = 212 uM. Table 2 prints no kcat/Km column, and this article prints no catalytic-efficiency cell for this measurement.

row_label: Table 2, strain row R134A, site Latch


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P54205 and applied mutation signature K305E with inferred residue-numbering offset -5 to reconstruct the assayed variant sequence.

column_label: Table 2 (Kinetic properties of Rubisco mutants), strain row 'K305E'; column 'Site' = Latch; column 'Kcat (min-1)' = 185; column 'Km(RuBP) (uM)' = 242; column 'apparent Km (CO2) (uM)' = 190; column 'Ki(Pi) (mM)' = 5.7. Table 2 prints no kcat/Km column.

normalized_value_unit_evidence: kcat: printed Table 2 cell 185 under the column head Kcat (min-1); one min^-1 is 1/60 s^-1, so 185 / 60 = 3.0833333333333335 s^(-1). km: printed Table 2 cell 242 under the column head Km(RuBP) (uM); one uM is 1/1000 mM, so 242 / 1000 = 0.242 mM. kcat/Km: Table 2 has no kcat/Km column, so nothing is converted for the ratio; the canonical catalytic efficiency is the quotient of those two converted cells of the same strain row, 3.0833333333333335 / 0.242 = 12.741046831955924 s^(-1)*mM^(-1), typed derived_same_measurement against them.

raw_value_unit_evidence: Table 2, strain row K305E, site Latch: Kcat = 185 min^-1; Km(RuBP) = 242 uM. Table 2 prints no kcat/Km column, and this article prints no catalytic-efficiency cell for this measurement.

row_label: Table 2, strain row K305E, site Latch


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P54205 and applied mutation signature H310D with inferred residue-numbering offset -5 to reconstruct the assayed variant sequence.

column_label: Table 2 (Kinetic properties of Rubisco mutants), strain row 'H310D'; column 'Site' = Latch; column 'Kcat (min-1)' = 185; column 'Km(RuBP) (uM)' = 387; column 'apparent Km (CO2) (uM)' = NM; column 'Ki(Pi) (mM)' = NM. Table 2 prints no kcat/Km column.

normalized_value_unit_evidence: kcat: printed Table 2 cell 185 under the column head Kcat (min-1); one min^-1 is 1/60 s^-1, so 185 / 60 = 3.0833333333333335 s^(-1). km: printed Table 2 cell 387 under the column head Km(RuBP) (uM); one uM is 1/1000 mM, so 387 / 1000 = 0.387 mM. kcat/Km: Table 2 has no kcat/Km column, so nothing is converted for the ratio; the canonical catalytic efficiency is the quotient of those two converted cells of the same strain row, 3.0833333333333335 / 0.387 = 7.967269595176572 s^(-1)*mM^(-1), typed derived_same_measurement against them.

raw_value_unit_evidence: Table 2, strain row H310D, site Latch: Kcat = 185 min^-1; Km(RuBP) = 387 uM. Table 2 prints no kcat/Km column, and this article prints no catalytic-efficiency cell for this measurement.

row_label: Table 2, strain row H310D, site Latch


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature H310A with inferred residue-numbering offset -5 to reconstruct the assayed variant sequence.


proof_lines: wild type enzyme, in 50 mM HEPES, pH 8.0, at 30°C

proof_lines: pH 8.0, 30°C, wild-type, oxidized, mutant C172A, reduced


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature R134A with inferred residue-numbering offset -8 to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature K305E with inferred residue-numbering offset +6 to reconstruct the assayed variant sequence.


organism: Thermosynechococcus vestitus

sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:Q8DIS5 and applied mutation signature F345I to reconstruct the assayed variant sequence.

assay_conditions_summary: pH 8.1; 298.15 K; buffer reaction

column_label: Table 1: E. coli L8S8 Rubisco content and catalytic parameters at 25 C (J. Biol. Chem. 2018, 293(1):18-27), Rubisco row 'Te-F345I' with RbcL/RbcS mutation columns as printed in Table 1, row Te-F345I, RbcL F345I, RbcS None; column 'Expression (% (w/w) sol E. coli protein)' = 14.6 +/- 0.7**; column 'kcat c (s-1)' = 4.8 +/- 0.3**; column 'Kc 21% O2 (uM)' = 101 +/- 1; column 'kcat c/Kc21%O2 (mM-1 s-1)' = 47 +/- 2**; column 'SC/O (mol mol-1)' = 48.0 +/- 0.5**; column 'Tm (C)' = 72.3 +/- 0.3.

normalized_value_unit_evidence: kcat: printed Table 1 cell 4.8 s-1; the cell is already in s^-1, so no unit conversion applies and the paper value is 4.8 s^(-1); the exported value is 4.8 s^(-1). Km: printed Table 1 cell 101 uM; uM to mM is a division by 1000, so 101 / 1000 = 0.101 mM; the exported value is 0.101 mM. kcat/Km: printed Table 1 cell 47 mM-1 s-1; the cell is already in s^-1 mM^-1, so no unit conversion applies and the paper value is 47.0 s^(-1)*mM^(-1); the exported value 47.52475247524752 s^(-1)*mM^(-1) is the quotient of the exported kcat and km, and this record adopts the paper's own printed efficiency cell.

raw_value_unit_evidence: Table 1, row Te-F345I, RbcL F345I, RbcS None: kcat c = 4.8 s-1; Kc 21% O2 = 101 uM; printed kcat c/Kc21%O2 = 47 mM-1 s-1.


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:Q8DIS5 and applied mutation signature F345I/P415A to reconstruct the assayed variant sequence.

column_label: Table 1: E. coli L8S8 Rubisco content and catalytic parameters at 25 C (J. Biol. Chem. 2018, 293(1):18-27), Rubisco row 'Te-FIPA' with RbcL/RbcS mutation columns as printed in Table 1, row Te-FIPA, RbcL F345I, P415A, RbcS None; column 'Expression (% (w/w) sol E. coli protein)' = 17.5 +/- 1.2*; column 'kcat c (s-1)' = 4.8 +/- 0.4**; column 'Kc 21% O2 (uM)' = 102 +/- 5; column 'kcat c/Kc21%O2 (mM-1 s-1)' = 47 +/- 6**; column 'SC/O (mol mol-1)' = 49.2 +/- 0.4**; column 'Tm (C)' = 75.9 +/- 0.1**.

normalized_value_unit_evidence: kcat: printed Table 1 cell 4.8 s-1; the cell is already in s^-1, so no unit conversion applies and the paper value is 4.8 s^(-1); the exported value is 4.8 s^(-1). Km: printed Table 1 cell 102 uM; uM to mM is a division by 1000, so 102 / 1000 = 0.102 mM; the exported value is 0.102 mM. kcat/Km: printed Table 1 cell 47 mM-1 s-1; the cell is already in s^-1 mM^-1, so no unit conversion applies and the paper value is 47.0 s^(-1)*mM^(-1); the exported value 47.05882352941177 s^(-1)*mM^(-1) is the quotient of the exported kcat and km, and this record adopts the paper's own printed efficiency cell.

raw_value_unit_evidence: Table 1, row Te-FIPA, RbcL F345I, P415A, RbcS None: kcat c = 4.8 s-1; Kc 21% O2 = 102 uM; printed kcat c/Kc21%O2 = 47 mM-1 s-1.


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:Q8DIS5 and applied mutation signature A398T/P415A to reconstruct the assayed variant sequence.

column_label: Table 1: E. coli L8S8 Rubisco content and catalytic parameters at 25 C (J. Biol. Chem. 2018, 293(1):18-27), Rubisco row 'Te-2Gj (15)' with RbcL/RbcS mutation columns as printed in Table 1, row Te-2Gj (15), RbcL A398T, P415A, RbcS None; column 'Expression (% (w/w) sol E. coli protein)' = 16.6 +/- 3.6**; column 'kcat c (s-1)' = 6.4 +/- 0.2**; column 'Kc 21% O2 (uM)' = 110 +/- 4; column 'kcat c/Kc21%O2 (mM-1 s-1)' = 59 +/- 3*; column 'SC/O (mol mol-1)' = 50.5 +/- 0.5**; column 'Tm (C)' = NM.

normalized_value_unit_evidence: kcat: printed Table 1 cell 6.4 s-1; the cell is already in s^-1, so no unit conversion applies and the paper value is 6.4 s^(-1); the exported value is 6.4 s^(-1). Km: printed Table 1 cell 110 uM; uM to mM is a division by 1000, so 110 / 1000 = 0.11 mM; this record carries the printed cell 0.11 mM in place of the exported 0.1 mM. kcat/Km: printed Table 1 cell 59 mM-1 s-1; the cell is already in s^-1 mM^-1, so no unit conversion applies and the paper value is 59.0 s^(-1)*mM^(-1); the exported value 64.0 s^(-1)*mM^(-1) is the quotient of the exported kcat and km, and this record adopts the paper's own printed efficiency cell.

raw_value_unit_evidence: Table 1, row Te-2Gj (15), RbcL A398T, P415A, RbcS None: kcat c = 6.4 s-1; Kc 21% O2 = 110 uM; printed kcat c/Kc21%O2 = 59 mM-1 s-1.


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:Q8DIS5 and applied mutation signature V300A to reconstruct the assayed variant sequence.

column_label: Table 1: E. coli L8S8 Rubisco content and catalytic parameters at 25 C (J. Biol. Chem. 2018, 293(1):18-27), Rubisco row 'Te-V300A' with RbcL/RbcS mutation columns as printed in Table 1, row Te-V300A, RbcL V300A, RbcS None; column 'Expression (% (w/w) sol E. coli protein)' = 7.1 +/- 0.2; column 'kcat c (s-1)' = 6.6 +/- 0.2*; column 'Kc 21% O2 (uM)' = 135 +/- 9**; column 'kcat c/Kc21%O2 (mM-1 s-1)' = 49 +/- 6**; column 'SC/O (mol mol-1)' = 51.9 +/- 0.6; column 'Tm (C)' = 71.4 +/- 0.6.

normalized_value_unit_evidence: kcat: printed Table 1 cell 6.6 s-1; the cell is already in s^-1, so no unit conversion applies and the paper value is 6.6 s^(-1); the exported value is 6.6 s^(-1). Km: printed Table 1 cell 135 uM; uM to mM is a division by 1000, so 135 / 1000 = 0.135 mM; the exported value is 0.135 mM. kcat/Km: printed Table 1 cell 49 mM-1 s-1; the cell is already in s^-1 mM^-1, so no unit conversion applies and the paper value is 49.0 s^(-1)*mM^(-1); the exported value 48.888888888888886 s^(-1)*mM^(-1) is the quotient of the exported kcat and km, and this record adopts the paper's own printed efficiency cell.

raw_value_unit_evidence: Table 1, row Te-V300A, RbcL V300A, RbcS None: kcat c = 6.6 s-1; Kc 21% O2 = 135 uM; printed kcat c/Kc21%O2 = 49 mM-1 s-1.


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:Q8DIS5 and applied mutation signature P415A to reconstruct the assayed variant sequence.

column_label: Table 1: E. coli L8S8 Rubisco content and catalytic parameters at 25 C (J. Biol. Chem. 2018, 293(1):18-27), Rubisco row 'Te-P415A' with RbcL/RbcS mutation columns as printed in Table 1, row Te-P415A, RbcL P415A, RbcS None; column 'Expression (% (w/w) sol E. coli protein)' = 10.4 +/- 0.8**; column 'kcat c (s-1)' = 6.9 +/- 0.2*; column 'Kc 21% O2 (uM)' = 111 +/- 2; column 'kcat c/Kc21%O2 (mM-1 s-1)' = 62 +/- 2*; column 'SC/O (mol mol-1)' = 52.6 +/- 0.5; column 'Tm (C)' = 73.7 +/- 0.1**.

normalized_value_unit_evidence: kcat: printed Table 1 cell 6.9 s-1; the cell is already in s^-1, so no unit conversion applies and the paper value is 6.9 s^(-1); the exported value is 6.9 s^(-1). Km: printed Table 1 cell 111 uM; uM to mM is a division by 1000, so 111 / 1000 = 0.111 mM; the exported value is 0.111 mM. kcat/Km: printed Table 1 cell 62 mM-1 s-1; the cell is already in s^-1 mM^-1, so no unit conversion applies and the paper value is 62.0 s^(-1)*mM^(-1); the exported value 62.16216216216216 s^(-1)*mM^(-1) is the quotient of the exported kcat and km, and this record adopts the paper's own printed efficiency cell.

raw_value_unit_evidence: Table 1, row Te-P415A, RbcL P415A, RbcS None: kcat c = 6.9 s-1; Kc 21% O2 = 111 uM; printed kcat c/Kc21%O2 = 62 mM-1 s-1.


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

column_label: Table 1: E. coli L8S8 Rubisco content and catalytic parameters at 25 C (J. Biol. Chem. 2018, 293(1):18-27), Rubisco row 'Te-LS (WT)' with RbcL/RbcS mutation columns as printed in Table 1, row Te-LS (WT), RbcL None, RbcS None; column 'Expression (% (w/w) sol E. coli protein)' = 6.6 +/- 0.7; column 'kcat c (s-1)' = 7.4 +/- 0.1; column 'Kc 21% O2 (uM)' = 107 +/- 2; column 'kcat c/Kc21%O2 (mM-1 s-1)' = 70 +/- 2; column 'SC/O (mol mol-1)' = 53.3 +/- 0.5; column 'Tm (C)' = 72.8 +/- 0.2.

normalized_value_unit_evidence: kcat: printed Table 1 cell 7.4 s-1; the cell is already in s^-1, so no unit conversion applies and the paper value is 7.4 s^(-1); the exported value is 7.4 s^(-1). Km: printed Table 1 cell 107 uM; uM to mM is a division by 1000, so 107 / 1000 = 0.107 mM; the exported value is 0.107 mM. kcat/Km: printed Table 1 cell 70 mM-1 s-1; the cell is already in s^-1 mM^-1, so no unit conversion applies and the paper value is 70.0 s^(-1)*mM^(-1); the exported value 69.1588785046729 s^(-1)*mM^(-1) is the quotient of the exported kcat and km, and this record adopts the paper's own printed efficiency cell.

raw_value_unit_evidence: Table 1, row Te-LS (WT), RbcL None, RbcS None: kcat c = 7.4 s-1; Kc 21% O2 = 107 uM; printed kcat c/Kc21%O2 = 70 mM-1 s-1.


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:Q8DIS5 and applied mutation signature I393M/P415A to reconstruct the assayed variant sequence.

column_label: Table 1: E. coli L8S8 Rubisco content and catalytic parameters at 25 C (J. Biol. Chem. 2018, 293(1):18-27), Rubisco row 'Te-2Gi (13)' with RbcL/RbcS mutation columns as printed in Table 1, row Te-2Gi (13), RbcL I393M, P415A, RbcS None; column 'Expression (% (w/w) sol E. coli protein)' = 16.6 +/- 2.4**; column 'kcat c (s-1)' = 7.8 +/- 0.4; column 'Kc 21% O2 (uM)' = 90 +/- 2**; column 'kcat c/Kc21%O2 (mM-1 s-1)' = 87 +/- 1**; column 'SC/O (mol mol-1)' = 48.1 +/- 0.4**; column 'Tm (C)' = NM.

normalized_value_unit_evidence: kcat: printed Table 1 cell 7.8 s-1; the cell is already in s^-1, so no unit conversion applies and the paper value is 7.8 s^(-1); the exported value is 7.8 s^(-1). Km: printed Table 1 cell 90 uM; uM to mM is a division by 1000, so 90 / 1000 = 0.09 mM; the exported value is 0.09 mM. kcat/Km: printed Table 1 cell 87 mM-1 s-1; the cell is already in s^-1 mM^-1, so no unit conversion applies and the paper value is 87.0 s^(-1)*mM^(-1); the exported value 86.66666666666667 s^(-1)*mM^(-1) is the quotient of the exported kcat and km, and this record adopts the paper's own printed efficiency cell.

raw_value_unit_evidence: Table 1, row Te-2Gi (13), RbcL I393M, P415A, RbcS None: kcat c = 7.8 s-1; Kc 21% O2 = 90 uM; printed kcat c/Kc21%O2 = 87 mM-1 s-1.


sequence_variant_note: Mutation signature P415A/Y36N/R51H could not be applied safely because the resolved sequence does not match the expected reference residue(s).

proof_lines: mutation P415A in subunit RbcL, plus mutation Y36N/R51H in subunit RbcS, pH 8.1, 25°C


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:Q8DIS5 and applied mutation signature A414T/P415A to reconstruct the assayed variant sequence.

column_label: Table 1: E. coli L8S8 Rubisco content and catalytic parameters at 25 C (J. Biol. Chem. 2018, 293(1):18-27), Rubisco row 'Te-2Gh (12)' with RbcL/RbcS mutation columns as printed in Table 1, row Te-2Gh (12), RbcL A414T, P415A, RbcS None; column 'Expression (% (w/w) sol E. coli protein)' = 13.9 +/- 3.0*; column 'kcat c (s-1)' = 8.0 +/- 0.1; column 'Kc 21% O2 (uM)' = 102 +/- 2; column 'kcat c/Kc21%O2 (mM-1 s-1)' = 78 +/- 1; column 'SC/O (mol mol-1)' = 55.8 +/- 0.5**; column 'Tm (C)' = NM.

normalized_value_unit_evidence: kcat: printed Table 1 cell 8.0 s-1; the cell is already in s^-1, so no unit conversion applies and the paper value is 8.0 s^(-1); the exported value is 8.0 s^(-1). Km: printed Table 1 cell 102 uM; uM to mM is a division by 1000, so 102 / 1000 = 0.102 mM; the exported value is 0.102 mM. kcat/Km: printed Table 1 cell 78 mM-1 s-1; the cell is already in s^-1 mM^-1, so no unit conversion applies and the paper value is 78.0 s^(-1)*mM^(-1); the exported value 78.43137254901961 s^(-1)*mM^(-1) is the quotient of the exported kcat and km, and this record adopts the paper's own printed efficiency cell.

raw_value_unit_evidence: Table 1, row Te-2Gh (12), RbcL A414T, P415A, RbcS None: kcat c = 8.0 s-1; Kc 21% O2 = 102 uM; printed kcat c/Kc21%O2 = 78 mM-1 s-1.


sequence_variant_note: Mutation signature A414T/P415A/A48V could not be applied safely because the resolved sequence does not match the expected reference residue(s).

proof_lines: mutations A414T/P415A in subunit RbcL, plus mutation A48V in subunit RbcS, pH 8.1, 25°C


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:Q8DIS5 and applied mutation signature L74M/D397N/P415A to reconstruct the assayed variant sequence.

column_label: Table 1: E. coli L8S8 Rubisco content and catalytic parameters at 25 C (J. Biol. Chem. 2018, 293(1):18-27), Rubisco row 'Te-2Gg (11)' with RbcL/RbcS mutation columns as printed in Table 1, row Te-2Gg (11), RbcL L74M, D397N, P415A, RbcS None; column 'Expression (% (w/w) sol E. coli protein)' = 12.5 +/- 0.8**; column 'kcat c (s-1)' = 8.2 +/- 0.5; column 'Kc 21% O2 (uM)' = 92 +/- 3**; column 'kcat c/Kc21%O2 (mM-1 s-1)' = 90 +/- 6**; column 'SC/O (mol mol-1)' = 55.4 +/- 0.3**; column 'Tm (C)' = NM.

normalized_value_unit_evidence: kcat: printed Table 1 cell 8.2 s-1; the cell is already in s^-1, so no unit conversion applies and the paper value is 8.2 s^(-1); the exported value is 8.2 s^(-1). Km: printed Table 1 cell 92 uM; uM to mM is a division by 1000, so 92 / 1000 = 0.092 mM; the exported value is 0.092 mM. kcat/Km: printed Table 1 cell 90 mM-1 s-1; the cell is already in s^-1 mM^-1, so no unit conversion applies and the paper value is 90.0 s^(-1)*mM^(-1); the exported value 89.13043478260869 s^(-1)*mM^(-1) is the quotient of the exported kcat and km, and this record adopts the paper's own printed efficiency cell.

raw_value_unit_evidence: Table 1, row Te-2Gg (11), RbcL L74M, D397N, P415A, RbcS None: kcat c = 8.2 s-1; Kc 21% O2 = 92 uM; printed kcat c/Kc21%O2 = 90 mM-1 s-1.


sequence_variant_note: Mutation signature P415A/H37L could not be applied safely because the resolved sequence does not match the expected reference residue(s).

proof_lines: mutation P415A in subunit RbcL, plus mutation H37L in subunit RbcS, pH 8.1, 25°C


sequence_variant_note: Mutation signature P415A/A48M could not be applied safely because the resolved sequence does not match the expected reference residue(s).

proof_lines: mutation P415A in subunit RbcL, plus mutation A48M in subunit RbcS, pH 8.1, 25°C


sequence_variant_note: Mutation signature P415A/Y36N/G112D could not be applied safely because the resolved sequence does not match the expected reference residue(s).

proof_lines: mutation P415A in subunit RbcL, plus mutations Y36N/G112D in subunit RbcS, pH 8.1, 25°C


sequence_variant_note: Mutation signature P415A/V98M could not be applied safely because the resolved sequence does not match the expected reference residue(s).

proof_lines: mutation P415A in subunit RbcL, plus mutation V98M in subunit RbcS, pH 8.1, 25°C


organism: Chlamydomonas reinhardtii

sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_mutation_ranked_match and applied mutation signature Y32A with inferred residue-numbering offset -13 to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_mutation_ranked_match and applied mutation signature P79A to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_mutation_ranked_match and applied mutation signature W73A with inferred residue-numbering offset -13 to reconstruct the assayed variant sequence.


proof_lines:
pH 8.0, 30°C, wild-type, oxidized
wild-type enzyme
pH 8.0, 30°C, wild-type, reduced


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature C192A with inferred residue-numbering offset -5 to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature C172A/C192A with inferred residue-numbering offset -5 to reconstruct the assayed variant sequence.

proof_lines: pH 8.0, 30°C, mutant C172A/C192A, reduced


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature C172A with inferred residue-numbering offset -5 to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature T65A with inferred residue-numbering offset -5 to reconstruct the assayed variant sequence.

proof_lines: mutant enzyme T65A, in 50 mM HEPES, pH 8.0, at 30°C


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature G404A with inferred residue-numbering offset -5 to reconstruct the assayed variant sequence.

proof_lines: mutant enzyme G404A, in 50 mM HEPES, pH 8.0, at 30°C


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature T65S with inferred residue-numbering offset -5 to reconstruct the assayed variant sequence.

proof_lines: mutant enzyme T65S, in 50 mM HEPES, pH 8.0, at 30°C


organism: Thiobacillus denitrificans (strain ATCC 25259 / T1)

substrate_name: ribulose 1,5-bisphosphate

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

proof_lines: The CO(2)/O(2) specificity factor (tau) is 14.

substrate: ribulose 1,5-bisphosphate


proof_lines: The CO(2)/O(2) specificity factor (tau) is 46.


organism: Arabidopsis thaliana

smiles: CC(CCOP(=O)(O)O)(CC(=O)O)O

proof_lines: kcat is 2.0 sec(-1) with (R)-5-diphosphomevalonate as substrate (PubMed:24327557). kcat is 3.2 sec(-1) with (R)-5-diphosphomevalonate as substrate (PubMed:26216978). kcat is 0.033 sec(-1) with (R)-5-phosphomevalonate as substrate (PubMed:26


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

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

proof_lines: kcat is 3.2 sec(-1) with (R)-5-diphosphomevalonate as substrate. kcat is 0.034 sec(-1) with (R)-5-phosphomevalonate as substrate.


organism: Methanococcoides burtonii

assay_conditions_summary: pH 8

proof_lines:
pH 8.0, for both dimer and pentamer
pH 6.0, for both dimer and pentamer
pentamer


organism: Homo sapiens

sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_mutation_ranked_match and applied mutation signature R161Q to reconstruct the assayed variant sequence.

assay_conditions_summary: 303.15 K; cofactor ATP


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


organism: Plasmodium falciparum


substrate_name: Uroporphyrinogen I

substrate: Uroporphyrinogen I


organism: Anethum foeniculum

proof_lines: 20°C, pH not specified in the publication

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

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


organism: Synechococcus sp.

sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_mutation_ranked_match and applied mutation signature G176D to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_mutation_ranked_match and applied mutation signature G176N to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_mutation_ranked_match and applied mutation signature G176A to reconstruct the assayed variant sequence.


organism: Artemisia myriantha


organism: Bradyrhizobium diazoefficiens (strain JCM 10833 / BCRC 13528 / IAM 13628 / NBRC 14792 / USDA 110)

proof_lines: The CO(2)/O(2) specificity factor (tau) is 75.


organism: Blitum petiolare

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


organism: Bromus anomalus


organism: Puccinellia lemmonii


organism: Desmodium cinereum


organism: Oryza barthii x Oryza glaberrima


organism: Thermococcus kodakarensis

proof_lines: wild type enzyme, in 100 mM Bicine-NaOH (pH 8.3) and 10 mM MgCl2, temperature not specified in the publication


organism: Chrysanthellum indicum


organism: Phaseolus carteri


substrate_name: UDP-D-glucuronate

proof_lines: kcat is 0.3 min(-1) with UDP-D-galacturonate as substrate (PubMed:12969423). kcat is 0.49 min(-1) with UDP-D-galacturonate as substrate (PubMed:31844840).

substrate: UDP-D-glucuronate


organism: Euphorbia microsphaera


organism: Xanthobacter flavus

proof_lines: The CO(2)/O(2) specificity factor (tau) is 44.


organism: Agave victoriae-reginae

proof_lines: in 100 mM Bicine-NaOH pH 8.0, 20 mM MgCl2, at 25°C


organism: Cereibacter sphaeroides

proof_lines: The CO(2)/O(2) specificity factor (tau) is 56.


organism: Homo sapiens

substrate_name: UDP-alpha-D-glucuronate

proof_lines: kcat is 0.2 sec(-1) for UDP-alpha-D-glucuronate.

substrate: UDP-alpha-D-glucuronate


enzyme_display_name: dehydro-L-gulonate decarboxylase

proof_lines: kcat is 4.27 sec(-1) for the decarboxylation of 3-dehydro-L-gulonate (at pH 7.9 and 37 degrees Celsius).

enzyme: dehydro-L-gulonate decarboxylase


organism: Griffithsia monilis


organism: Drosera venusta


organism: Hydrogenovibrio crunogenus (strain DSM 25203 / XCL-2)


organism: Pallenis maritima


organism: Hordeum vulgare

proof_lines: oxygenase catalytic efficiency, pH 8.0, 25°C


organism: Limonium stenophyllum


organism: Iris douglasiana


organism: Sideritis cretica subsp. spicata


organism: Arabidopsis thaliana


organism: Prochlorococcus marinus subsp. pastoris (strain CCMP1986 / NIES-2087 / MED4)


organism: Calamagrostis foliosa


organism: Synechococcus sp.

sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_mutation_ranked_match and applied mutation signature F342V/D103V with inferred residue-numbering offset -34 to reconstruct the assayed variant sequence.


organism: Synechococcus elongatus (strain ATCC 33912 / PCC 7942 / FACHB-805)

proof_lines: The CO(2)/O(2) specificity factor (tau) is 39.


organism: Teucrium heterophyllum


organism: Nitrosomonas sp.


organism: Thermococcus kodakarensis


organism: Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1)


organism: Halothiobacillus neapolitanus (strain ATCC 23641 / DSM 15147 / CIP 104769 / NCIMB 8539 / c2)


substrate_name: Unknown

substrate: Unknown


organism: Hydrogenophaga pseudoflava


organism: Hydrogenovibrio crunogenus (strain DSM 25203 / XCL-2)


organism: Hydrogenovibrio marinus

proof_lines: The CO(2)/O(2) specificity factor (tau) is 26.6.


proof_lines: The CO(2)/O(2) specificity factor (tau) is 14.8.


proof_lines: The CO(2)/O(2) specificity factor (tau) is 33.1.


organism: Saccharomyces cerevisiae

sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature D302A to reconstruct the assayed variant sequence.


organism: Homo sapiens


organism: Allochromatium vinosum (strain ATCC 17899 / DSM 180 / NBRC 103801 / NCIMB 10441 / D)

substrate_name: CO2 purified from A.vinosum in vivo

proof_lines: This enzyme requires a lac or tac promoter for expression in E.coli and has different kinetics than the enzyme purified in vivo, suggesting this is not expressed in A.vinosum.

substrate: CO2 purified from A.vinosum in vivo


organism: Bradyrhizobium diazoefficiens (strain JCM 10833 / BCRC 13528 / IAM 13628 / NBRC 14792 / USDA 110)


organism: Cereibacter sphaeroides


organism: Euglena gracilis

substrate_name: H2O; CO2; D-Ribulose 1,5-bisphosphate

substrate: H2O; CO2; D-Ribulose 1,5-bisphosphate


organism: Xanthobacter flavus


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature V330T with inferred residue-numbering offset -15 to reconstruct the assayed variant sequence.

proof_lines: mutant enzyme V330T, in 100 mM Bicine-NaOH (pH 8.3) and 10 mM MgCl2, temperature not specified in the publication


organism: Synechocystis sp.

proof_lines: wild type enzyme, in 50 mM HEPES, pH 8.0, at 30°C


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature H298A with inferred residue-numbering offset -5 to reconstruct the assayed variant sequence.


proof_lines: mutant enzyme T65A, in 50 mM HEPES, pH 8.0, at 30°C


proof_lines: mutant enzyme G404A, in 50 mM HEPES, pH 8.0, at 30°C


organism: Thiobacillus denitrificans (strain ATCC 25259 / T1)

proof_lines: The CO(2)/O(2) specificity factor (tau) is 14.


proof_lines: The CO(2)/O(2) specificity factor (tau) is 46.


organism: Methanococcoides burtonii


organism: Prochlorococcus marinus subsp. pastoris (strain CCMP1986 / NIES-2087 / MED4)


sequence_variant_note: Resolved canonical sequence from identity matching and applied mutation signature H327Q with inferred residue-numbering offset -5 to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from identity matching and applied mutation signature K305E with inferred residue-numbering offset -5 to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from identity matching and applied mutation signature R134A to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P54205 and applied mutation signature R134A with inferred residue-numbering offset -5 to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature C172A with inferred residue-numbering offset -5 to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature C172A/C192A with inferred residue-numbering offset -5 to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature C192A with inferred residue-numbering offset -5 to reconstruct the assayed variant sequence.


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


proof_lines:
Synechocystis sp. PCC 6803
RuBisCO
redox regulation


proof_lines:
Synechocystis sp. PCC 6803
RuBisCO
Cys172


proof_lines:
Synechocystis sp. PCC 6803
Rubisco
Km(RuBP)


verification_status: verified

sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature R134A to reconstruct the assayed variant sequence.

column_label: PMID 15937184 Table 2; row R134A / CO2; Kcat and app Km(CO2) (uM) columns; kcat/Km locked from the same row.

raw_value_unit_evidence: Table 2 line 168: R134A kcat 178 min^-1 and app Km(CO2) 161 uM.

table_label: Table 2. Kinetic properties of Rubisco mutants

status: verified


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature H327Q with inferred residue-numbering offset -5 to reconstruct the assayed variant sequence.

column_label: PMID 15937184 Table 2; row H327Q / CO2; Kcat and app Km(CO2) (uM) columns; kcat/Km locked from the same row.

raw_value_unit_evidence: Table 2 line 175: H327Q kcat 92 min^-1 and app Km(CO2) 175 uM.


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature K305A with inferred residue-numbering offset -5 to reconstruct the assayed variant sequence.

column_label: PMID 15937184 Table 2; row K305A / CO2; Kcat and app Km(CO2) (uM) columns; kcat/Km locked from the same row.

raw_value_unit_evidence: Table 2 line 170: K305A kcat 177 min^-1 and app Km(CO2) 185 uM.


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature K305E with inferred residue-numbering offset -5 to reconstruct the assayed variant sequence.

column_label: PMID 15937184 Table 2; row K305E / CO2; Kcat and app Km(CO2) (uM) columns; kcat/Km locked from the same row.

raw_value_unit_evidence: Table 2 line 169: K305E kcat 185 min^-1 and app Km(CO2) 190 uM.


column_label: PMID 15937184 Table 2; row H298A / D-Ribulose 1,5-bisphosphate; Kcat and Km(RuBP) (uM) columns; kcat/Km locked from the same row.

raw_value_unit_evidence: Table 2 line 173: H298A kcat 43 min^-1 and Km(RuBP) 267 uM.

row_label: H298A / D-Ribulose 1,5-bisphosphate


sequence_variant_note: Mutation signature H310A matches the mutant residue at offset +0 and the reference residue at offset -5; variant reconstruction was not applied because multiple plausible residue-numbering offsets are present.


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature H310D with inferred residue-numbering offset -5 to reconstruct the assayed variant sequence.

column_label: PMID 15937184 Table 2; row H310D / D-Ribulose 1,5-bisphosphate; Kcat and Km(RuBP) (uM) columns; kcat/Km locked from the same row.

raw_value_unit_evidence: Table 2 line 171: H310D kcat 185 min^-1 and Km(RuBP) 387 uM.

row_label: H310D / D-Ribulose 1,5-bisphosphate


column_label: PMID 15937184 Table 2; row H327Q / D-Ribulose 1,5-bisphosphate; Kcat and Km(RuBP) (uM) columns; kcat/Km locked from the same row.

raw_value_unit_evidence: Table 2 line 175: H327Q kcat 92 min^-1 and Km(RuBP) 490 uM.

row_label: H327Q / D-Ribulose 1,5-bisphosphate


column_label: PMID 15937184 Table 2; row K305A / D-Ribulose 1,5-bisphosphate; Kcat and Km(RuBP) (uM) columns; kcat/Km locked from the same row.

raw_value_unit_evidence: Table 2 line 170: K305A kcat 177 min^-1 and Km(RuBP) 199 uM.

row_label: K305A / D-Ribulose 1,5-bisphosphate


column_label: PMID 15937184 Table 2; row K305E / D-Ribulose 1,5-bisphosphate; Kcat and Km(RuBP) (uM) columns; kcat/Km locked from the same row.

raw_value_unit_evidence: Table 2 line 169: K305E kcat 185 min^-1 and Km(RuBP) 242 uM.

row_label: K305E / D-Ribulose 1,5-bisphosphate


organism: Hevea brasiliensis

substrate_name: ATP; (R)-5-Diphosphomevalonate

substrate: ATP; (R)-5-Diphosphomevalonate


organism: Mus musculus

substrate_name: mevalonate diphosphate

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

assay_conditions_summary: pH 7.2; cofactor ATP

substrate: mevalonate diphosphate


organism: Rattus norvegicus


organism: Arabidopsis thaliana

substrate_name: UDP-D-glucuronate at 30 degrees Celsius

substrate: UDP-D-glucuronate at 30 degrees Celsius


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

substrate_name: uroporphyrinogen I

column_label: Abstract reports Km values of 1.8 microM and 6.0 microM for conversion of uroporphyrinogen I and III respectively.

raw_value_unit_evidence: Km raw_value=1.8 microM raw_unit=microM

row_label: Rhodobacter sphaeroides uroporphyrinogen decarboxylase / uroporphyrinogen I

table_label: PubMed XML abstract PMID 8352737

substrate: uroporphyrinogen I


raw_value_unit_evidence: Km raw_value=6.0 microM raw_unit=microM

row_label: Rhodobacter sphaeroides uroporphyrinogen decarboxylase / uroporphyrinogen III


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P32377 and applied mutation signature K18M to reconstruct the assayed variant sequence.

assay_conditions_summary: pH 7; 303.15 K; cofactor ATP

column_label: Table 2; row K18M; columns Km(Mg-ATP), kcat, and kcat/Km(Mg-ATP).

normalized_value_unit_evidence: normalized Km=1.066 mM from 1066 uM; normalized kcat/Km=0.14 s^-1 mM^-1.

table_label: Table 2


column_label: Table 2; row Wild type; columns Km(Mg-ATP), kcat, and kcat/Km(Mg-ATP).

normalized_value_unit_evidence: normalized Km=0.061 mM from 61 uM; table-rounded kcat/Km=80 s^-1 mM^-1; export-derived kcat/Km=4.9/0.061=80.32786885245902 s^-1 mM^-1.

raw_value_unit_evidence: Table 2 row Wild type; Km(Mg-ATP)=61 +/- 6 uM; kcat=4.9 sec^-1; kcat/Km(Mg-ATP)=8 x 10^-2 s^-1 uM^-1.

row_label: Wild type


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature D302N to reconstruct the assayed variant sequence.


column_label: Table 2; row K18M; columns Km(D,L-MPP), kcat, and kcat/Km(D,L-MPP).

normalized_value_unit_evidence: normalized Km=0.177 mM from 177 uM; table-rounded kcat/Km=0.87 s^-1 mM^-1; export-derived kcat/Km=0.15/0.177=0.847457627118644 s^-1 mM^-1.


column_label: Table 2; row Wild type; columns Km(D,L-MPP), kcat, and kcat/Km(D,L-MPP).

normalized_value_unit_evidence: normalized Km=0.123 mM from 123 uM; table-rounded kcat/Km=40 s^-1 mM^-1; export-derived kcat/Km=4.9/0.123=39.837398373983746 s^-1 mM^-1.

raw_value_unit_evidence: Table 2 row Wild type; Km(D,L-MPP)=123 +/- 22 uM; kcat=4.9 sec^-1; kcat/Km(D,L-MPP)=4 x 10^-2 s^-1 uM^-1.


organism: Oryza sativa

assay_conditions_summary: pH 6.5; buffer pH 6

column_label: ScienceDirect Table 2, OsUXS2 row, Km (M), kcat (s^-1), and kcat/Km (M^-1 s^-1) columns.


column_label: ScienceDirect Table 2, OsUXS3 row, Km (M), kcat (s^-1), and kcat/Km (M^-1 s^-1) columns.


organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)


organism: Escherichia coli


substrate_name: heptacarboxylate porphyrinogen I

substrate: heptacarboxylate porphyrinogen I


organism: Allochromatium vinosum (strain ATCC 17899 / DSM 180 / NBRC 103801 / NCIMB 10441 / D)

substrate_name: D-Ribulose 1,5-bisphosphate

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

substrate: D-Ribulose 1,5-bisphosphate


organism: Polypodium aureum


organism: Rhodospirillum rubrum


sequence_source: multiple


organism: Flaveria trinervia


proof_lines:
AtUxs2
UDP-glucuronic acid decarboxylase
UDP-xylose


organism: Flaveria pringlei


organism: Thermosynechococcus vestitus

proof_lines:
green-like type rubisco
almost 2-fold higher specificity factor
enzyme thermostability


proof_lines: first characterization of a green-like type rubisco


organism: Homo sapiens

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

source_databases_merged: skid uniprot


organism: Synechococcus sp.

sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_mutation_ranked_match and applied mutation signature Y17C to reconstruct the assayed variant sequence.


organism: Cryptococcus neoformans

substrate_name: UDPglucuronate

proof_lines:
UDP-glucuronic acid
UDP-xylose

substrate: UDPglucuronate


organism: Acrosiphonia arcta


organism: Flaveria floridana


enzyme_display_name: UniProt Q8TDX5

substrate_name: 2-aminomuconate semialdehyde

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

enzyme: UniProt Q8TDX5

substrate: 2-aminomuconate semialdehyde


organism: Griffithsia monilis

proof_lines:
RuBisCO
mathematical models
fallover


organism: Flaveria cronquistii


organism: Nitrosomonas sp.

substrate_name: D-ribulose 1,5-bisphosphate

column_label: Abstract reports Km values for RuBP, NaHCO3, and Mg2+ were 0.112, 0.415, and 1.063 mM, respectively.

raw_value_unit_evidence: Km raw_value=0.112 mM raw_unit=mM

row_label: Nitrosomonas sp. K1 RubisCO / RuBP

table_label: PubMed XML abstract PMID 16232884

substrate: D-ribulose 1,5-bisphosphate


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.

proof_lines:
wild type enzyme, at 25°C, pH 8
wild-type enzyme


proof_lines:
mutant enzyme D117V, at 25°C, pH 8
mutant enzyme D117V, at 25°C, pH 8


proof_lines:
mutant enzyme D117H, at 25°C, pH 8
mutant enzyme D117H, at 25°C, pH 8


proof_lines:
mutant enzyme H44Q, at 25°C, pH 8
mutant enzyme H44Q, at 25°C, pH 8


proof_lines:
mutant enzyme H44N, at 25°C, pH 8
mutant enzyme H44N, at 25°C, pH 8


organism: Saccharomyces cerevisiae


substrate_name: ATP

substrate: ATP


organism: Acidovorax facilis


organism: Synechococcus elongatus PCC 6301

proof_lines: mutant M259T, pH not specified in the publication, temperature not specified in the publication


proof_lines: mutant R214H, pH not specified in the publication, temperature not specified in the publication


proof_lines: mutant V186I, pH not specified in the publication, temperature not specified in the publication


proof_lines: mutant M259T/A575V/M57I, pH not specified in the publication, temperature not specified in the publication


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


proof_lines: mutant S325L, pH not specified in the publication, temperature not specified in the publication


proof_lines: mutant V186I/T327A, pH not specified in the publication, temperature not specified in the publication


proof_lines: mutant T327A, pH not specified in the publication, temperature not specified in the publication


proof_lines: mutant R214H/A375S, pH not specified in the publication, temperature not specified in the publication


proof_lines: mutant S325L/T327A, pH not specified in the publication, temperature not specified in the publication


organism: Archaeoglobus fulgidus


organism: Staphylococcus epidermidis


proof_lines: wild type enzyme, at 30°C in 100 mM HEPES-NaOH (pH 7.0)


organism: Rhodospirillum rubrum

proof_lines:
mutant D263Q, cosubstrate: CO2
mutant D263Q


proof_lines: mutant D263Q, cosubstrate: D-ribulose 1,5-bisphosphate


proof_lines:
mutant D263S, cosubstrate: CO2
mutant D263S


proof_lines: mutant D263S, cosubstrate: D-ribulose 1,5-bisphosphate


proof_lines:
mutant D263A, cosubstrate: CO2
mutant D263A


proof_lines: mutant D263A, cosubstrate: D-ribulose 1,5-bisphosphate


proof_lines:
mutant D263N, cosubstrate: CO2
mutant D263N


proof_lines: mutant D263N, cosubstrate: D-ribulose 1,5-bisphosphate


proof_lines:
mutant D263E, cosubstrate: CO2
mutant D263E


proof_lines: mutant D263E, cosubstrate: D-ribulose 1,5-bisphosphate


proof_lines:
mutant enzyme M295D, at 83°C
mutant M295D, pH 8.3, 83°C


proof_lines:
wild type enzyme, at 83°C
wild-type, pH 8.3, 83°C


organism: Synechococcus

proof_lines:
mutant A375V, co-substrate: CO2
mutant A375V


proof_lines: mutant A375V, co-substrate: D-ribulose 1,5-bisphosphate


proof_lines:
mutant D103V/A375V, co-substrate: CO2
mutant D103V/A375V


proof_lines: mutant A375V/D103V, co-substrate: D-ribulose 1,5-bisphosphate


proof_lines:
wild-type, co-substrate: CO2
wild-type


proof_lines:
mutant D103V, co-substrate: CO2
mutant D103V


proof_lines: wild-type, co-substrate: D-ribulose 1,5-bisphosphate


proof_lines: mutant D103V, co-substrate: D-ribulose 1,5-bisphosphate


organism: Rattus norvegicus


organism: Chlamydomonas reinhardtii


organism: Homo sapiens


substrate_name: uroporphyrinogen-I

substrate: uroporphyrinogen-I


substrate_name: uroporphyrinogen-III

substrate: uroporphyrinogen-III


organism: Allochromatium vinosum

proof_lines:
mutants rbcL-rbcS, rbcA-rbcD
mutant rbcL-rbcS


organism: Nicotiana tabacum

proof_lines: ANtS40L Rubisco oligomer complex, using soluble leaf protein extract

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

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


proof_lines: wild-type, using soluble leaf protein extract

proof_lines: wild-type, measured using fractions 12 and 13 following Superdex 200 HR purification

proof_lines: pH 7.8, 25°C, wild-type and mutant Val-335, in vivo


proof_lines: rubisco oligomer (S40L)8 composed of linked small and large subunits, measured using fractions 7 and 8 following Superdex 200 HR purification

proof_lines: rubisco oligomer (S40L)16 composed of linked small and large subunits, measured using fractions 7 and 8 following Superdex 200 HR purification


organism: Porphyridium purpureum


organism: Cylindrotheca sp.


substrate_name: 6-COOH-porphyrinogen I

substrate: 6-COOH-porphyrinogen I


substrate_name: uroporphyrinogen III

substrate: uroporphyrinogen III


substrate_name: Uroporphyrinogen I

substrate: Uroporphyrinogen I


assay_conditions_summary: pH 8; 298.15 K; buffer CO2- and O2-free 200 mM Bicine-NaOH

proof_lines: mutant enzyme K122R, in CO2- and O2-free 200 mM Bicine-NaOH buffer (pH 8.0) containing 20 mM MgCl2, at 25°C


proof_lines: wild type enzyme, in CO2- and O2-free 200 mM Bicine-NaOH buffer (pH 8.0) containing 20 mM MgCl2, at 25°C

proof_lines: wild-type, cosubstrate: D-ribulose 1,5-bisphosphate


organism: Olisthodiscus luteus


proof_lines:
pH 7.8, 25°C, mutant Val-335, in vitro
pH 7.8, 25°C, mutant Val-335, in vivo


proof_lines:
pH 7.8, 25°C, wild-type, in vivo
pH 7.8, 25°C, wild-type, in vitro


organism: Cylindrotheca fusiformis


organism: Acidithiobacillus ferrooxidans


organism: Agriophyllum squarrosum

proof_lines: 20°C, pH not specified in the publication


organism: Agrostis stolonifera


organism: Synechococcus sp.

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


proof_lines:
pH 8.0, 23°C, wild-type
wild-type enzyme


organism: Saccharomyces cerevisiae


substrate_name: 7-COOH-porphyrinogen I

substrate: 7-COOH-porphyrinogen I


organism: Staphylococcus epidermidis

proof_lines: mutant enzyme S192A, at 30°C in 100 mM HEPES-NaOH (pH 7.0)


substrate_name: Unknown

proof_lines: wild type enzyme, at 30°C in 100 mM HEPES-NaOH (pH 7.0)

proof_lines: wild-type, substrate (R)-5-diphosphomevalonate, pH 7.0, 30°C

substrate: Unknown


organism: Arabidopsis thaliana

proof_lines: 30°C growth temperature, assay at 25°C, pH not specified in the publication

proof_lines: 20°C growth temperature, assay at 25°C, pH not specified in the publication

proof_lines: 10°C growth temperature, assay at 25°C, pH not specified in the publication


organism: Arctagrostis latifolia

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

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


organism: Bacopa monnieri

assay_conditions_summary: pH 8; cofactor ATP

proof_lines: pH 8.0, temperature not specified in the publication


enzyme_display_name: UniProt A0A0G4DBU7

organism: Streptomyces sp. 590 KI-2014

substrate_name: L-norleucine

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

enzyme: UniProt A0A0G4DBU7

substrate: L-norleucine


substrate_name: L-methionine

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

substrate: L-methionine


enzyme_display_name: UniProt A0A060TAG5

organism: Blastobotrys adeninivorans

substrate_name: gallic acid

enzyme: UniProt A0A060TAG5

substrate: gallic acid


substrate_name: protocatechuic acid

substrate: protocatechuic acid


enzyme_display_name: phenylalanine decarboxylase

organism: Cavia aperea

enzyme: phenylalanine decarboxylase


substrate_name: tryptophan

substrate: tryptophan


substrate_name: p-tyrosine

substrate: p-tyrosine


substrate_name: phenylalanine

substrate: phenylalanine


substrate_name: histidine

substrate: histidine


organism: Beta vulgaris


organism: Rhodospirillum rubrum

substrate_name: D-ribulose 1,5-bisphosphate

substrate: D-ribulose 1,5-bisphosphate


organism: Agrostis scabra


organism: Artemisia vulgaris


organism: Calamagrostis canescens


organism: Bradyrhizobium japonicum

proof_lines: oxygenation carboxylation


organism: Amphicarpaea bracteata


enzyme_display_name: 4-hydroxybenzoate decarboxylase

organism: Enterobacter cloacae

assay_conditions_summary: pH 7; buffer 100 mM potassium phosphate

proof_lines: in 100 mM potassium phosphate buffer (pH 7.0)

enzyme: 4-hydroxybenzoate decarboxylase


substrate_name: phenol

proof_lines: 20 mM phenol, 3 MKHCO3, 10 mM dithiothreitol in 100 mM potassium phosphate buffer (pH 7.0)

substrate: phenol


enzyme_display_name: methionine decarboxylase

enzyme: methionine decarboxylase


enzyme_display_name: gallate decarboxylase

enzyme: gallate decarboxylase


organism: Methanospirillum hungatei

proof_lines:
carboxylase with pH-optimum 7.8
carboxylase with pH-optimum 6.4


organism: Desulfovibrio sp.


sequence_variant_note: Resolved canonical sequence from unresolved_mutant_sequence and applied mutation signature Q64A to reconstruct the assayed variant sequence.


assay_conditions_summary: pH 6


organism: Calamagrostis arundinacea


organism: Streptomyces sp.


substrate_name: S-ethyl-L-Cys

substrate: S-ethyl-L-Cys


organism: Dryopteris filix-mas

substrate_name: L-Met

proof_lines:
at pH 4.5 and below
at pH 4.8

substrate: L-Met


substrate_name: L-Leu

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

substrate: L-Leu


substrate_name: L-norvaline

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

substrate: L-norvaline


substrate_name: L-Ile

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

substrate: L-Ile


substrate_name: L-Val

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

substrate: L-Val


enzyme_display_name: UniProt Q05115

organism: Bordetella bronchiseptica

enzyme: UniProt Q05115


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


enzyme_display_name: UniProt Q1XGK3

organism: Pseudomonas putida

proof_lines:
Raw SKiD Env: Temp=25°C, pH=6
Raw SKiD Env: Temp=25°C, pH=8
Raw SKiD Env: Temp=25°C, pH=6.5

enzyme: UniProt Q1XGK3


enzyme_display_name: orsellinate decarboxylase

organism: Lasallia pustulata

enzyme: orsellinate decarboxylase


organism: Clonostachys rosea


organism: Citrobacter sp.


organism: Pseudomonas sp.

substrate_name: Phenylphosphate

proof_lines: CO2:4-hydroxybenzoate isotope exchange reaction

substrate: Phenylphosphate


organism: Homo sapiens

proof_lines: pH 6.6, temperature not specified in the publication


organism: uncultured bacterium


organism: Klebsiella aerogenes


organism: Sedimentibacter hydroxybenzoicus

proof_lines: kcat is 3300 min(-1) with 4-hydroxybenzoate as substrate. kcat is 1100 min(-1) with 3,4-dihydroxybenzoate as substrate.

source_databases_merged: brenda uniprot


proof_lines: dissolved, CO2:4-hydroxybenzoate isotope exchange reaction


organism: Chlamydia pneumoniae

substrate_name: Unknown

substrate: Unknown


organism: Pantoea agglomerans


organism: Chlamydophila pneumoniae


organism: Streptomyces sp. 590 KI-2014

substrate_name: L-norleucine

substrate: L-norleucine


substrate_name: L-Methionine

substrate: L-Methionine


enzyme_display_name: protocatechuate decarboxylase

sequence: MNKVTDLRSAIELLKTIPGQLIETNXDV

column_label: Abstract states the Km for 3,4-dihydroxybenzoate is 0.6 mM at pH 7.0 and 25 degrees C.

raw_value_unit_evidence: Km raw_value=0.6 raw_unit=mM

row_label: Clostridium hydroxybenzoicum 3,4-dihydroxybenzoate decarboxylase with 3,4-dihydroxybenzoate

table_label: PubMed abstract PMID 8655551

enzyme: protocatechuate decarboxylase


organism: Vibrio alginolyticus

substrate_name: carboxynorspermidine (at 37 degrees Celsius and pH 8.25)

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


substrate_name: pyridoxal 5'-phosphate (at 37 degrees Celsius and pH 8.25)


organism: Burkholderia cepacia

substrate_name: 2-Amino-2-methylpropanoate; Pyruvate

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

substrate: 2-Amino-2-methylpropanoate; Pyruvate


substrate_name: pyruvate

substrate: pyruvate


enzyme_display_name: ribulose-bisphosphate carboxylase

organism: Calamagrostis nutkaensis

proof_lines: 20°C, pH not specified in the publication

enzyme: ribulose-bisphosphate carboxylase


substrate_name: Gly

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

proof_lines: with pyruvate as cosubstrate, decarboxylation

substrate: Gly


substrate_name: alpha-aminomalonate

proof_lines: with pyruvate as cosubstrate, oxidative decarboxylation

substrate: alpha-aminomalonate


substrate_name: L-Ala

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

substrate: L-Ala


organism: Calamagrostis stricta subsp. inexpansa


smiles: O=O


column_label: Abstract reports apparent Km and kcat values for 4-hydroxybenzoate were 0.40 mM and 3.3 x 10(3) min-1 at pH 6.0 and 25 degrees C.

raw_value_unit_evidence: Km raw_value=0.40 mM raw_unit=mM

row_label: Clostridium/Sedimentibacter 4-hydroxybenzoate decarboxylase / 4-hydroxybenzoate

table_label: PubMed XML abstract PMID 7744052


column_label: Abstract reports apparent Km and kcat values for 3,4-dihydroxybenzoate were 1.2 mM and 1.1 x 10(3) min-1 at pH 6.0 and 25 degrees C.

raw_value_unit_evidence: Km raw_value=1.2 mM raw_unit=mM

row_label: Clostridium/Sedimentibacter 4-hydroxybenzoate decarboxylase / 3,4-dihydroxybenzoate


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


organism: Chenopodiastrum murale


organism: Cereibacter sphaeroides

substrate_name: Uroporphyrinogen I

substrate: Uroporphyrinogen I


substrate_name: uroporphyrinogen III

substrate: uroporphyrinogen III


organism: Citrullus lanatus


organism: Citrus sinensis


substrate_name: D-ribulose 1,5-bisphosphate

substrate: D-ribulose 1,5-bisphosphate


organism: Cynodon dactylon

proof_lines: Vmax carboxylation: 3.41 micromol/min/mg


enzyme_display_name: UniProt A6T925

organism: Klebsiella pneumoniae

enzyme: UniProt A6T925


enzyme_display_name: UniProt C6F3U5

organism: Enterobacter sp.

substrate_name: ferulate

enzyme: UniProt C6F3U5

substrate: ferulate


enzyme_display_name: UniProt Q03034

organism: Saccharomyces cerevisiae

substrate_name: trans-cinnamate

enzyme: UniProt Q03034

substrate: trans-cinnamate


proof_lines:
Raw SKiD Env: Temp=25°C, pH=7
Raw SKiD Env: Temp=30°C, pH=6.5


organism: Deschampsia danthonioides

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

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


organism: Elymus farctus


organism: Citrullus ecirrhosus


organism: Erythrina flabelliformis


organism: Desmodium psilocarpum


organism: Coffea arabica


organism: Desmodium intortum


organism: Eragrostis tef


organism: Galdieria sulphuraria


enzyme_display_name: uroporphyrinogen decarboxylase

organism: Gallus gallus

enzyme: uroporphyrinogen decarboxylase


substrate_name: uroporphyrinogen

substrate: uroporphyrinogen


organism: Glycine canescens


organism: Glycine max


organism: Hordeum murinum


organism: Hydrogenophaga pseudoflava


organism: Flueggea suffruticosa


organism: Festuca pratensis


organism: Halothiobacillus neapolitanus


proof_lines: apparent Km for mutant carboxysome lacking carbonic anhydrase


organism: Lablab purpureus


organism: Hordeum brachyantherum


organism: Helianthus annuus


organism: Lolium rigidum


organism: Macrotyloma uniflorum


organism: Lolium multiflorum


organism: Manihot esculenta


organism: Mercurialis annua


enzyme_display_name: deoxyribose-phosphate aldolase

organism: Pyrobaculum calidifontis

substrate_name: 2-deoxy-D-ribose 5-phosphate

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

enzyme: deoxyribose-phosphate aldolase

substrate: 2-deoxy-D-ribose 5-phosphate


organism: Hyperthermus butylicus

assay_conditions_summary: pH 5.5; 298.15 K; buffer 100 mM sodium acetate

proof_lines: in 100 mM sodium acetate buffer (pH 5.5) at 25°C


enzyme_display_name: Deoxyribose-phosphate aldolase

organism: Aciduliprofundum boonei (strain DSM 19572 / T469)

enzyme: Deoxyribose-phosphate aldolase


organism: Oryza glaberrima


organism: Musa velutina


organism: Lepidium campestre


organism: Oryza longistaminata


organism: Oryza sativa

proof_lines: oxygenation carboxylation


organism: Euphorbia helioscopia


organism: Oryza meridionalis


organism: Oryza eichingeri


organism: Oryza sativa Indica Group


organism: Oryza punctata


organism: Oryza nivara


organism: Burkholderia cepacia

sequence_source: uniprot


organism: Oryza sativa Japonica Group


organism: Panicum amarum


organism: Oxybasis rubra


organism: Oryza glumipatula


organism: Panicum dichotomiflorum


organism: Panicum phragmitoides


organism: Phaeodactylum tricornutum


organism: Phaseolus lunatus


organism: Phaseolus vulgaris


organism: Poa palustris


organism: Pseudomonas sp.


organism: Phaseolus coccineus


organism: Puccinellia distans


organism: Paspalum dilatatum

proof_lines: Vmax carboxylation: 2.54 micromol/min/mg

proof_lines: Vmax carboxylation: 3.11 micromol/min/mg


proof_lines:
Vmax oxygenation: 0.79 micromol/min/mg
Vmax oxygenation: 0.71 micromol/min/mg


organism: Pueraria montana


organism: Puccinellia maritima


organism: Sorghum bicolor

proof_lines: recombinant enzyme expressed in Oryza sativa transgenic line SS16, in 100 mM Bicine-NaOH, 1 mM EDTA, 5 mM MgCl2, 2 mM NaH2PO4, 0.4% (w/v) bovine serum albumin, 5 mM dithiothreitol, 4 mM amino-n-caproic acid, and 0.8 mM benzamidine, pH 8.0,

proof_lines: recombinant enzyme expressed in Oryza sativa transgenic line SS5, in 100 mM Bicine-NaOH, 1 mM EDTA, 5 mM MgCl2, 2 mM NaH2PO4, 0.4% (w/v) bovine serum albumin, 5 mM dithiothreitol, 4 mM amino-n-caproic acid, and 0.8 mM benzamidine, pH 8.0, a

proof_lines: recombinant enzyme expressed in Oryza sativa transgenic line SS10, in 100 mM Bicine-NaOH, 1 mM EDTA, 5 mM MgCl2, 2 mM NaH2PO4, 0.4% (w/v) bovine serum albumin, 5 mM dithiothreitol, 4 mM amino-n-caproic acid, and 0.8 mM benzamidine, pH 8.0,


proof_lines: wild type enzyme, in 100 mM Bicine-NaOH, 1 mM EDTA, 5 mM MgCl2, 2 mM NaH2PO4, 0.4% (w/v) bovine serum albumin, 5 mM dithiothreitol, 4 mM amino-n-caproic acid, and 0.8 mM benzamidine, pH 8.0, at 28°C


organism: Sphenostylis stenocarpa

proof_lines: 20°C, pH not specified in the publication


organism: Sulfobacillus thermosulfidooxidans


organism: Symphytum sp.


organism: Puccinellia nuttalliana


enzyme_display_name: diphosphomevalonate decarboxylase

organism: Sus scrofa

substrate_name: ATP

proof_lines: 1 mM ATP4- above that complexed at the substrate. MgATP2- deceases the Km from 0.45 mM to 0.15 mM

enzyme: diphosphomevalonate decarboxylase

substrate: ATP


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


organism: Synechococcus sp.


organism: Rattus norvegicus


substrate_name: Unknown

assay_conditions_summary: pH 7.5; 298.15 K; buffer 100 mM Tris


organism: Tephrosia rhodesica


organism: Trichormus variabilis


organism: Rhodospirillum rubrum


organism: Zoysia japonica

proof_lines: Vmax carboxylation: 3.78 micromol/min/mg


organism: Tephrosia purpurea


organism: Abelmoschus esculentus


organism: Alaria esculenta


organism: Amaranthus hybridus


enzyme_display_name: UDP-glucuronate decarboxylase

organism: Arabidopsis thaliana

substrate_name: UDP-D-glucuronate

enzyme: UDP-glucuronate decarboxylase

substrate: UDP-D-glucuronate


organism: Tephrosia candida


proof_lines: in 100 mM Bicine-NaOH pH 8.0, 20 mM MgCl2, at 25°C


organism: Agrostis scabra


organism: Atrichum undulatum


organism: Allochromatium vinosum


organism: Triticum monococcum subsp. aegilopoides


organism: Bos taurus

substrate_name: 6-COOH-porphyrinogen I

substrate: 6-COOH-porphyrinogen I


organism: Burkholderia cepacia

proof_lines:
activated by Ca2+
activated by Mg2+
activated by Li+


organism: Chlamydia pneumoniae

proof_lines: in 20 mM Tris-HCl (pH 7.5) containing 1 mM Mg2+, at 30°C


organism: Cupriavidus necator


organism: Carpobrotus edulis


organism: Crithmum maritimum


organism: Dactylis glomerata


organism: Drosera capensis


organism: Ceratophyllum demersum


organism: Echeveria elegans


organism: Cycas panzhihuaensis


organism: Gallus gallus

proof_lines:
ATP in form of MnATP2-
ATP in form of CdATP2-
ATP in form of MgATP2-


organism: Galdieria sulphuraria


organism: Escherichia coli


organism: Bifidobacterium animalis subsp. lactis (strain DSM 10140 / CCUG 37979 / JCM 10602 / LMG 18314 / NRRL B-41405 / UR1)

substrate_name: fructose 6-phosphate

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

substrate: fructose 6-phosphate


enzyme_display_name: UniProt A0A0H5BR52

organism: Chamberlinius hualienensis

enzyme: UniProt A0A0H5BR52


substrate_name: benzaldehyde

substrate: benzaldehyde


enzyme_display_name: UniProt A0A1C9V3S9

organism: Davallia tyermanii

substrate_name: (R)-mandelonitrile

assay_conditions_summary: pH 5

enzyme: UniProt A0A1C9V3S9

substrate: (R)-mandelonitrile


enzyme_display_name: UniProt A0A1L7NZN4

organism: Passiflora edulis

enzyme: UniProt A0A1L7NZN4


enzyme_display_name: UniProt B9X0I1

organism: Prunus mume

enzyme: UniProt B9X0I1


enzyme_display_name: hydroxymandelonitrile lyase

organism: Sorghum bicolor

enzyme: hydroxymandelonitrile lyase


enzyme_display_name: UniProt I3EBM6

organism: Bacillus methanolicus

substrate_name: glycerone phosphate

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

enzyme: UniProt I3EBM6

substrate: glycerone phosphate


substrate_name: D-glyceraldehyde 3-phosphate

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

substrate: D-glyceraldehyde 3-phosphate


enzyme_display_name: UniProt P56109

organism: Helicobacter pylori

enzyme: UniProt P56109


enzyme_display_name: UniProt P58315

organism: Thermoproteus tenax

substrate_name: fructose 1,6-bisphosphate

enzyme: UniProt P58315

substrate: fructose 1,6-bisphosphate


enzyme_display_name: UniProt P0A955

enzyme: UniProt P0A955


organism: Glycine max

substrate_name: UDPglucuronate

substrate: UDPglucuronate


enzyme_display_name: ribulose-bisphosphate carboxylase

organism: Devaleraea ramentacea

enzyme: ribulose-bisphosphate carboxylase


organism: Himantothallus grandifolius


organism: Chlamydomonas reinhardtii


organism: Hibiscus cannabinus


organism: Desmarestia aculeata


organism: Homo sapiens

substrate_name: Uroporphyrinogen I

proof_lines: enzyme from patients with sporadic porphyria cutanea tarda

proof_lines: enzyme from patients with familial porphyria cutanea tarda

substrate: Uroporphyrinogen I


organism: Gallus gallus


substrate_name: uroporphyrinogen III

substrate: uroporphyrinogen III


organism: Lactuca sativa

proof_lines: oxygenase catalytic efficiency, pH 8.0, 25°C


enzyme_display_name: UniProt P23522

organism: Escherichia coli

enzyme: UniProt P23522


substrate_name: 2-dehydro-3-deoxy-L-rhamnonic acid

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

substrate: 2-dehydro-3-deoxy-L-rhamnonic acid


organism: Bifidobacterium animalis subsp. lactis (strain DSM 10140 / CCUG 37979 / JCM 10602 / LMG 18314 / NRRL B-41405 / UR1)


organism: Limonium latebracteatum

substrate_name: D-ribulose 1,5-bisphosphate

substrate: D-ribulose 1,5-bisphosphate


organism: Laminaria digitata


organism: Limonium virgatum


organism: Hordeum vulgare


organism: Mallomonas papillosa


organism: Laminaria solidungula


organism: Medicago sativa

verification_method: identity_resolution_snapshot + shared_family_context + candidate_conflict_review


organism: Marchantia polymorpha


organism: Metasequoia glyptostroboides


organism: Limonium gibertii

proof_lines: enzyme from well-watered plant grown at 25°C, pH and temperature not specified in the publication


organism: Nicotiana tabacum

proof_lines: enzyme assembled with small subunit isoform RbcS-s1H, pH 8.0, 25°C

proof_lines: ANtS40L Rubisco oligomer complex, using soluble leaf protein extract


organism: Nitrobacter winogradskyi


organism: Oryza sativa


substrate_name: UDP-glucuronic acid

substrate: UDP-glucuronic acid


organism: Palmaria palmata


organism: Palmaria decipiens


organism: Nymphaea alba


proof_lines: carboxylase catalytic efficiency, pH 8.0, 25°C


organism: Phycodrys rubens


organism: Pteridium aquilinum


organism: Phaeodactylum tricornutum


organism: Ptilota gunneri


organism: Rattus norvegicus

proof_lines:
37000 MW enzyme form
45000 MW enzyme form


organism: Sarracenia flava


organism: Platycerium superbum


organism: Saccharina latissima


organism: Skeletonema costatum

proof_lines: pH 7.5, temperature not specified in the publication


organism: Spinacia oleracea


organism: Staphylococcus epidermidis

proof_lines: pH and temperature not specified in the publication

substrate: Unknown


organism: Staphylococcus aureus


organism: Rhodospirillum rubrum


organism: Synura petersenii


enzyme_display_name: UniProt D1MX73

organism: Baliospermum montanum

enzyme: UniProt D1MX73


substrate_name: 2-thiophene carboxaldehyde

substrate: 2-thiophene carboxaldehyde


substrate_name: piperonal

substrate: piperonal


enzyme_display_name: UniProt P52704

organism: Hevea brasiliensis

proof_lines:
Raw SKiD Env: Temp=-----, pH=-----
Raw SKiD Env: Temp=-----, pH=5

enzyme: UniProt P52704


enzyme_display_name: UniProt P52705

organism: Manihot esculenta

substrate_name: 4-biphenyl carboxaldehyde

enzyme: UniProt P52705

substrate: 4-biphenyl carboxaldehyde


proof_lines:
Raw SKiD Env: Temp=-----, pH=5
Raw SKiD Env: Temp=25°C, pH=4
Raw SKiD Env: Temp=-----, pH=7.5


substrate_name: CN-

proof_lines:
Raw SKiD Env: Temp=-----, pH=-----
Raw SKiD Env: Temp=25°C, pH=4
Raw SKiD Env: Temp=-----, pH=7.5

substrate: CN-


enzyme_display_name: UniProt P75823

organism: Escherichia coli

substrate_name: L-threonine

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

proof_lines:
Raw SKiD Env: Temp=30°C, pH=7
Raw SKiD Env: Temp=30°C, pH=8

enzyme: UniProt P75823

substrate: L-threonine


enzyme_display_name: low-specificity L-threonine aldolase

organism: Caulobacter vibrioides

substrate_name: L-allo-Threonine

sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature D95C to reconstruct the assayed variant sequence.

enzyme: low-specificity L-threonine aldolase

substrate: L-allo-Threonine


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature D95G/E96G to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature D95W to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature D95Y to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature D95Y/E96T to reconstruct the assayed variant sequence.


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


substrate_name: L-Threonine

substrate: L-Threonine


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature D95L to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature D95M to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature D95N/E96S to reconstruct the assayed variant sequence.


organism: Synechococcus sp.

proof_lines:
cosubstrate: CO2
carboxylation


enzyme_display_name: protocatechuate decarboxylase

organism: Sedimentibacter hydroxybenzoicus

enzyme: protocatechuate decarboxylase


organism: Synura uvella


organism: Triticum aestivum

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

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


organism: Trachycarpus fortunei

proof_lines: in 100 mM Bicine-NaOH pH 8.0, 20 mM MgCl2, at 25°C


organism: Thiobacillus denitrificans

proof_lines:
enzyme form I
enzyme form II


proof_lines: enzyme from well-watered plant grown at 38°C, pH and temperature not specified in the publication


proof_lines:
pH 8.1, 4°C
pH 8.1, 25°C
at pH 8


enzyme_display_name: UniProt Q6KZI8

organism: Picrophilus torridus

enzyme: UniProt Q6KZI8


enzyme_display_name: UniProt Q47098

substrate_name: 3-deoxy-D-manno-oct-2-ulosonic acid

enzyme: UniProt Q47098

substrate: 3-deoxy-D-manno-oct-2-ulosonic acid


substrate_name: 4-hydroxy-2-oxopentanoic acid

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

substrate: 4-hydroxy-2-oxopentanoic acid


enzyme_display_name: UniProt P76469

enzyme: UniProt P76469


enzyme_display_name: UniProt O54288

organism: Saccharolobus solfataricus

enzyme: UniProt O54288


enzyme_display_name: UDP-glucuronate decarboxylase

enzyme: UDP-glucuronate decarboxylase


organism: Amaranthus hybridus

substrate_name: D-Ribulose 1,5-bisphosphate; CO2; H2O

substrate: D-Ribulose 1,5-bisphosphate; CO2; H2O


organism: Echinochloa crus-galli


enzyme_display_name: diphosphomevalonate decarboxylase

organism: Arachis hypogaea

substrate_name: (R)-5-Diphosphomevalonate; ATP

enzyme: diphosphomevalonate decarboxylase

substrate: (R)-5-Diphosphomevalonate; ATP


enzyme_display_name: UniProt P0DTQ0

organism: Bacillus thuringiensis serovar kurstaki

substrate_name: 5-deoxy-D-ribulose 1-phosphate

enzyme: UniProt P0DTQ0

substrate: 5-deoxy-D-ribulose 1-phosphate


organism: Glycine max

substrate_name: CO2; D-Ribulose 1,5-bisphosphate; H2O

substrate: CO2; D-Ribulose 1,5-bisphosphate; H2O


organism: Portulaca oleracea

substrate_name: CO2; H2O; D-Ribulose 1,5-bisphosphate

substrate: CO2; H2O; D-Ribulose 1,5-bisphosphate


organism: Zea mays


organism: Rhodospirillum rubrum


organism: Medicago sativa

substrate_name: H2O; D-Ribulose 1,5-bisphosphate; CO2

substrate: H2O; D-Ribulose 1,5-bisphosphate; CO2


organism: Setaria italica


organism: Solanum lycopersicum


organism: Spinacia oleracea


organism: Sorghum bicolor


organism: Bos taurus


organism: Streptococcus pneumoniae


proof_lines: Km (CO2): 0.485 mbar, V (oxygenation) max/V (carboxylation) max: 0.11, pH 7.95, 25°C


organism: Petroselinum crispum

substrate_name: H2O; CO2; D-Ribulose 1,5-bisphosphate

substrate: H2O; CO2; D-Ribulose 1,5-bisphosphate


organism: Aphanizomenon flos-aquae


enzyme_display_name: isocitrate lyase

organism: Aspergillus nidulans

substrate_name: threo-Ds-isocitrate

enzyme: isocitrate lyase

substrate: threo-Ds-isocitrate


enzyme_display_name: UniProt P0CT06

organism: Pyricularia oryzae

substrate_name: isocitrate

enzyme: UniProt P0CT06

substrate: isocitrate


enzyme_display_name: UniProt Q9I0K4

organism: Pseudomonas aeruginosa

enzyme: UniProt Q9I0K4


enzyme_display_name: UniProt Q05957

organism: Dianthus caryophyllus

enzyme: UniProt Q05957


substrate_name: oxalacetate

substrate: oxalacetate


enzyme_display_name: UniProt P0A6L4

organism: Escherichia coli K-12

substrate_name: N-acetyl-D-mannosamine

enzyme: UniProt P0A6L4

substrate: N-acetyl-D-mannosamine


substrate_name: pyruvate

substrate: pyruvate


enzyme_display_name: UniProt Q8NMD2

organism: Corynebacterium glutamicum

substrate_name: N-acetylneuraminate

proof_lines:
Raw SKiD Env: Temp=37°C, pH=7.5
Raw SKiD Env: Temp=37°C, pH=8.5

enzyme: UniProt Q8NMD2

substrate: N-acetylneuraminate


enzyme_display_name: UniProt Q9CKB0

organism: Pasteurella multocida

enzyme: UniProt Q9CKB0


organism: Citrullus lanatus


substrate_name: Ds-isocitrate

substrate: Ds-isocitrate


organism: Euglena gracilis

substrate_name: glyoxylate

assay_conditions_summary: pH 6.5; 303.15 K; cofactor CoA

proof_lines: D475N mutant protein, 0.15 mM acetyl-CoA, 10 mM succinate, pH 6.5, 30°C

proof_lines: D475N mutant protein, 10 mM succinate, pH 6.5, 30°C

substrate: glyoxylate


substrate_name: succinate

proof_lines: D475N mutant protein, 1.5 mM glyoxylate, sharply decreased with increasing acetyl-CoA concentration, pH 6.5, 30°C

substrate: succinate


proof_lines: when acetyl-CoA is present at concentrations higher than 5 mM, the Km value for isocitrate decreased by about one-third and the Vmax value increased about 2-fold, pH not specified in the publication, temperature not specified in the publica


organism: Pinus pinea

assay_conditions_summary: pH 7

proof_lines: pH 7, microgravity, condensation reaction


enzyme_display_name: N-acetylneuraminate lyase

proof_lines:
at pH 7.5 and 37°C
at pH 8.5 and 37°C

enzyme: N-acetylneuraminate lyase


organism: Turbatrix aceti


organism: Amaranthus caudatus

substrate_name: DL-isocitrate

proof_lines: isoform ICL1, with 5 mM MgCl2, at pH 7.5 and 25°C

proof_lines: isoform ICL2, with 5 mM MgCl2, at pH 7.5 and 25°C

substrate: DL-isocitrate


organism: Papilio machaon


substrate_name: Unknown

substrate: Unknown


organism: Candida brassicae

assay_conditions_summary: pH 6.85; buffer conditions ('imidazole-HCl buffer pH 6

proof_lines:
imidazole-HCl buffer pH 6.85
sodium phosphate buffer, pH 6.85


proof_lines:
pH 7, standard g, cleavage reaction
pH 7, microgravity, cleavage reaction
TRA, pH 7.0


organism: Rattus norvegicus


organism: Pinus densiflora


substrate_name: acetyl-CoA

assay_conditions_summary: pH 8; 303.15 K; cofactor CoA

substrate: acetyl-CoA


substrate_name: (2R,3S)-2,3-dimethyl malate

assay_conditions_summary: pH 7.5; 298.15 K; cofactor NADH

column_label: Table 1 columns reactant, kcat (s^-1), Km (uM), kcat/Km (M^-1 s^-1); (2R,3S)-2,3-dimethyl malate footnote b Km cell 26 uM; footnote b continuous LDH/NADH coupling assay.

raw_value_unit_evidence: (2R,3S)-2,3-dimethyl malate footnote b row: Km 26 uM in Table 1.

row_label: (2R,3S)-2,3-dimethyl malate; footnote b continuous LDH/NADH coupling assay

table_label: ACS institutional HTML Table 1, Steady-State Kinetic Constants for C-C Bond Cleavage Reactions Catalyzed by PDP

substrate: (2R,3S)-2,3-dimethyl malate


column_label: Table 1 columns reactant, kcat (s^-1), Km (uM), kcat/Km (M^-1 s^-1); (2R,3S)-isocitrate Km cell 42 uM.

raw_value_unit_evidence: (2R,3S)-isocitrate row: Km 42 uM in Table 1.


column_label: Table 1 columns reactant, kcat (s^-1), Km (uM), kcat/Km (M^-1 s^-1); oxaloacetate Km cell 130 uM.

raw_value_unit_evidence: Oxaloacetate row: Km 130 uM in Table 1.

row_label: oxaloacetate


organism: Linum usitatissimum


organism: Aliivibrio salmonicida

substrate_name: N-acetyl-D-neuraminic acid

sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature N168A with inferred residue-numbering offset -7 to reconstruct the assayed variant sequence.

substrate: N-acetyl-D-neuraminic acid


sequence_variant_note: Mutation signature N168T could not be applied safely because the resolved sequence does not match the expected reference residue(s).


organism: Limosilactobacillus antri

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

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 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.

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_ec_organism_unique and applied mutation signature P193Y to reconstruct the assayed variant sequence.


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

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.


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 4. Enzyme column header: LaNAL. Activity: Cleavage. Substrate: Neu5Ac. Cells read: K M (mM) 1.1±0.1, k cat (s -1 ) 1.9±0.2, k cat /K M (mM -1 s -1 ) 1.7. metric: kcat; raw value: 1.9; raw unit: s^-1; normalized value: 1.9 s^(-1); metric: Km; raw value: 1.1; raw unit: mM; normalized value: 1.1 mM; metric: kcat/Km; raw unit: s^-1 mM^-1; normalized value: 1.727272727272727 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 4 (LaNAL | Cleavage | Neu5Ac): K M 1.1 mM = 1.1 mM, already the export's unit, no conversion needed; k cat 1.9 s^-1 = 1.9 s^(-1), already the export's unit; k cat /K M 1.727272727272727 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 '±0.1' on the K M cell and '±0.2' 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 4 of Table 2 (enzyme LaNAL, activity Cleavage, substrate Neu5Ac) reads: K M (mM) cell 1.1±0.1; k cat (s -1 ) cell 1.9±0.2; k cat /K M (mM -1 s -1 ) cell 1.7. 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: LaNAL | Cleavage | Neu5Ac


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:C8P490 and applied mutation signature P193Y 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 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 (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.


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 5. Enzyme column header: LaNAL. Activity: Synthesis. Substrate: ManNAc. Cells read: K M (mM) 333±2, k cat (s -1 ) 5.4±0.2, k cat /K M (mM -1 s -1 ) 0.016. metric: kcat; raw value: 5.4; raw unit: s^-1; normalized value: 5.4 s^(-1); metric: Km; raw value: 333; raw unit: mM; normalized value: 333.0 mM; metric: kcat/Km; raw unit: s^-1 mM^-1; normalized value: 0.016216216216216217 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 5 (LaNAL | Synthesis | ManNAc): K M 333 mM = 333.0 mM, already the export's unit, no conversion needed; k cat 5.4 s^-1 = 5.4 s^(-1), already the export's unit; k cat /K M 0.016216216216216217 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 '±2' on the K M cell and '±0.2' 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 5 of Table 2 (enzyme LaNAL, activity Synthesis, substrate ManNAc) reads: K M (mM) cell 333±2; k cat (s -1 ) cell 5.4±0.2; k cat /K M (mM -1 s -1 ) cell 0.016. 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: LaNAL | Synthesis | ManNAc


column_label: Table label: Table 2. Kinetic parameters of LsNAL, LaNAL and three mutants of LaNAL. Data column 6. Enzyme column header: LaNAL. Activity: Synthesis. Substrate: Pyr. Cells read: K M (mM) 1.1±0.2, k cat (s -1 ) 5.6±0.1, k cat /K M (mM -1 s -1 ) 5.1. metric: kcat; raw value: 5.6; raw unit: s^-1; normalized value: 5.6 s^(-1); metric: Km; raw value: 1.1; raw unit: mM; normalized value: 1.1 mM; metric: kcat/Km; raw unit: s^-1 mM^-1; normalized value: 5.09090909090909 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 6 (LaNAL | Synthesis | Pyr): K M 1.1 mM = 1.1 mM, already the export's unit, no conversion needed; k cat 5.6 s^-1 = 5.6 s^(-1), already the export's unit; k cat /K M 5.09090909090909 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 6 of Table 2 (enzyme LaNAL, activity Synthesis, substrate Pyr) reads: K M (mM) cell 1.1±0.2; k cat (s -1 ) cell 5.6±0.1; k cat /K M (mM -1 s -1 ) cell 5.1. 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: LaNAL | Synthesis | Pyr


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.


organism: Escherichia coli (strain K12)

substrate_name: glyoxylate (at pH 7.3)

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

substrate: glyoxylate (at pH 7.3)


substrate_name: succinate (at pH 7.3)

substrate: succinate (at pH 7.3)


organism: Staphylococcus hominis

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


organism: Colwellia maris

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

proof_lines:
mutant Q217K, 10°C
mutant Q217K, 30°C


proof_lines:
wild-type, 10°C
wild-type, 20°C


sequence_variant_note: Resolved sequence already matches the mutant residue(s) after applying an inferred residue-numbering offset +14, so it is treated as a source-provided variant sequence.

proof_lines:
mutant Q207H, 10°C
mutant Q207H, 30°C