substrate_name: NADH

assay_conditions_summary: cofactor NADH

substrate: NADH


enzyme_display_name: nucleotide diphosphatase

organism: Homo sapiens

substrate_name: thymidine 5'-monophosphate p-nitrophenyl ester

source_db: brenda

verification_status: unverified

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.

enzyme: nucleotide diphosphatase

status: unverified

source: brenda


substrate_name: UDP-glucose

substrate: UDP-glucose


substrate_name: CDP-choline

substrate: CDP-choline


enzyme_display_name: glucosamine-6-phosphate deaminase

organism: Bos taurus

substrate_name: D-glucosamine 6-phosphate

proof_lines: pH 8.0, 30°C, in presence of N-acetylglucosamine 6-phosphate

enzyme: glucosamine-6-phosphate deaminase

substrate: D-glucosamine 6-phosphate


substrate_name: D-fructose 6-phosphate

substrate: D-fructose 6-phosphate


substrate_name: Unknown

km_display: Not reported

ki_unit: mM

substrate: Unknown


organism: Campylobacter jejuni

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

mutation_type: substitution


organism: Mus musculus

substrate_name: CTP

proof_lines: pH and temperature not specified in the publication

substrate: CTP


substrate_name: ATP

assay_conditions_summary: cofactor ATP

substrate: ATP


substrate_name: UTP

substrate: UTP


substrate_name: GTP

substrate: GTP


organism: Pseudomonas fluorescens


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


organism: Arthrobacter sp.


enzyme_display_name: 4-chlorobenzoyl-CoA dehalogenase

assay_conditions_summary: cofactor CoA

enzyme: 4-chlorobenzoyl-CoA dehalogenase


substrate_name: dITP

substrate: dITP


substrate_name: ITP

substrate: ITP


substrate_name: xanthosine 5'-triphosphate

substrate: xanthosine 5'-triphosphate


enzyme_display_name: 8-oxoguanine deaminase

organism: Pseudomonas aeruginosa

substrate_name: guanine

enzyme: 8-oxoguanine deaminase

substrate: guanine


substrate_name: isocytosine

substrate: isocytosine


organism: Pseudomonas sp.


substrate_name: beta-Chloro-D-alanine

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

substrate: beta-Chloro-D-alanine


substrate_name: O-acetyl-D-serine

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

substrate: O-acetyl-D-serine


organism: Rattus sp.

substrate_name: thymidine 5'-monophosphate p-nitrophenyl ester


substrate_name: NAD+

assay_conditions_summary: cofactor NAD+

substrate: NAD+


substrate_name: D-vinylglycine

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

substrate: D-vinylglycine


substrate_name: GDP-mannose

substrate: GDP-mannose


substrate_name: p-nitrophenyl 5'-TMP

proof_lines: potent inhibition at nearly stoichiometric concentrations

substrate: p-nitrophenyl 5'-TMP


substrate_name: FAD

assay_conditions_summary: cofactor FAD

substrate: FAD


substrate_name: NADH

substrate: NADH


substrate_name: UDP-glucose

substrate: UDP-glucose


substrate_name: ADP-ribose

assay_conditions_summary: cofactor ADP

substrate: ADP-ribose


organism: Aspergillus niger

substrate_name: fructose 6-phosphate

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

substrate: fructose 6-phosphate


substrate_name: glucosamine 6-phosphate

substrate: glucosamine 6-phosphate


organism: Escherichia coli

substrate_name: dTTP

substrate: dTTP


substrate_name: UTP

substrate: UTP


enzyme_display_name: aminopyrimidine aminohydrolase

organism: Helicobacter pylori

proof_lines: mutant enzyme F47Y, in 30 mM Tris, 50 mM NaCl (pH 8.0), at 20°C

enzyme: aminopyrimidine aminohydrolase


proof_lines: wild type enzyme, in 30 mM Tris, 50 mM NaCl (pH 8.0), at 20°C


substrate_name: D-fructose 6-phosphate

proof_lines: pH 8.5, 37°C, in presence of N-acetylglucosamine 6-phosphate and Mn2+

substrate: D-fructose 6-phosphate


enzyme_display_name: single-stranded DNA cytosine deaminase

substrate_name: CCCA

enzyme: single-stranded DNA cytosine deaminase

substrate: CCCA


substrate_name: TTCA

substrate: TTCA


organism: Mycobacterium tuberculosis


enzyme_display_name: haloalkane dehalogenase

organism: Mycobacterium tuberculosis variant bovis

smiles: CCCCCl

enzyme: haloalkane dehalogenase


smiles: C(CBr)CBr


enzyme_display_name: exopolyphosphatase

mutation_signature: truncated enzyme

mutation_type: truncation

enzyme: exopolyphosphatase


organism: Pseudomonas putida

substrate_name: D-Cystine

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

proof_lines: mutant enzyme E295S/L322T, pH and temperature not specified in the publication

substrate: D-Cystine


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


organism: Staphylococcus aureus

substrate_name: thiamine

substrate: thiamine


proof_lines: mutant enzyme D111A/K115A, at pH 7.5 and 37°C


enzyme_display_name: nucleoside-triphosphate phosphatase

organism: West Nile virus

substrate_name: ATP

assay_conditions_summary: pH 7.5; 303.15 K; cofactor ATP

enzyme: nucleoside-triphosphate phosphatase

substrate: ATP


substrate_name: DNA duplex

substrate: DNA duplex


enzyme_display_name: ADP-ribose diphosphatase

organism: Arabidopsis sp.

enzyme: ADP-ribose diphosphatase


organism: Arabidopsis thaliana

assay_conditions_summary: pH 8; 310.15 K; cofactor ADP

proof_lines:
37°C, pH 8.0, AtNUDT10
37°C, pH 8.0, AtNUDT6
37°C, pH 8.0, AtNUDT2


organism: Archaeoglobus fulgidus


organism: Bacillus sp. (in: firmicutes)

proof_lines:
at 60°C
at 25°C


enzyme_display_name: GTP cyclohydrolase II

organism: Bacillus subtilis

proof_lines: mutant enzyme Y210C/A290T/Q293R/A296T/K322R/F339Y/M361I, at pH 8.5 and 30°C

enzyme: GTP cyclohydrolase II


substrate_name: D-glucosamine 6-phosphate

proof_lines:
22°C, pH 8.0
recombinant enzyme, pH 7.4, 37°C

substrate: D-glucosamine 6-phosphate


organism: Bos taurus

substrate_name: UDP-N-acetyl-alpha-D-galactosamine

proof_lines: in the presence of B4 lectin from Vicia villosa

substrate: UDP-N-acetyl-alpha-D-galactosamine


organism: Campylobacter jejuni


organism: Candida albicans


organism: Canis lupus familiaris

proof_lines: per subunit, hyperbolic kinetic conditions, in presence of 1 mM N-acetylglucosamine 6-phosphate, pH 8.8

proof_lines: hexameric enzyme, hyperbolic kinetic conditions, in presence of 1 mM N-acetylglucosamine 6-phosphate, pH 8.8


organism: Dengue virus

assay_conditions_summary: pH 7.4; 303.15 K; cofactor ATP

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


organism: Enterovirus C


organism: Escherichia coli


organism: Haemophilus influenzae

substrate_name: alpha-D-glucosamine 6-phosphate

substrate: alpha-D-glucosamine 6-phosphate


organism: Homo sapiens

assay_conditions_summary: pH 7.5; 310.15 K; cofactor ADP

proof_lines:
pH 7.5, 37°C
at pH 8.0 and 37°C
pH 7.0, 37°C


substrate_name: ADPribose

substrate: ADPribose


substrate_name: ADP-mannose

assay_conditions_summary: pH 7; 310.15 K; cofactor ADP

substrate: ADP-mannose


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


enzyme_display_name: double-stranded RNA adenine deaminase

substrate_name: adenine in double-stranded RNA

enzyme: double-stranded RNA adenine deaminase

substrate: adenine in double-stranded RNA


enzyme_display_name: 8-oxo-dGDP phosphatase

substrate_name: GDP

assay_conditions_summary: pH 8; 303.15 K; cofactor ADP

enzyme: 8-oxo-dGDP phosphatase

substrate: GDP


assay_conditions_summary: pH 10; 310.15 K; cofactor ADP

proof_lines:
at pH 10.0 and 37°C
at pH 8.0 and 37°C


substrate_name: 7-methylguanosine 5'-diphosphate

substrate: 7-methylguanosine 5'-diphosphate


proof_lines: N-terminally tagged protein, pH 7.2, 20°C

proof_lines: C-terminally tagged protein, pH 7.2, 20°C


proof_lines: pH 8.5, 37°C, in presence of N-acetylglucosamine 6-phosphate and Mn2+


enzyme_display_name: endothelin-converting enzyme 1

substrate_name: Big endothelin-1

enzyme: endothelin-converting enzyme 1

substrate: Big endothelin-1


organism: Methylorubrum extorquens


substrate_name: formyl-tetrahydromethanopterin

substrate: formyl-tetrahydromethanopterin


organism: Methanosarcina barkeri


enzyme_display_name: ADAMTS-4 endopeptidase

organism: Mus musculus

substrate_name: Unknown

enzyme: ADAMTS-4 endopeptidase

substrate: Unknown


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


substrate_name: UDP-alpha-D-galactose

substrate: UDP-alpha-D-galactose


organism: Mycobacterium tuberculosis


organism: Oryctolagus cuniculus


enzyme_display_name: GPR endopeptidase

organism: Priestia megaterium

substrate_name: spore protein A

proof_lines:
spore protein A, Km lower than 0.014 mM
Km lower than 0.008 mM
pH 7.4, 37°C

enzyme: GPR endopeptidase

substrate: spore protein A


organism: Pseudomonas putida


substrate_name: D-cysteine

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

proof_lines: double mutant Pseudomonas putida E295S+L322T

substrate: D-cysteine


organism: Rattus norvegicus

substrate_name: H2O; p-Nitrophenylthymidine phosphate

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

assay_conditions_summary: pH 8.9; 310.15 K; cofactor ATP

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

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

substrate: H2O; p-Nitrophenylthymidine phosphate


proof_lines:
ADPRibase I
ADPRibase-Mn
ADPRibase II


organism: Rattus sp.

substrate_name: ATP

substrate: ATP


enzyme_display_name: tRNA(adenine(34)) deaminase

organism: Saccharomyces cerevisiae

substrate_name: adenine34 in tRNASer(AGA)

proof_lines: pH and temperature not specified in the publication

enzyme: tRNA(adenine(34)) deaminase

substrate: adenine34 in tRNASer(AGA)


enzyme_display_name: endopolyphosphatase

enzyme: endopolyphosphatase


organism: Staphylococcus aureus

substrate_name: thiamine

proof_lines: apparent value, in 100 mM Tris-HCl, pH 7.5, at 37°C

substrate: thiamine


enzyme_display_name: lysostaphin

organism: Staphylococcus simulans

proof_lines: value from Grafit and Hanes plot analyses

enzyme: lysostaphin


substrate_name: pentaglycine

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

proof_lines: 37°C, pH 7.5, pentaglycine incorporated into the cell wall

substrate: pentaglycine


enzyme_display_name: glucosamine-6-phosphate deaminase

organism: Sus scrofa

substrate_name: D-glucosamine 6-phosphate

proof_lines: pH 7.9, 37°C, activated by N-acetylglucosamine 6-phosphate

enzyme: glucosamine-6-phosphate deaminase

substrate: D-glucosamine 6-phosphate


enzyme_display_name: 4-chlorobenzoyl-CoA dehalogenase

organism: Arthrobacter sp.

assay_conditions_summary: pH 7.5; 303.15 K; cofactor CoA

enzyme: 4-chlorobenzoyl-CoA dehalogenase


substrate_name: ADP

assay_conditions_summary: pH 7; 295.15 K; cofactor ADP

proof_lines: pH 7.0, 22°C, recombinant wild-type enzyme

substrate: ADP


substrate_name: UTP

substrate: UTP


substrate_name: CTP

substrate: CTP


substrate_name: TTP

substrate: TTP


substrate_name: GTP

substrate: GTP


assay_conditions_summary: pH 7; 295.15 K; cofactor ATP


organism: Bacillus subtilis

substrate_name: ADPribose

substrate: ADPribose


organism: Escherichia coli


organism: Haemophilus influenzae


enzyme_display_name: alpha-D-ribose 1-methylphosphonate 5-triphosphate diphosphatase

proof_lines: pH 8.5, temperature not specified in the publication


proof_lines: full-length bifunctional enzyme ribA2, at pH 8.0 and 37°C

proof_lines: GCHII-domain of enzyme ribA2, at pH 8.0 and 37°C


organism: Homo sapiens

substrate_name: ADPribose; H2O

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

substrate: ADPribose; H2O


enzyme_display_name: GTP cyclohydrolase IIa

organism: Methanocaldococcus jannaschii

substrate_name: diphosphate

protein_accession_database: UniProt

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

data_origin: experimental

enzyme: GTP cyclohydrolase IIa

substrate: diphosphate


organism: Pseudomonas sp.

substrate_name: (R)-2-chloropropionic acid; 2-chloropropionic acid; (S)-2-chloropropionic acid

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

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


enzyme_display_name: peroxisome-assembly ATPase

assay_conditions_summary: pH 7.4; 310.15 K; cofactor ATP

proof_lines: recombinant Pex1p/Pex6p complex, pH 7.4, 37°C

proof_lines: recombinant Pex1-FLAG/His-Pex6 complex, pH and temperature not specified in the publication

enzyme: peroxisome-assembly ATPase


enzyme_display_name: non-chaperonin molecular chaperone ATPase

organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

substrate_name: ATP (at 2.5 mM potassium acetate)

source_db: uniprot

assay_conditions_summary: cofactor ATP

proof_lines: kcat is 0.95 min(-1) with ATP as substrate (at 2.5 mM potassium acetate) and 0.81 min(-1) with ATP as substrate (at 100 mM potassium acetate).

substrate: ATP (at 2.5 mM potassium acetate)

source: uniprot


enzyme_display_name: vesicle-fusing ATPase

proof_lines: higher order oligomer of the enzyme, pH and temperature not specified in the publication

enzyme: vesicle-fusing ATPase


substrate_name: ATP; H2O

enzyme: non-chaperonin molecular chaperone ATPase

substrate: ATP; H2O


substrate_name: H2O; ATP

substrate: H2O; ATP


organism: Pseudomonas aeruginosa


organism: Arabidopsis thaliana


substrate_name: Unknown

substrate: Unknown


substrate_name: ATP

proof_lines:
human Hsp90alpha and Hsp90beta
ATP hydrolysis
Hsp90 ATPase cycle

substrate: ATP


source_db: oed

kcat_over_km_origin: calculated

sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature R826M with inferred residue-numbering offset +4 to reconstruct the assayed variant sequence.

source: oed


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature Y819W with inferred residue-numbering offset -2 to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature N728A to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature T317A with inferred residue-numbering offset -1 to reconstruct the assayed variant sequence.


organism: Agrobacterium tumefaciens


substrate_name: ATP (at pH 7.8 and 30 degrees Celsius)

assay_conditions_summary: pH 7.8; cofactor ATP

substrate: ATP (at pH 7.8 and 30 degrees Celsius)


verification_status: verified

column_label: Full text reports wild type Drg1p exhibited ATPase activity with a Km(app) for ATP of 35 uM.

raw_value_unit_evidence: Km raw_value=35 uM raw_unit=microM

row_label: Wild type Drg1p ATPase activity

table_label: JBC full text Figure 4 / ATPase kinetics prose

status: verified


organism: Caenorhabditis elegans

substrate_name: ATP (at 30 degrees Celsius)

substrate: ATP (at 30 degrees Celsius)


organism: Rattus norvegicus


enzyme_display_name: UniProt P06672

organism: Zymomonas mobilis

substrate_name: 2-ketohexanoic acid

source_db: skid

source_license: CC BY-NC-ND 4.0

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

enzyme: UniProt P06672

substrate: 2-ketohexanoic acid

source: skid


substrate_name: 2-ketopentanoic acid

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

substrate: 2-ketopentanoic acid


substrate_name: benzoylformate

substrate: benzoylformate


enzyme_display_name: UniProt A9H275

organism: Ipomoea batatas

substrate_name: pyruvate

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

enzyme: UniProt A9H275

substrate: pyruvate


enzyme_display_name: UniProt P20906

organism: Pseudomonas putida

substrate_name: 2-oxohexanoic acid

enzyme: UniProt P20906

substrate: 2-oxohexanoic acid


substrate_name: 2-oxo-4-methylhexanoic acid

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

substrate: 2-oxo-4-methylhexanoic acid


substrate_name: 2-oxopentanoic acid

substrate: 2-oxopentanoic acid


smiles: CSCCC(=O)C(=O)[O-]


proof_lines:
Raw SKiD Env: Temp=30°C, pH=6.5
Raw SKiD Env: Temp=-----, pH=7
Raw SKiD Env: Temp=30°C, pH=6


substrate_name: phenylpyruvate

substrate: phenylpyruvate


substrate_name: methyl benzoylphosphonate

substrate: methyl benzoylphosphonate


substrate_name: benzaldehyde

substrate: benzaldehyde


substrate_name: acetaldehyde

smiles: CC=O

substrate: acetaldehyde


enzyme_display_name: benzoylformate decarboxylase

sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature T377L/A460Y to reconstruct the assayed variant sequence.

enzyme: benzoylformate decarboxylase


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


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


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


enzyme_display_name: pyruvate decarboxylase

organism: Saccharomyces cerevisiae

enzyme: pyruvate decarboxylase


proof_lines:
per subunit, pH 6.0, 30°C, mutant E91D
pH 6, 25°C, E91D mutant PDC


organism: Mycolicibacterium smegmatis


organism: Lactococcus lactis subsp. lactis

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


proof_lines: per subunit, pH 6.0, 30°C, wild-type enzyme


substrate_name: 2 pyruvate

proof_lines:
wild type enzyme, at pH 6.0 and 30°C
pH 6, wild-type YPDC

substrate: 2 pyruvate


proof_lines: mutant enzyme A143T/T156A/Q367H/N396I/K478R, at pH 6.0 and 30°C


organism: [Bacillus] caldolyticus


organism: Lactococcus lactis

substrate_name: Pyruvic acid

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

proof_lines:
pH 6.0, 30C, recombinant mutant V461I
pH 6.0, 30°C, recombinant mutant V461I

substrate: Pyruvic acid


proof_lines:
pH 6.0, 30C, recombinant mutant M538W
pH 6.0, 30°C, recombinant mutant M538W


proof_lines:
pH 6.0, 30C, recombinant mutant S286Y
pH 6.0, 30°C, recombinant mutant S286Y


proof_lines:
pH 6.0, 30C, recombinant mutant F381W
pH 6.0, 30°C, recombinant mutant F381W


proof_lines: pH 6, 25°C, C221E/C222A double mutant YPDC

proof_lines: per subunit, pH 6.0, 30°C, mutant C221E/C222A


proof_lines: pH 6, 25°C, C221D/C222A double mutant YPDC


assay_conditions_summary: pH 6


proof_lines:
pH 6, D28A mutant YPDC
D28A mutant YPDC


proof_lines: histidine buffer, enzyme from healthy tissue

proof_lines: histidine buffer, enzyme from diseased tissue

proof_lines: phosphate buffer, enzyme from healthy tissue


organism: Komagataella pastoris


organism: Pyrococcus furiosus

proof_lines: pH and temperature not specified in the publication


organism: Rhizopus arrhizus

proof_lines:
pH 6.5, 35C, isozyme 1
pH 6.5, 35°C, isozyme 2


organism: Rhodopseudomonas palustris


proof_lines: pH 6, 4°C, C221A/C222A double mutant PDC

proof_lines: pH 6, 30°C, C221A/C222A double mutant PDC

proof_lines: mutant enzyme C221A/C222A, at pH 6.5 and 10°C


substrate_name: Pyruvate

proof_lines:
isoform PDC6, at pH 7.0 and 25°C
isoform PDC1, at pH 7.0 and 25°C
isoform PDC5, at pH 7.0 and 25°C

substrate: Pyruvate


organism: Thermococcus kodakarensis


organism: Tritrichomonas suis

proof_lines:
pH 6.2, 25°C
pH 6.2, 25°C, presence of 0.1 M NaCl


organism: uncultured bacterium


enzyme_display_name: oxalate decarboxylase

organism: Cavia porcellus

substrate_name: oxalate

enzyme: oxalate decarboxylase

substrate: oxalate


organism: Zygosaccharomyces rouxii


organism: Lactiplantibacillus plantarum


enzyme_display_name: acetoacetate decarboxylase

organism: Rattus norvegicus

substrate_name: Acetoacetate

enzyme: acetoacetate decarboxylase

substrate: Acetoacetate


organism: Pseudothermotoga hypogea


organism: Stutzerimonas stutzeri


proof_lines: recombinant, his-tagged enzyme at pH 6.0 and 35°C


organism: Thermococcus guaymasensis


organism: Thermotoga maritima


enzyme_display_name: oxalyl-CoA decarboxylase

organism: Oxalobacter formigenes

substrate_name: Oxalyl-CoA

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

sequence_source: multiple

assay_conditions_summary: pH 6.7; 303.15 K; cofactor CoA

proof_lines:
pH 6.7, 30°C
at 37°C
Raw SKiD Env: Temp=30°C, pH=6.7

source_databases_merged: sabio_rk brenda skid uniprot

enzyme: oxalyl-CoA decarboxylase

substrate: Oxalyl-CoA


substrate_name: oxalyl-CoA

sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_consensus_sequence and applied mutation signature E121A to reconstruct the assayed variant sequence.

assay_conditions_summary: pH 6.5; buffer 25 mM sodium phosphate; cofactor CoA

proof_lines: mutant enzyme E121A, in 25 mM sodium phosphate buffer, pH 6.5, containing 300 mM NaCl

substrate: oxalyl-CoA


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_consensus_sequence and applied mutation signature Y120A to reconstruct the assayed variant sequence.

proof_lines: mutant enzyme Y120A, in 25 mM sodium phosphate buffer, pH 6.5, containing 300 mM NaCl


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_consensus_sequence and applied mutation signature Y483A with inferred residue-numbering offset -15 to reconstruct the assayed variant sequence.

proof_lines: mutant enzyme Y483A, in 25 mM sodium phosphate buffer, pH 6.5, containing 300 mM NaCl


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_consensus_sequence and applied mutation signature Y483F with inferred residue-numbering offset -15 to reconstruct the assayed variant sequence.

proof_lines: mutant enzyme Y483F, in 25 mM sodium phosphate buffer, pH 6.5, containing 300 mM NaCl


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_consensus_sequence and applied mutation signature E121Q to reconstruct the assayed variant sequence.

proof_lines: mutant enzyme E121Q, in 25 mM sodium phosphate buffer, pH 6.5, containing 300 mM NaCl


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_consensus_sequence and applied mutation signature Y120F to reconstruct the assayed variant sequence.

proof_lines: mutant enzyme Y120F, in 25 mM sodium phosphate buffer, pH 6.5, containing 300 mM NaCl


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_consensus_sequence and applied mutation signature S553A to reconstruct the assayed variant sequence.

proof_lines: mutant enzyme S553A, in 25 mM sodium phosphate buffer, pH 6.5, containing 300 mM NaCl


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_consensus_sequence and applied mutation signature R555A to reconstruct the assayed variant sequence.

proof_lines: mutant enzyme R555A, in 25 mM sodium phosphate buffer, pH 6.5, containing 300 mM NaCl


proof_lines: wild type enzyme, in 25 mM sodium phosphate buffer, pH 6.5, containing 300 mM NaCl


enzyme_display_name: cis-aconitate decarboxylase

organism: Homo sapiens

substrate_name: cis-aconitate

enzyme: cis-aconitate decarboxylase

substrate: cis-aconitate


organism: Kluyveromyces lactis

proof_lines:
pH 6, 30°C, enzyme monomer
pH 6, 30°C


organism: Nakaseomyces glabratus

proof_lines: pH and temperature not specified in the publication


assay_conditions_summary: pH 6.5; buffer pH 6

proof_lines: wild-type, pH 6.5, 37°C, 167 mM phosphate buffer

proof_lines: pH 6.5, 37°C, recombinant wild-type enzyme


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature R273H to reconstruct the assayed variant sequence.

proof_lines: mutant R273H, pH 6.5, 37°C, 167 mM phosphate buffer


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature N152S to reconstruct the assayed variant sequence.

proof_lines: mutant N152S, pH 6.5, 37°C, 167 mM phosphate buffer


organism: Zygosaccharomyces bisporus

proof_lines: pH 6, 25°C, sigmoidal dependence of the reaction rate from substrate concentration, Hill coefficient 2.10


organism: Zea mays

sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_mutation_ranked_match and applied mutation signature E50D with inferred residue-numbering offset -10 to reconstruct the assayed variant sequence.


organism: Sarcina ventriculi

sequence: MKITIAEYLLKRLKEVNVEHMFGVPGDYNLGFLDYV

wild_type_sequence: MKITIAEYLLKRLKEVNVEHMFGVPGDYNLGFLDYV

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

proof_lines: pH 6.5, potassium MES buffer, two affinities for pyruvate, sigmoidal kinetics

proof_lines: pH 6.5, sodium hydrogen maleate buffer, two affinities for pyruvate, sigmoidal kinetics


organism: Flammulina velutipes

proof_lines: recombinant OXDC, expressed in Nicotiana tabaccum


organism: Bacillus subtilis

sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_mutation_ranked_match and applied mutation signature E161A to reconstruct the assayed variant sequence.

assay_conditions_summary: pH 4


organism: Zymomonas mobilis

source_databases_merged: sabio_rk brenda skid


organism: Chromobacterium violaceum

substrate_name: acetoacetate

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

proof_lines: kcat is 350 sec(-1) at pH 6. kcat is 440 sec(-1) at pH 5.4. kcat is 420 sec(-1) at pH 4.8.

source_databases_merged: skid uniprot

substrate: acetoacetate


organism: Aspergillus terreus (strain NIH 2624 / FGSC A1156)


organism: Clostridium acetobutylicum


organism: Escherichia coli

assay_conditions_summary: pH 6.5; 303.15 K; cofactor CoA

proof_lines: kcat is 69.7 sec(-1) for decarboxylase activity with oxalyl-CoA as substrate (with 300 uM ADP at pH 6.5 and 30 degrees Celsius). kcat is 60.7 sec(-1) for decarboxylase activity with oxalyl-CoA as substrate (at pH 6.5 and 30 degrees Celsius)


organism: Mus musculus


substrate_name: Oxalate

substrate: Oxalate


organism: Bacillus subtilis (strain 168)

substrate_name: Unknown

substrate: Unknown


organism: Pseudomonas putida

substrate_name: alpha-Oxo-benzeneacetic acid

substrate: alpha-Oxo-benzeneacetic acid


organism: Oxalobacter formigenes


substrate_name: 2-Keto-4-methylhexanoic acid

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

substrate: 2-Keto-4-methylhexanoic acid


proof_lines:
Raw SKiD Env: Temp=25°C, pH=-----
Raw SKiD Env: Temp=30°C, pH=6


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

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


smiles: CCCCC(=O)C(=O)[O-]


verification_status: corrected

sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P06672 and applied mutation signature I472A to reconstruct the assayed variant sequence.

assay_conditions_summary: pH 6.5; 303.15 K; cofactor NADH

column_label: Table III, compound row 2-Keto-4-methylhexanoic acid (10), column PDCI472A; column 'Km (mM)' = 1.7; column 'kcat (s^-1)' = 7.7; column 'kcat/Km (mM^-1 s^-1)' = 4.5.

normalized_value_unit_evidence: Km: printed Table III cell 1.7 mM; the column is already millimolar, so no conversion is applied and the value is 1.7 mM. kcat: printed Table III cell 7.7 s^-1; the column is already per second, so no conversion is applied and the value is 7.7 s^(-1). kcat/Km: printed Table III cell 4.5 mM^-1 s^-1; mM^-1 s^-1 is the canonical s^-1 mM^-1 with the two factors written in the other order, so no conversion is applied and the value is 4.5 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table III, compound row 2-Keto-4-methylhexanoic acid (10), column PDCI472A: Km = 1.7 mM; kcat = 7.7 s^-1; printed kcat/Km = 4.5 mM^-1 s^-1.

table_label: Table III: Michaelis-Menten constants for decarboxylation of branched chain 2-keto acids (Protein Engineering, Design & Selection 2005, 18(7):345-357)

status: corrected


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P06672 and applied mutation signature I472A/I476F to reconstruct the assayed variant sequence.

column_label: Table III, compound row 2-Keto-4-methylhexanoic acid (10), column PDCI472A/I476F; column 'Km (mM)' = 3.7; column 'kcat (s^-1)' = 8.1; column 'kcat/Km (mM^-1 s^-1)' = 2.2.

normalized_value_unit_evidence: Km: printed Table III cell 3.7 mM; the column is already millimolar, so no conversion is applied and the value is 3.7 mM. kcat: printed Table III cell 8.1 s^-1; the column is already per second, so no conversion is applied and the value is 8.1 s^(-1). kcat/Km: printed Table III cell 2.2 mM^-1 s^-1; mM^-1 s^-1 is the canonical s^-1 mM^-1 with the two factors written in the other order, so no conversion is applied and the value is 2.2 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table III, compound row 2-Keto-4-methylhexanoic acid (10), column PDCI472A/I476F: Km = 3.7 mM; kcat = 8.1 s^-1; printed kcat/Km = 2.2 mM^-1 s^-1.


column_label: Table II, compound row 2-Ketobutanoic acid (2), column I472A; column 'Km (mM)' = 6.7; column 'kcat (s^-1)' = 250; column 'kcat/Km (mM^-1 s^-1)' = 37; the same cell prints the relative value (54) in parentheses, which Table II defines as a percentage of the wild-type value.

normalized_value_unit_evidence: Km: printed Table II cell 6.7 mM; the column is already millimolar, so no conversion is applied and the value is 6.7 mM. kcat: printed Table II cell 250 s^-1; the column is already per second, so no conversion is applied and the value is 250.0 s^(-1). kcat/Km: printed Table II cell 37 mM^-1 s^-1; mM^-1 s^-1 is the canonical s^-1 mM^-1 with the two factors written in the other order, so no conversion is applied and the value is 37.0 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table II, compound row 2-Ketobutanoic acid (2), column I472A: Km = 6.7 mM; kcat = 250 s^-1; printed kcat/Km = 37 mM^-1 s^-1.

table_label: Table II: Michaelis-Menten constants for decarboxylase activity of PDC variants (Protein Engineering, Design & Selection 2005, 18(7):345-357)


column_label: Table II, compound row 2-Ketobutanoic acid (2), column I472A/I476F; column 'Km (mM)' = 50; column 'kcat (s^-1)' = 9.0; column 'kcat/Km (mM^-1 s^-1)' = 0.2; the same cell prints the relative value (0.3) in parentheses, which Table II defines as a percentage of the wild-type value.

normalized_value_unit_evidence: Km: printed Table II cell 50 mM; the column is already millimolar, so no conversion is applied and the value is 50.0 mM. kcat: printed Table II cell 9.0 s^-1; the column is already per second, so no conversion is applied and the value is 9.0 s^(-1). kcat/Km: printed Table II cell 0.2 mM^-1 s^-1; mM^-1 s^-1 is the canonical s^-1 mM^-1 with the two factors written in the other order, so no conversion is applied and the value is 0.2 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table II, compound row 2-Ketobutanoic acid (2), column I472A/I476F: Km = 50 mM; kcat = 9.0 s^-1; printed kcat/Km = 0.2 mM^-1 s^-1.


column_label: Table II, compound row 2-Ketobutanoic acid (2), column WT; column 'Km (mM)' = 4.7; column 'kcat (s^-1)' = 320; column 'kcat/Km (mM^-1 s^-1)' = 68; the same cell prints the relative value (100) in parentheses, which Table II defines as a percentage of the wild-type value.

normalized_value_unit_evidence: Km: printed Table II cell 4.7 mM; the column is already millimolar, so no conversion is applied and the value is 4.7 mM. kcat: printed Table II cell 320 s^-1; the column is already per second, so no conversion is applied and the value is 320.0 s^(-1). kcat/Km: printed Table II cell 68 mM^-1 s^-1; mM^-1 s^-1 is the canonical s^-1 mM^-1 with the two factors written in the other order, so no conversion is applied and the value is 68.0 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table II, compound row 2-Ketobutanoic acid (2), column WT: Km = 4.7 mM; kcat = 320 s^-1; printed kcat/Km = 68 mM^-1 s^-1.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature I472A to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from accession_anchored:P20906/AY143338/AAC15502.1/1MCZ and applied mutation signature A460Y to reconstruct the assayed variant sequence.

raw_value_unit_evidence: Table 3 row A460Y; column 2KB; kcat=6.0 ± 0.4 s^-1; Km=1.3 ± 0.2 mM; kcat/Km=4.6 mM^-1 s^-1 (parenthetical 9-fold over wt).

table_label: Table 3


sequence_variant_note: Resolved canonical sequence from accession_anchored:P20906/AY143338/AAC15502.1/1MCZ and applied mutation signature T377L to reconstruct the assayed variant sequence.

raw_value_unit_evidence: Table 3 row T377L; column 2KB; kcat=7.5 ± 0.3 s^-1; Km=4.3 ± 0.4 mM; kcat/Km=1.7 mM^-1 s^-1 (parenthetical 3-fold over wt).


sequence_variant_note: Resolved canonical sequence from accession_anchored:P20906/AY143338/AAC15502.1/1MCZ and applied mutation signature T377L/A460Y to reconstruct the assayed variant sequence.

raw_value_unit_evidence: Table 3 row T377L-A460Y; column 2KB; kcat=5.8 ± 0.2 s^-1; Km=0.42 ± 0.02 mM; kcat/Km=14 mM^-1 s^-1 (parenthetical 28-fold over wt).


column_label: Table 3 | row wt | column 2KB | kcat (s^-1)=4 ± 1 | Km (mM)=7.5 ± 0.6 | kcat/Km (mM^-1 s^-1)=0.5

raw_value_unit_evidence: Table 3 row wt; column 2KB; kcat=4 ± 1 s^-1; Km=7.5 ± 0.6 mM; kcat/Km=0.5 mM^-1 s^-1 (parenthetical 1-fold over wt).

row_label: wt


raw_value_unit_evidence: Table 3 row A460Y; column 2KH; kcat=4.4 ± 0.2 s^-1; Km=0.28 ± 0.05 mM; kcat/Km=16 mM^-1 s^-1 (parenthetical 12-fold over wt).


raw_value_unit_evidence: Table 3 row T377L; column 2KH; kcat=1.1 ± 0.1 s^-1; Km=1.3 ± 0.3 mM; kcat/Km=0.86 mM^-1 s^-1 (parenthetical 0.6-fold over wt).


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature T377L/A460Y to reconstruct the assayed variant sequence.


raw_value_unit_evidence: Table 3 row A460Y; column 2KP; kcat=6.2 ± 0.2 s^-1; Km=0.28 ± 0.03 mM; kcat/Km=22 mM^-1 s^-1 (parenthetical 12-fold over wt).


raw_value_unit_evidence: Table 3 row T377L; column 2KP; kcat=3.3 ± 0.1 s^-1; Km=1.1 ± 0.1 mM; kcat/Km=3 mM^-1 s^-1 (parenthetical 1.6-fold over wt).


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature I472A/I476F with inferred residue-numbering offset -11 to reconstruct the assayed variant sequence.


column_label: PMID 15930043, Table II. Michaelis-Menten constants for decarboxylase activity of PDC variants; row Compound 2-Ketohexanoic acid (4); PDC variant WT; columns kcat (s^-1)=4.0, Km (mM)=12.7, kcat/Km (mM^-1 s^-1)=0.3.

normalized_value_unit_evidence: kcat normalized_value=4.0 normalized_unit=s^-1; Km normalized_value=12.7 normalized_unit=mM; kcat/Km normalized_value=0.3 normalized_unit=s^-1*mM^-1

raw_value_unit_evidence: kcat raw_value=4.0 raw_unit=s^-1; Km raw_value=12.7 raw_unit=mM; kcat/Km raw_value=0.3 raw_unit=s^-1*mM^-1; source_context=PDC from Zymomonas mobilis; wild-type variant column in Table II. 2-Oxohexanoate maps to 2-ketohexanoic acid.


column_label: Table II, compound row 2-Ketopentanoic acid (3), column I472A; column 'Km (mM)' = 2.5; column 'kcat (s^-1)' = 220; column 'kcat/Km (mM^-1 s^-1)' = 87; the same cell prints the relative value (1260) in parentheses, which Table II defines as a percentage of the wild-type value.

normalized_value_unit_evidence: Km: printed Table II cell 2.5 mM; the column is already millimolar, so no conversion is applied and the value is 2.5 mM. kcat: printed Table II cell 220 s^-1; the column is already per second, so no conversion is applied and the value is 220.0 s^(-1). kcat/Km: printed Table II cell 87 mM^-1 s^-1; mM^-1 s^-1 is the canonical s^-1 mM^-1 with the two factors written in the other order, so no conversion is applied and the value is 87.0 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table II, compound row 2-Ketopentanoic acid (3), column I472A: Km = 2.5 mM; kcat = 220 s^-1; printed kcat/Km = 87 mM^-1 s^-1.


column_label: Table II, compound row 2-Ketopentanoic acid (3), column I472A/I476F; column 'Km (mM)' = 11; column 'kcat (s^-1)' = 30; column 'kcat/Km (mM^-1 s^-1)' = 2.7; the same cell prints the relative value (39) in parentheses, which Table II defines as a percentage of the wild-type value.

normalized_value_unit_evidence: Km: printed Table II cell 11 mM; the column is already millimolar, so no conversion is applied and the value is 11.0 mM. kcat: printed Table II cell 30 s^-1; the column is already per second, so no conversion is applied and the value is 30.0 s^(-1). kcat/Km: printed Table II cell 2.7 mM^-1 s^-1; mM^-1 s^-1 is the canonical s^-1 mM^-1 with the two factors written in the other order, so no conversion is applied and the value is 2.7 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table II, compound row 2-Ketopentanoic acid (3), column I472A/I476F: Km = 11 mM; kcat = 30 s^-1; printed kcat/Km = 2.7 mM^-1 s^-1.


column_label: PMID 15930043, Table II. Michaelis-Menten constants for decarboxylase activity of PDC variants; row Compound 2-Ketopentanoic acid (3); PDC variant WT; columns kcat (s^-1)=53, Km (mM)=7.6, kcat/Km (mM^-1 s^-1)=7.0.

normalized_value_unit_evidence: kcat normalized_value=53.0 normalized_unit=s^-1; Km normalized_value=7.6 normalized_unit=mM; kcat/Km normalized_value=7.0 normalized_unit=s^-1*mM^-1

raw_value_unit_evidence: kcat raw_value=53 raw_unit=s^-1; Km raw_value=7.6 raw_unit=mM; kcat/Km raw_value=7.0 raw_unit=s^-1*mM^-1; source_context=PDC from Zymomonas mobilis; wild-type variant column in Table II. 2-Oxopentanoate maps to 2-ketopentanoic acid.


column_label: Table II, compound row Benzoylformate (12), column I472A; column 'Km (mM)' = 1.8; column 'kcat (s^-1)' = 6.9; column 'kcat/Km (mM^-1 s^-1)' = 3.8.

normalized_value_unit_evidence: Km: printed Table II cell 1.8 mM; the column is already millimolar, so no conversion is applied and the value is 1.8 mM. kcat: printed Table II cell 6.9 s^-1; the column is already per second, so no conversion is applied and the value is 6.9 s^(-1). kcat/Km: printed Table II cell 3.8 mM^-1 s^-1; mM^-1 s^-1 is the canonical s^-1 mM^-1 with the two factors written in the other order, so no conversion is applied and the value is 3.8 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table II, compound row Benzoylformate (12), column I472A: Km = 1.8 mM; kcat = 6.9 s^-1; printed kcat/Km = 3.8 mM^-1 s^-1.


column_label: Table II, compound row Benzoylformate (12), column I472A/I476F; column 'Km (mM)' = 4.4; column 'kcat (s^-1)' = 1.2; column 'kcat/Km (mM^-1 s^-1)' = 0.3.

normalized_value_unit_evidence: Km: printed Table II cell 4.4 mM; the column is already millimolar, so no conversion is applied and the value is 4.4 mM. kcat: printed Table II cell 1.2 s^-1; the column is already per second, so no conversion is applied and the value is 1.2 s^(-1). kcat/Km: printed Table II cell 0.3 mM^-1 s^-1; mM^-1 s^-1 is the canonical s^-1 mM^-1 with the two factors written in the other order, so no conversion is applied and the value is 0.3 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table II, compound row Benzoylformate (12), column I472A/I476F: Km = 4.4 mM; kcat = 1.2 s^-1; printed kcat/Km = 0.3 mM^-1 s^-1.


substrate_name: pyruvate

column_label: Table II, compound row Pyruvate (1), column I472A; column 'Km (mM)' = 7.8; column 'kcat (s^-1)' = 200; column 'kcat/Km (mM^-1 s^-1)' = 26; the same cell prints the relative value (6) in parentheses, which Table II defines as a percentage of the wild-type value.

normalized_value_unit_evidence: Km: printed Table II cell 7.8 mM; the column is already millimolar, so no conversion is applied and the value is 7.8 mM. kcat: printed Table II cell 200 s^-1; the column is already per second, so no conversion is applied and the value is 200.0 s^(-1). kcat/Km: printed Table II cell 26 mM^-1 s^-1; mM^-1 s^-1 is the canonical s^-1 mM^-1 with the two factors written in the other order, so no conversion is applied and the value is 26.0 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table II, compound row Pyruvate (1), column I472A: Km = 7.8 mM; kcat = 200 s^-1; printed kcat/Km = 26 mM^-1 s^-1.

substrate: pyruvate


column_label: Table II, compound row Pyruvate (1), column I472A/I476F; column 'Km (mM)' = 50; column 'kcat (s^-1)' = 8.0; column 'kcat/Km (mM^-1 s^-1)' = 0.2; the same cell prints the relative value (2) in parentheses, which Table II defines as a percentage of the wild-type value.

normalized_value_unit_evidence: Km: printed Table II cell 50 mM; the column is already millimolar, so no conversion is applied and the value is 50.0 mM. kcat: printed Table II cell 8.0 s^-1; the column is already per second, so no conversion is applied and the value is 8.0 s^(-1). kcat/Km: printed Table II cell 0.2 mM^-1 s^-1; mM^-1 s^-1 is the canonical s^-1 mM^-1 with the two factors written in the other order, so no conversion is applied and the value is 0.2 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table II, compound row Pyruvate (1), column I472A/I476F: Km = 50 mM; kcat = 8.0 s^-1; printed kcat/Km = 0.2 mM^-1 s^-1.


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P06672 and applied mutation signature I476F to reconstruct the assayed variant sequence.

column_label: Table II, compound row Pyruvate (1), column I476F; column 'Km (mM)' = 2.6; column 'kcat (s^-1)' = 77; column 'kcat/Km (mM^-1 s^-1)' = 30; the same cell prints the relative value (7) in parentheses, which Table II defines as a percentage of the wild-type value.

normalized_value_unit_evidence: Km: printed Table II cell 2.6 mM; the column is already millimolar, so no conversion is applied and the value is 2.6 mM. kcat: printed Table II cell 77 s^-1; the column is already per second, so no conversion is applied and the value is 77.0 s^(-1). kcat/Km: printed Table II cell 30 mM^-1 s^-1; mM^-1 s^-1 is the canonical s^-1 mM^-1 with the two factors written in the other order, so no conversion is applied and the value is 30.0 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table II, compound row Pyruvate (1), column I476F: Km = 2.6 mM; kcat = 77 s^-1; printed kcat/Km = 30 mM^-1 s^-1.


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P20906 and applied mutation signature A460I to reconstruct the assayed variant sequence.

assay_conditions_summary: pH 6; 303.15 K; buffer 50 mM potassium phosphate; cofactor NADH

column_label: Table IV, compound row 2-Ketopentanoic acid (3), column A460I; column 'Km (mM)' = 1.2; column 'kcat (s^-1)' = 40.6; column 'kcat/Km (mM^-1 s^-1)' = 33.8; the same cell prints the relative value (457) in parentheses, which Table IV defines as a percentage of the wild-type value; the Km cell carries the table footnote marker for substrate inhibition (Displays substrate inhibition with Ki = 20 mM.).

normalized_value_unit_evidence: Km: printed Table IV cell 1.2 mM; the column is already millimolar, so no conversion is applied and the value is 1.2 mM. kcat: printed Table IV cell 40.6 s^-1; the column is already per second, so no conversion is applied and the value is 40.6 s^(-1). kcat/Km: printed Table IV cell 33.8 mM^-1 s^-1; mM^-1 s^-1 is the canonical s^-1 mM^-1 with the two factors written in the other order, so no conversion is applied and the value is 33.8 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table IV, compound row 2-Ketopentanoic acid (3), column A460I: Km = 1.2 mM; kcat = 40.6 s^-1; printed kcat/Km = 33.8 mM^-1 s^-1.

table_label: Table IV: Michaelis-Menten constants for decarboxylase activity of BFD variants (Protein Engineering, Design & Selection 2005, 18(7):345-357)


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature A460I to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P20906 and applied mutation signature A460I/F464I to reconstruct the assayed variant sequence.

column_label: Table IV, compound row Benzoylformate (12), column A460I/F464I; column 'Km (mM)' = 1.1; column 'kcat (s^-1)' = 21; column 'kcat/Km (mM^-1 s^-1)' = 19; the same cell prints the relative value (1) in parentheses, which Table IV defines as a percentage of the wild-type value.

normalized_value_unit_evidence: Km: printed Table IV cell 1.1 mM; the column is already millimolar, so no conversion is applied and the value is 1.1 mM. kcat: printed Table IV cell 21 s^-1; the column is already per second, so no conversion is applied and the value is 21.0 s^(-1). kcat/Km: printed Table IV cell 19 mM^-1 s^-1; mM^-1 s^-1 is the canonical s^-1 mM^-1 with the two factors written in the other order, so no conversion is applied and the value is 19.0 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table IV, compound row Benzoylformate (12), column A460I/F464I: Km = 1.1 mM; kcat = 21 s^-1; printed kcat/Km = 19 mM^-1 s^-1.


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P20906 and applied mutation signature F464I to reconstruct the assayed variant sequence.

column_label: Table IV, compound row Benzoylformate (12), column F464I; column 'Km (mM)' = 2.3; column 'kcat (s^-1)' = 123; column 'kcat/Km (mM^-1 s^-1)' = 53; the same cell prints the relative value (3) in parentheses, which Table IV defines as a percentage of the wild-type value.

normalized_value_unit_evidence: Km: printed Table IV cell 2.3 mM; the column is already millimolar, so no conversion is applied and the value is 2.3 mM. kcat: printed Table IV cell 123 s^-1; the column is already per second, so no conversion is applied and the value is 123.0 s^(-1). kcat/Km: printed Table IV cell 53 mM^-1 s^-1; mM^-1 s^-1 is the canonical s^-1 mM^-1 with the two factors written in the other order, so no conversion is applied and the value is 53.0 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table IV, compound row Benzoylformate (12), column F464I: Km = 2.3 mM; kcat = 123 s^-1; printed kcat/Km = 53 mM^-1 s^-1.


sequence_variant_note: Mutation signature F464I matches the mutant residue at offset +0 and the reference residue at offset -14; variant reconstruction was not applied because multiple plausible residue-numbering offsets are present.


proof_lines:
Pseudomonas putida
benzoylformate decarboxylase
substrate specificity exchange


proof_lines:
pyruvate
BFDA460I
benzoylformate decarboxylase


substrate_name: 2-Keto-4-methylpentanoic acid

proof_lines:
substrate-spectrum shift
branch-chain substrate context
benzoylformate decarboxylase

substrate: 2-Keto-4-methylpentanoic acid


column_label: Table III, compound row 2-Keto-4-methylhexanoic acid (10), column BFDA460I; column 'Km (mM)' = 1.1; column 'kcat (s^-1)' = 9.8; column 'kcat/Km (mM^-1 s^-1)' = 8.9; the Km cell carries the table footnote marker for substrate inhibition (Displays substrate inhibition with Ki = 48 mM.).

normalized_value_unit_evidence: Km: printed Table III cell 1.1 mM; the column is already millimolar, so no conversion is applied and the value is 1.1 mM. kcat: printed Table III cell 9.8 s^-1; the column is already per second, so no conversion is applied and the value is 9.8 s^(-1). kcat/Km: printed Table III cell 8.9 mM^-1 s^-1; mM^-1 s^-1 is the canonical s^-1 mM^-1 with the two factors written in the other order, so no conversion is applied and the value is 8.9 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table III, compound row 2-Keto-4-methylhexanoic acid (10), column BFDA460I: Km = 1.1 mM; kcat = 9.8 s^-1; printed kcat/Km = 8.9 mM^-1 s^-1.


column_label: Table III, compound row 2-Keto-4-methylpentanoic acid (8), column BFDA460I; column 'Km (mM)' = 3.4; column 'kcat (s^-1)' = 38; column 'kcat/Km (mM^-1 s^-1)' = 11; the same cell prints the relative value (975) in parentheses, which Table III defines as a percentage of the wild-type value; the Km cell carries the table footnote marker for substrate inhibition (Displays substrate inhibition with Ki = 60 mM.).

normalized_value_unit_evidence: Km: printed Table III cell 3.4 mM; the column is already millimolar, so no conversion is applied and the value is 3.4 mM. kcat: printed Table III cell 38 s^-1; the column is already per second, so no conversion is applied and the value is 38.0 s^(-1). kcat/Km: printed Table III cell 11 mM^-1 s^-1; mM^-1 s^-1 is the canonical s^-1 mM^-1 with the two factors written in the other order, so no conversion is applied and the value is 11.0 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table III, compound row 2-Keto-4-methylpentanoic acid (8), column BFDA460I: Km = 3.4 mM; kcat = 38 s^-1; printed kcat/Km = 11 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 III, compound row 2-Keto-4-methylpentanoic acid (8), column BFD WT; column 'Km (mM)' = 9.6; column 'kcat (s^-1)' = 11; column 'kcat/Km (mM^-1 s^-1)' = 1.1; the same cell prints the relative value (100) in parentheses, which Table III defines as a percentage of the wild-type value.

normalized_value_unit_evidence: Km: printed Table III cell 9.6 mM; the column is already millimolar, so no conversion is applied and the value is 9.6 mM. kcat: printed Table III cell 11 s^-1; the column is already per second, so no conversion is applied and the value is 11.0 s^(-1). kcat/Km: printed Table III cell 1.1 mM^-1 s^-1; mM^-1 s^-1 is the canonical s^-1 mM^-1 with the two factors written in the other order, so no conversion is applied and the value is 1.1 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table III, compound row 2-Keto-4-methylpentanoic acid (8), column BFD WT: Km = 9.6 mM; kcat = 11 s^-1; printed kcat/Km = 1.1 mM^-1 s^-1.


column_label: Table IV, compound row 2-Ketobutanoic acid (2), column A460I; column 'Km (mM)' = 18.3; column 'kcat (s^-1)' = 18.8; column 'kcat/Km (mM^-1 s^-1)' = 1.0.

normalized_value_unit_evidence: Km: printed Table IV cell 18.3 mM; the column is already millimolar, so no conversion is applied and the value is 18.3 mM. kcat: printed Table IV cell 18.8 s^-1; the column is already per second, so no conversion is applied and the value is 18.8 s^(-1). kcat/Km: printed Table IV cell 1.0 mM^-1 s^-1; mM^-1 s^-1 is the canonical s^-1 mM^-1 with the two factors written in the other order, so no conversion is applied and the value is 1.0 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table IV, compound row 2-Ketobutanoic acid (2), column A460I: Km = 18.3 mM; kcat = 18.8 s^-1; printed kcat/Km = 1.0 mM^-1 s^-1.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature E121A to reconstruct the assayed variant sequence.

column_label: PMID 17637344 Table 2. Summary of Kinetic Data for OXC Mutants; row E121A; columns KM (uM)=41 +/- 8, kcat (s^-1)=0.1 +/- 0.01, and printed kcat/KM=2.4 x 10^3 s^-1 M^-1; strict kcat/Km value is locked from the same-row kcat and KM central values for oxalyl-CoA.

normalized_value_unit_evidence: kcat normalized_value=0.1 normalized_unit=s^-1; km normalized_value=0.041 normalized_unit=mM; kcat_over_km normalized_value=2.4390243902439024 normalized_unit=s^-1*mM^-1.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature E121Q to reconstruct the assayed variant sequence.

column_label: PMID 17637344 Table 2. Summary of Kinetic Data for OXC Mutants; row E121Q; columns KM (uM)=18 +/- 4, kcat (s^-1)=3.3 +/- 0.3, and printed kcat/KM=1.8 x 10^5 s^-1 M^-1; strict kcat/Km value is locked from the same-row kcat and KM central values for oxalyl-CoA.

normalized_value_unit_evidence: kcat normalized_value=3.3 normalized_unit=s^-1; km normalized_value=0.018 normalized_unit=mM; kcat_over_km normalized_value=183.33333333333334 normalized_unit=s^-1*mM^-1.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature R555A to reconstruct the assayed variant sequence.

column_label: PMID 17637344 Table 2. Summary of Kinetic Data for OXC Mutants; row R555A; columns KM (uM)=66 +/- 8, kcat (s^-1)=85 +/- 4, and printed kcat/KM=1.3 x 10^6 s^-1 M^-1; strict kcat/Km value is locked from the same-row kcat and KM central values for oxalyl-CoA.

normalized_value_unit_evidence: kcat normalized_value=85.0 normalized_unit=s^-1; km normalized_value=0.066 normalized_unit=mM; kcat_over_km normalized_value=1287.8787878787878 normalized_unit=s^-1*mM^-1.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature S553A to reconstruct the assayed variant sequence.

column_label: PMID 17637344 Table 2. Summary of Kinetic Data for OXC Mutants; row S553A; columns KM (uM)=21 +/- 5, kcat (s^-1)=13 +/- 1.5, and printed kcat/KM=6.2 x 10^5 s^-1 M^-1; strict kcat/Km value is locked from the same-row kcat and KM central values for oxalyl-CoA.

normalized_value_unit_evidence: kcat normalized_value=13.0 normalized_unit=s^-1; km normalized_value=0.021 normalized_unit=mM; kcat_over_km normalized_value=619.047619047619 normalized_unit=s^-1*mM^-1.


column_label: PMID 17637344 Table 2. Summary of Kinetic Data for OXC Mutants; row OXC; columns KM (uM)=23 +/- 3.5, kcat (s^-1)=88 +/- 4, and printed kcat/KM=3.8 x 10^6 s^-1 M^-1; strict kcat/Km value is locked from the same-row kcat and KM central values for oxalyl-CoA.

normalized_value_unit_evidence: kcat normalized_value=88.0 normalized_unit=s^-1; km normalized_value=0.023 normalized_unit=mM; kcat_over_km normalized_value=3826.086956521739 normalized_unit=s^-1*mM^-1.

raw_value_unit_evidence: Table 2 row OXC: KM 23 +/- 3.5 uM; kcat 88 +/- 4 s^-1; printed kcat/KM 3.8 x 10^6 s^-1 M^-1.

row_label: OXC


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature Y120A to reconstruct the assayed variant sequence.

column_label: PMID 17637344 Table 2. Summary of Kinetic Data for OXC Mutants; row Y120A; columns KM (uM)=60 +/- 14, kcat (s^-1)=0.26 +/- 0.03, and printed kcat/KM=4.1 x 10^3 s^-1 M^-1; strict kcat/Km value is locked from the same-row kcat and KM central values for oxalyl-CoA.

normalized_value_unit_evidence: kcat normalized_value=0.26 normalized_unit=s^-1; km normalized_value=0.06 normalized_unit=mM; kcat_over_km normalized_value=4.333333333333334 normalized_unit=s^-1*mM^-1.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature Y120F to reconstruct the assayed variant sequence.

column_label: PMID 17637344 Table 2. Summary of Kinetic Data for OXC Mutants; row Y120F; columns KM (uM)=43 +/- 9, kcat (s^-1)=7.2 +/- 0.6, and printed kcat/KM=1.7 x 10^5 s^-1 M^-1; strict kcat/Km value is locked from the same-row kcat and KM central values for oxalyl-CoA.

normalized_value_unit_evidence: kcat normalized_value=7.2 normalized_unit=s^-1; km normalized_value=0.043 normalized_unit=mM; kcat_over_km normalized_value=167.4418604651163 normalized_unit=s^-1*mM^-1.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature Y483A with inferred residue-numbering offset -15 to reconstruct the assayed variant sequence.

column_label: PMID 17637344 Table 2. Summary of Kinetic Data for OXC Mutants; row Y483A; columns KM (uM)=24 +/- 7, kcat (s^-1)=1.4 +/- 0.1, and printed kcat/KM=5.6 x 10^4 s^-1 M^-1; strict kcat/Km value is locked from the same-row kcat and KM central values for oxalyl-CoA.

normalized_value_unit_evidence: kcat normalized_value=1.4 normalized_unit=s^-1; km normalized_value=0.024 normalized_unit=mM; kcat_over_km normalized_value=58.33333333333333 normalized_unit=s^-1*mM^-1.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature Y483F with inferred residue-numbering offset -15 to reconstruct the assayed variant sequence.

column_label: PMID 17637344 Table 2. Summary of Kinetic Data for OXC Mutants; row Y483F; columns KM (uM)=40 +/- 11, kcat (s^-1)=1.7 +/- 0.2, and printed kcat/KM=4.1 x 10^4 s^-1 M^-1; strict kcat/Km value is locked from the same-row kcat and KM central values for oxalyl-CoA.

normalized_value_unit_evidence: kcat normalized_value=1.7 normalized_unit=s^-1; km normalized_value=0.04 normalized_unit=mM; kcat_over_km normalized_value=42.5 normalized_unit=s^-1*mM^-1.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature T377L/A460Y to reconstruct the assayed variant sequence.


substrate_name: benzylformate

sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P20906 and applied mutation signature A460Y to reconstruct the assayed variant sequence.

assay_conditions_summary: pH 6; 303.15 K; cofactor NADH

column_label: Table 3 (Steady-State Kinetic Characterization of BFDC Variants Showing Improved PDC Activity); the five substrate column heads are 'BF', '2KH', '2KP', '2KB' and 'Pyr' and the three parameter rows of each BFDC variant block are 'kcat (s-1)', 'Km (mM)' and 'kcat/Km (mM-1 s-1)'. For BFDC variant 'A460Y' in column 'BF': kcat = 1.7; Km = 0.04; kcat/Km = 43. The second number printed in parentheses inside each kcat/Km cell is the -fold increase over wt stated in footnote a, not a kinetic value.

normalized_value_unit_evidence: kcat: printed Table 3 cell 1.7 s-1; the paper already prints this metric in s^(-1), so no unit conversion applies and the normalized value is 1.7 s^(-1). Km: printed Table 3 cell 0.04 mM; the paper already prints this metric in mM, so no unit conversion applies and the normalized value is 0.04 mM. kcat/Km: printed Table 3 cell 43 mM-1 s-1; mM^-1 s^-1 is the canonical efficiency unit, so no unit conversion applies and the normalized value is 43.0 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table 3, BFDC variant row 'A460Y', substrate column 'BF': kcat = 1.7 s-1; Km = 0.04 mM; printed kcat/Km = 43 mM-1 s-1.

table_label: Table 3: Steady-State Kinetic Characterization of BFDC Variants Showing Improved PDC Activity (Biochemistry 2009, 48, 8387-8395)

substrate: benzylformate


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P20906 and applied mutation signature T377L to reconstruct the assayed variant sequence.

column_label: Table 3 (Steady-State Kinetic Characterization of BFDC Variants Showing Improved PDC Activity); the five substrate column heads are 'BF', '2KH', '2KP', '2KB' and 'Pyr' and the three parameter rows of each BFDC variant block are 'kcat (s-1)', 'Km (mM)' and 'kcat/Km (mM-1 s-1)'. For BFDC variant 'T377L' in column 'BF': kcat = 110; Km = 0.45; kcat/Km = 244. The second number printed in parentheses inside each kcat/Km cell is the -fold increase over wt stated in footnote a, not a kinetic value.

normalized_value_unit_evidence: kcat: printed Table 3 cell 110 s-1; the paper already prints this metric in s^(-1), so no unit conversion applies and the normalized value is 110.0 s^(-1). Km: printed Table 3 cell 0.45 mM; the paper already prints this metric in mM, so no unit conversion applies and the normalized value is 0.45 mM. kcat/Km: printed Table 3 cell 244 mM-1 s-1; mM^-1 s^-1 is the canonical efficiency unit, so no unit conversion applies and the normalized value is 244.0 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table 3, BFDC variant row 'T377L', substrate column 'BF': kcat = 110 s-1; Km = 0.45 mM; printed kcat/Km = 244 mM-1 s-1.


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P20906 and applied mutation signature T377L/A460Y to reconstruct the assayed variant sequence.

column_label: Table 3 (Steady-State Kinetic Characterization of BFDC Variants Showing Improved PDC Activity); the five substrate column heads are 'BF', '2KH', '2KP', '2KB' and 'Pyr' and the three parameter rows of each BFDC variant block are 'kcat (s-1)', 'Km (mM)' and 'kcat/Km (mM-1 s-1)'. For BFDC variant 'T377L-A460Y' in column 'BF': kcat = 25; Km = 1.5; kcat/Km = 16. The second number printed in parentheses inside each kcat/Km cell is the -fold increase over wt stated in footnote a, not a kinetic value.

normalized_value_unit_evidence: kcat: printed Table 3 cell 25 s-1; the paper already prints this metric in s^(-1), so no unit conversion applies and the normalized value is 25.0 s^(-1). Km: printed Table 3 cell 1.5 mM; the paper already prints this metric in mM, so no unit conversion applies and the normalized value is 1.5 mM. kcat/Km: printed Table 3 cell 16 mM-1 s-1; mM^-1 s^-1 is the canonical efficiency unit, so no unit conversion applies and the normalized value is 16.0 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table 3, BFDC variant row 'T377L-A460Y', substrate column 'BF': kcat = 25 s-1; Km = 1.5 mM; printed kcat/Km = 16 mM-1 s-1.


column_label: Table 3 (Steady-State Kinetic Characterization of BFDC Variants Showing Improved PDC Activity); the five substrate column heads are 'BF', '2KH', '2KP', '2KB' and 'Pyr' and the three parameter rows of each BFDC variant block are 'kcat (s-1)', 'Km (mM)' and 'kcat/Km (mM-1 s-1)'. For BFDC variant 'wt' in column 'BF': kcat = 320; Km = 0.27; kcat/Km = 1180. The second number printed in parentheses inside each kcat/Km cell is the -fold increase over wt stated in footnote a, not a kinetic value.

normalized_value_unit_evidence: kcat: printed Table 3 cell 320 s-1; the paper already prints this metric in s^(-1), so no unit conversion applies and the normalized value is 320.0 s^(-1). Km: printed Table 3 cell 0.27 mM; the paper already prints this metric in mM, so no unit conversion applies and the normalized value is 0.27 mM. kcat/Km: printed Table 3 cell 1180 mM-1 s-1; mM^-1 s^-1 is the canonical efficiency unit, so no unit conversion applies and the normalized value is 1180.0 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table 3, BFDC variant row 'wt', substrate column 'BF': kcat = 320 s-1; Km = 0.27 mM; printed kcat/Km = 1180 mM-1 s-1.


column_label: Table 3 (Steady-State Kinetic Characterization of BFDC Variants Showing Improved PDC Activity); the five substrate column heads are 'BF', '2KH', '2KP', '2KB' and 'Pyr' and the three parameter rows of each BFDC variant block are 'kcat (s-1)', 'Km (mM)' and 'kcat/Km (mM-1 s-1)'. For BFDC variant 'A460Y' in column 'Pyr': kcat = 1.4; Km = 21; kcat/Km = 0.065. The second number printed in parentheses inside each kcat/Km cell is the -fold increase over wt stated in footnote a, not a kinetic value.

normalized_value_unit_evidence: kcat: printed Table 3 cell 1.4 s-1; the paper already prints this metric in s^(-1), so no unit conversion applies and the normalized value is 1.4 s^(-1). Km: printed Table 3 cell 21 mM; the paper already prints this metric in mM, so no unit conversion applies and the normalized value is 21.0 mM. kcat/Km: printed Table 3 cell 0.065 mM-1 s-1; mM^-1 s^-1 is the canonical efficiency unit, so no unit conversion applies and the normalized value is 0.065 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table 3, BFDC variant row 'A460Y', substrate column 'Pyr': kcat = 1.4 s-1; Km = 21 mM; printed kcat/Km = 0.065 mM-1 s-1.


column_label: Table 3 (Steady-State Kinetic Characterization of BFDC Variants Showing Improved PDC Activity); the five substrate column heads are 'BF', '2KH', '2KP', '2KB' and 'Pyr' and the three parameter rows of each BFDC variant block are 'kcat (s-1)', 'Km (mM)' and 'kcat/Km (mM-1 s-1)'. For BFDC variant 'T377L' in column 'Pyr': kcat = 2.0; Km = 4.8; kcat/Km = 0.42. The second number printed in parentheses inside each kcat/Km cell is the -fold increase over wt stated in footnote a, not a kinetic value.

normalized_value_unit_evidence: kcat: printed Table 3 cell 2.0 s-1; the paper already prints this metric in s^(-1), so no unit conversion applies and the normalized value is 2.0 s^(-1). Km: printed Table 3 cell 4.8 mM; the paper already prints this metric in mM, so no unit conversion applies and the normalized value is 4.8 mM. kcat/Km: printed Table 3 cell 0.42 mM-1 s-1; mM^-1 s^-1 is the canonical efficiency unit, so no unit conversion applies and the normalized value is 0.42 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table 3, BFDC variant row 'T377L', substrate column 'Pyr': kcat = 2.0 s-1; Km = 4.8 mM; printed kcat/Km = 0.42 mM-1 s-1.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature E280Q to reconstruct the assayed variant sequence.

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

column_label: Table 1 row E280Q columns Km (mM), kcat (s^-1), and kcat/Km (M^-1 s^-1); Mn column preserved as condition/modifier evidence

table_label: Table 1. Mn Incorporation and Steady-State Kinetic Parameters for Metal-Binding OxDC Mutants


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature E280A to reconstruct the assayed variant sequence.

column_label: Table 1 row E280A columns Km (mM), kcat (s^-1), and kcat/Km (M^-1 s^-1); Mn column preserved as condition/modifier evidence


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature E280D to reconstruct the assayed variant sequence.

column_label: Table 1 row E280D columns Km (mM), kcat (s^-1), and kcat/Km (M^-1 s^-1); Mn column preserved as condition/modifier evidence


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature E101A to reconstruct the assayed variant sequence.

column_label: Table 1 row E101A columns Km (mM), kcat (s^-1), and kcat/Km (M^-1 s^-1); Mn column preserved as condition/modifier evidence


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature E101D to reconstruct the assayed variant sequence.

column_label: Table 1 row E101D columns Km (mM), kcat (s^-1), and kcat/Km (M^-1 s^-1); Mn column preserved as condition/modifier evidence


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature E101Q to reconstruct the assayed variant sequence.

column_label: Table 1 row E101Q columns Km (mM), kcat (s^-1), and kcat/Km (M^-1 s^-1); Mn column preserved as condition/modifier evidence


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature E101Q/E280Q to reconstruct the assayed variant sequence.

column_label: Table 1 row E101Q/E280Q columns Km (mM), kcat (s^-1), and kcat/Km (M^-1 s^-1); footnote c confirms both substitutions; Mn column preserved

raw_value_unit_evidence: Km 2.9 +/- 0.3 mM; kcat 0.012 +/- 0.0003 s^-1; kcat/Km 4 M^-1 s^-1; Mn 0.07 per monomer; footnote c identifies both glutamine substitutions


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

column_label: Table 1 row WT OxDC columns Km (mM), kcat (s^-1), and kcat/Km (M^-1 s^-1); Mn column preserved as condition/modifier evidence

row_label: WT OxDC


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature H281A with inferred residue-numbering offset -14 to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature H70A to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature S26A to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature E162D to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature E162Q to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature R92K with inferred residue-numbering offset -7 to reconstruct the assayed variant sequence.


organism: Saccharomyces cerevisiae

proof_lines:
yeast glycolysis
isoenzymes
pyruvate decarboxylase


assay_conditions_summary: pH 6.5; 303.15 K; buffer a standardised reaction; cofactor NADPH

column_label: Table label: Table 2, "Enzyme kinetics parameters determined in this project and contrasted with those of Ref. [23]". Reaction: PDC. Isoenzyme: Pdc6p. Rows read: PDC | Pdc6p | kcat -> Value cell 9.21, Unit cell s−1; PDC | Pdc6p | Kpyr -> Value cell 2.92, Unit cell mM. kcat/Km: no printed cell (Table 2 has no kcat/Km column).

normalized_value_unit_evidence: kcat 9.21 s−1 = 9.21 s^(-1) (printed unit s−1 is the export unit s^(-1), no conversion); decimal-equal to the catalog kcat 9.21; Km (Kpyr) 2.92 mM = 2.92 mM (already the export unit, no conversion); decimal-equal to the catalog km 2.92. In the on-disk transcription the printed superscript minus renders as the flattened `s−1` (U+2212) and empty SEM/Ref cells render as empty ` | ` fields.

raw_value_unit_evidence: Table 2, "Enzyme kinetics parameters determined in this project and contrasted with those of Ref. [23]" | header row: Reaction | Isoenzyme | Parameter | Value | SEM (%) | Ref. [23] | Unit | kcat evidence: PDC | Pdc6p | kcat | 9.21 |  |  | s−1 | Km evidence: PDC | Pdc6p | Kpyr | 2.92 |  | 4.33 | mM | cells read: kcat = 9.21 s−1 (Value column); Kpyr = 2.92 mM

row_label: PDC | Pdc6p


organism: Acetobacter pasteurianus

proof_lines:
Zymobacter palmae
pyruvate decarboxylase
three other bacteria


proof_lines:
pyruvate
n-butanol
neutral pH


organism: Hanseniaspora uvarum

column_label: Abstract states the Km for pyruvate was 0.75 mM.

raw_value_unit_evidence: Km raw_value=0.75 raw_unit=mM

row_label: Hanseniaspora uvarum pyruvate decarboxylase with pyruvate

table_label: PubMed abstract PMID 7725793


organism: Zymobacter palmae


column_label: PMID 15930043, Table II. Michaelis-Menten constants for decarboxylase activity of PDC variants; row Compound Pyruvate (1); PDC variant WT; columns kcat (s^-1)=486, Km (mM)=1.1, kcat/Km (mM^-1 s^-1)=442.

normalized_value_unit_evidence: kcat normalized_value=486.0 normalized_unit=s^-1; Km normalized_value=1.1 normalized_unit=mM; kcat/Km normalized_value=442.0 normalized_unit=s^-1*mM^-1

raw_value_unit_evidence: kcat raw_value=486 raw_unit=s^-1; Km raw_value=1.1 raw_unit=mM; kcat/Km raw_value=442 raw_unit=s^-1*mM^-1; source_context=PDC from Zymomonas mobilis; wild-type variant column in Table II.

row_label: Compound Pyruvate (1); PDC variant WT


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature W132F to reconstruct the assayed variant sequence.


proof_lines:
oxalyl-CoA decarboxylase
oxalyl coenzyme A
Escherichia coli


organism: Candida albicans

proof_lines:
Candida albicans
pyruvate decarboxylase
pyruvate


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

assay_conditions_summary: pH 6; 303.15 K; buffer 100 mM potassium phosphate

proof_lines: mutant enzyme T377L/A460Y, in 100 mM potassium phosphate buffer (pH 6.0), at 30°C


proof_lines: mutant enzyme T377L, in 100 mM potassium phosphate buffer (pH 6.0), at 30°C


proof_lines: mutant enzyme T377L/A460Y, at pH 6.0 and 30°C


proof_lines: mutant enzyme A460Y, in 100 mM potassium phosphate buffer (pH 6.0), at 30°C


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

proof_lines: wild type enzyme, in 100 mM potassium phosphate buffer (pH 6.0), at 30°C


proof_lines: pH 6.0, 30°C, wild-type enzyme and mutant enzyme A460I


assay_conditions_summary: cofactor NADPH

column_label: Table 2; reaction PDC; isoenzyme Pdc6p; parameter kcat value 9.21 s^-1; parameter Kpyr value 2.92 mM; kcat/Km computed from those explicit cells

normalized_value_unit_evidence: kcat normalized_value=9.21 normalized_unit=s^-1; Km normalized_value=2.92 normalized_unit=mM; kcat/Km normalized_value=3.1541095890410964 normalized_unit=s^-1*mM^-1

raw_value_unit_evidence: kcat raw_value=9.21 raw_unit=s^-1; Km raw_value=2.92 raw_unit=mM; kcat/Km computed from explicit Table 2 cells 9.21/2.92 raw_unit=s^-1*mM^-1

row_label: PDC / Pdc6p / Kpyr

table_label: Table 2. Enzyme kinetics parameters determined in this project and contrasted with those of [23].


substrate_name: 2-keto-4-methylhexanoic acid

proof_lines:
wild type, pH 6.5, 30°C
and above, wild type, pH 6.5, 30°C

substrate: 2-keto-4-methylhexanoic acid


substrate_name: 2-ketohexanoic acid

substrate: 2-ketohexanoic acid


substrate_name: benzoylformate

substrate: benzoylformate


substrate_name: 2-ketobutanoic acid

substrate: 2-ketobutanoic acid


substrate_name: 2-ketopentanoic acid

substrate: 2-ketopentanoic acid


proof_lines: mutant enzyme H281T, in 100 mM potassium phosphate buffer (pH 6.0), at 30°C


proof_lines: mutant enzyme H70F, in 100 mM potassium phosphate buffer (pH 6.0), at 30°C

proof_lines: pH and temperature not specified in the publication, mutant H70F


proof_lines: mutant enzyme H70S, in 100 mM potassium phosphate buffer (pH 6.0), at 30°C


proof_lines: mutant enzyme H281Y, in 100 mM potassium phosphate buffer (pH 6.0), at 30°C

proof_lines: pH and temperature not specified in the publication, mutant H281Y


proof_lines: mutant enzyme H281Q, in 100 mM potassium phosphate buffer (pH 6.0), at 30°C


proof_lines: mutant enzyme H70L, in 100 mM potassium phosphate buffer (pH 6.0), at 30°C

proof_lines: pH and temperature not specified in the publication, mutant H70L


proof_lines: mutant enzyme H281W, in 100 mM potassium phosphate buffer (pH 6.0), at 30°C


proof_lines: mutant enzyme H281N in 100 mM potassium phosphate buffer (pH 6.0), at 30°C


proof_lines: mutant enzyme S26M, in 100 mM potassium phosphate buffer (pH 6.0), at 30°C

proof_lines: pH and temperature not specified in the publication, mutant S26M


proof_lines: mutant enzyme H70T, in 100 mM potassium phosphate buffer (pH 6.0), at 30°C


proof_lines: mutant enzyme H281F, in 100 mM potassium phosphate buffer (pH 6.0), at 30°C

proof_lines: pH and temperature not specified in the publication, mutant H281F


proof_lines: mutant enzyme S26T, in 100 mM potassium phosphate buffer (pH 6.0), at 30°C


proof_lines: mutant enzyme S26L, in 100 mM potassium phosphate buffer (pH 6.0), at 30°C

proof_lines: pH and temperature not specified in the publication, mutant S26L


assay_conditions_summary: pH 7; 303.15 K; buffer 50 mM potassium phosphate

proof_lines: mutant enzyme L476G, in 50 mM potassium phosphate buffer pH 7.0, 0.5 mM thiamine diphosphate, 2.5 mM MgSO4, at 30°C


proof_lines: mutant enzyme S181T/L476P, in 50 mM potassium phosphate buffer pH 7.0, 0.5 mM thiamine diphosphate, 2.5 mM MgSO4, at 30°C


proof_lines: mutant enzyme L476H, in 50 mM potassium phosphate buffer pH 7.0, 0.5 mM thiamine diphosphate, 2.5 mM MgSO4, at 30°C


proof_lines: mutant enzyme L476T, in 50 mM potassium phosphate buffer pH 7.0, 0.5 mM thiamine diphosphate, 2.5 mM MgSO4, at 30°C


proof_lines: mutant enzyme L476P, in 50 mM potassium phosphate buffer pH 7.0, 0.5 mM thiamine diphosphate, 2.5 mM MgSO4, at 30°C


proof_lines: mutant enzyme L476Q/S525G, in 50 mM potassium phosphate buffer pH 7.0, 0.5 mM thiamine diphosphate, 2.5 mM MgSO4, at 30°C


proof_lines: mutant enzyme L476M, in 50 mM potassium phosphate buffer pH 7.0, 0.5 mM thiamine diphosphate, 2.5 mM MgSO4, at 30°C


proof_lines: mutant enzyme L476S, in 50 mM potassium phosphate buffer pH 7.0, 0.5 mM thiamine diphosphate, 2.5 mM MgSO4, at 30°C


proof_lines: mutant enzyme L476A, in 50 mM potassium phosphate buffer pH 7.0, 0.5 mM thiamine diphosphate, 2.5 mM MgSO4, at 30°C


proof_lines: mutant enzyme S181T, in 50 mM potassium phosphate buffer pH 7.0, 0.5 mM thiamine diphosphate, 2.5 mM MgSO4, at 30°C


proof_lines: mutant enzyme L476C, in 50 mM potassium phosphate buffer pH 7.0, 0.5 mM thiamine diphosphate, 2.5 mM MgSO4, at 30°C


proof_lines: mutant enzyme L476K, in 50 mM potassium phosphate buffer pH 7.0, 0.5 mM thiamine diphosphate, 2.5 mM MgSO4, at 30°C


proof_lines: mutant enzyme T377L/A460Y, at pH 6.0 and 30°C


substrate_name: phenylpyruvate

substrate: phenylpyruvate


substrate_name: 2-oxo-4-methylhexanoic acid

substrate: 2-oxo-4-methylhexanoic acid


substrate_name: 2-oxo-4-methylpentanoic acid

proof_lines:
pH 6.0, 30°C, wild-type enzyme
wild type enzyme, at pH 6.0 and 30°C

substrate: 2-oxo-4-methylpentanoic acid


substrate_name: 2-oxobutanoic acid

substrate: 2-oxobutanoic acid


proof_lines:
pH 6.0, 30°C, mutant enzyme A460I/F464I
mutant enzyme A460I/F464I


substrate_name: 2-oxohexanoic acid

substrate: 2-oxohexanoic acid


substrate_name: 2-oxopentanoic acid

substrate: 2-oxopentanoic acid


proof_lines:
pH 6.0, 30°C, mutant enzyme A460I
mutant enzyme A460I


proof_lines:
pH 6.0, 30°C, mutant enzyme F464I
mutant enzyme F464I


substrate_name: oxalate

substrate: oxalate


mutation_type: deletion

proof_lines: pH 4.0, 26°C, recombinant deletion mutant DELTA163-163


proof_lines: mutant enzyme E101Q/E280Q, in 50 mM NaOAc (pH 4.2), 0.2% (v/v) Triton X-100, 0.5 mM o-phenylenediamine, at 22°C


proof_lines: mutant enzyme E280A , in 50 mM NaOAc (pH 4.2), 0.2% (v/v) Triton X-100, 0.5 mM o-phenylenediamine, at 22°C


proof_lines: mutant enzyme E101A , in 50 mM NaOAc (pH 4.2), 0.2% (v/v) Triton X-100, 0.5 mM o-phenylenediamine, at 22°C


proof_lines: mutant enzyme E280D, in 50 mM NaOAc (pH 4.2), 0.2% (v/v) Triton X-100, 0.5 mM o-phenylenediamine, at 22°C


proof_lines: mutant enzyme E101D, in 50 mM NaOAc (pH 4.2), 0.2% (v/v) Triton X-100, 0.5 mM o-phenylenediamine, at 22°C


proof_lines: mutant enzyme E101Q, in 50 mM NaOAc (pH 4.2), 0.2% (v/v) Triton X-100, 0.5 mM o-phenylenediamine, at 22°C


proof_lines: mutant enzyme E280Q, in 50 mM NaOAc (pH 4.2), 0.2% (v/v) Triton X-100, 0.5 mM o-phenylenediamine, at 22°C


assay_conditions_summary: pH 7; 303.15 K; buffer 100 mM potassium phosphate

proof_lines: mutant enzyme H70A, in 100 mM potassium phosphate buffer (pH 6.0), at 30°C

proof_lines: pH and temperature not specified in the publication, mutant H70A


proof_lines: mutant enzyme H281A, in 100 mM potassium phosphate buffer (pH 6.0), at 30°C

proof_lines: pH and temperature not specified in the publication, mutant H281A


proof_lines: mutant enzyme S26A, in 100 mM potassium phosphate buffer (pH 6.0), at 30°C

proof_lines: pH and temperature not specified in the publication, mutant S26A


assay_conditions_summary: pH 7; 303.15 K; buffer pH 7

proof_lines: wild type enzyme, in 100 mM potassium phosphate buffer (pH 6.0), at 30°C

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


substrate_name: Unknown

substrate: Unknown


proof_lines: below, recombinant mutant W96F/W274F, pH and temperature not specified in the publication


proof_lines: recombinant mutant W96Y/W274Y, pH and temperature not specified in the publication


proof_lines: recombinant mutant W96F, pH and temperature not specified in the publication


proof_lines: recombinant mutant W274F, pH and temperature not specified in the publication


proof_lines: recombinant mutant W96Y, pH and temperature not specified in the publication


proof_lines: recombinant mutant W274Y, pH and temperature not specified in the publication


proof_lines: mutant enzyme D440E and mutant enzyme N467D


assay_conditions_summary: pH 6.5; buffer potassium phosphate

proof_lines: mutant enzyme L461V, in potassium phosphate buffer (pH 6.5, 50 mM)


proof_lines: mutant enzyme L461A, in potassium phosphate buffer (pH 6.5, 50 mM)


proof_lines: mutant enzyme P24A, in potassium phosphate buffer (pH 6.5, 50 mM)


proof_lines: mutant enzyme L461G, in potassium phosphate buffer (pH 6.5, 50 mM)


proof_lines: mutant enzyme A460G, in potassium phosphate buffer (pH 6.5, 50 mM)


organism: Methylorubrum extorquens

substrate_name: oxalyl-CoA

assay_conditions_summary: cofactor CoA

proof_lines: recombinant mutant Y497A/S568A, pH and temperature not specified in the publication, oxalyl-CoA decarboxylation

substrate: oxalyl-CoA


proof_lines: recombinant mutant Y497A, pH and temperature not specified in the publication, oxalyl-CoA decarboxylation


proof_lines: recombinant mutant S568A, pH and temperature not specified in the publication, oxalyl-CoA decarboxylation


proof_lines: recombinant wild-type enzyme, pH and temperature not specified in the publication, oxalyl-CoA decarboxylation

proof_lines: recombinant wild-type enzyme, pH and temperature not specified in the publication oxalyl-CoA decarboxylation


proof_lines:
pH 4, 26°C, E333A mutant OxdC
pH 4.0, 26°C, recombinant mutant E333A


proof_lines:
pH 4, 26°C, R270A mutant OxdC
pH 4.0, 26°C, recombinant mutant R270A


proof_lines:
pH 4.2, 23C, mutant E162Q
pH 4.0, 26°C, recombinant mutant E162Q
pH 4, 26°C, E162Q mutant OxdC


proof_lines:
pH 4.2, 23C, mutant R92K
pH 4.0, 26°C, recombinant mutant R92K
pH 4, 26°C, R92K mutant OxdC


proof_lines:
pH 4.2, 23C, mutant E162D
pH 4.0, 26°C, recombinant mutant E162D


proof_lines: pH 4.0, recombinant mutant E162A/N163S/S164N


proof_lines: pH 4.0, recombinant mutant S161D/N163S/S164N


substrate_name: pyruvate

assay_conditions_summary: pH 6; 303.15 K; buffer 50 mM MES

proof_lines: wild type enzyme, at 30°C in 50 mM MES buffer (pH 6.0) containing 1 mM MgSO4 and 0.1 mM thiamine diphosphate

substrate: pyruvate


substrate_name: benzaldehyde

assay_conditions_summary: pH 7

substrate: benzaldehyde


substrate_name: acetaldehyde

substrate: acetaldehyde


substrate_name: p-nitro-benzoylformate

proof_lines: prolonged incubation of BFD with benzoylphosphonate results in permanent inactivation of the enzyme

substrate: p-nitro-benzoylformate


assay_conditions_summary: pH 6.5; 303.15 K; buffer 50 mM potassium phosphate

proof_lines: at 30°C, in 50 mM potassium phosphate buffer, pH 6.5

proof_lines: in 50 mM potassium phosphate buffer, pH 6.5, at 30°C


assay_conditions_summary: pH 7.5; 293.15 K; buffer 50 mM phosphate

proof_lines: free mutant enzyme A460I/F464I, in 50 mM phosphate buffer at pH 7.5 and 20°C

proof_lines: immobilized mutant enzyme A460I/F464I, in 50 mM phosphate buffer at pH 7.5 and 20°C


proof_lines: mutant enzyme E473D, at 30°C in 50 mM MES buffer (pH 6.0) containing 1 mM MgSO4 and 0.1 mM thiamine diphosphate


proof_lines: mutant enzyme E473Q, at 30°C in 50 mM MES buffer (pH 6.0) containing 1 mM MgSO4 and 0.1 mM thiamine diphosphate


assay_conditions_summary: pH 6.5; buffer 50 mM potassium phosphate

proof_lines: pH and temperature not specified in the publication

proof_lines: in 50 mM potassium phosphate buffer pH 6.5, 2.5 mM MgSO4, 0.1 mM thiamine diphosphate


substrate_name: oxalic acid

proof_lines:
non-His-tagged recombinant enzyme
His-tagged recombinant enzyme

substrate: oxalic acid


proof_lines: apparent value, pH and temperature not specified in the publication


proof_lines: soluble enzyme, citrate buffer (0.05 M, pH 4.0), at 37°C


enzyme_display_name: acetolactate decarboxylase

enzyme: acetolactate decarboxylase


proof_lines: pH 7.2, 25°C, recombinant wild-type enzyme, decarboxylase activity

proof_lines: pH 4.2, 25°C, recombinant wild-type enzyme, decarboxylase activity

proof_lines: wild type enzyme, in 50 mM NaOAc (pH 4.2), 0.2% (v/v) Triton X-100, 0.5 mM o-phenylenediamine, at 22°C


organism: Enterobacter cloacae


organism: Gluconobacter oxydans

proof_lines:
pH 5.0, 55°C, recombinant enzyme
pH 6.5, 55°C, recombinant enzyme
pH 7.0, 55°C, recombinant enzyme


organism: Klebsiella aerogenes


organism: Lactococcus lactis

proof_lines:
in presence of Leu
in absence of Leu


substrate_name: methyl benzoylphosphonate

substrate: methyl benzoylphosphonate


substrate_name: benzoylformate

proof_lines: mutant enzyme L476Q, in 50 mM potassium phosphate buffer pH 7.0, 0.5 mM thiamine diphosphate, 2.5 mM MgSO4, at 30°C

substrate: benzoylformate


substrate_name: (p-methoxybenzoyl)formate

substrate: (p-methoxybenzoyl)formate


organism: Staphylococcus aureus


organism: Triticum aestivum

substrate_name: Pyruvate

substrate: Pyruvate


organism: Zea mays


organism: Zymomonas mobilis

assay_conditions_summary: pH 6


organism: Oryza sativa


organism: Pseudomonas putida


enzyme_display_name: (S)-2-haloacid dehalogenase

organism: Pseudoalteromonas sp.

substrate_name: monobromoacetic acid

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

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

enzyme: (S)-2-haloacid dehalogenase

substrate: monobromoacetic acid


enzyme_display_name: UniProt Q51645

organism: Burkholderia cepacia

substrate_name: monobromoacetate

enzyme: UniProt Q51645

substrate: monobromoacetate


enzyme_display_name: haloacetate dehalogenase

organism: Delftia acidovorans

substrate_name: difluoroacetate

proof_lines:
at pH 6.0 and 37°C
at pH 7.0 and 37°C

enzyme: haloacetate dehalogenase

substrate: difluoroacetate


substrate_name: fluoroacetate

proof_lines:
at pH 7.0 and 37°C
at pH 6.0 and 37°C

substrate: fluoroacetate


organism: Cupriavidus necator

substrate_name: 2-hydroxymuconic semialdehyde

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

proof_lines:
isoform HODHI, at pH 7.6 and 23°C
isoform HODHII, at pH 7.6 and 23°C

substrate: 2-hydroxymuconic semialdehyde


organism: Dechloromonas aromatica (nom. nud.)


organism: Rattus norvegicus


organism: Ancylobacter aquaticus

substrate_name: Monochloroacetate

substrate: Monochloroacetate


organism: Azotobacter sp.


organism: Mus musculus

substrate_name: monofluoroacetate

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

substrate: monofluoroacetate


organism: Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)

proof_lines: kcat is 6.7 min(-1) with fluoroacetate as substrate. kcat is 1.38 min(-1) with chloroacetate as substrate.


substrate_name: chloroacetate

substrate: chloroacetate


enzyme_display_name: 2,4-diacetylphloroglucinol hydrolase

organism: Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5)

substrate_name: DAPG

enzyme: 2,4-diacetylphloroglucinol hydrolase

substrate: DAPG


organism: Rhodococcus jostii RHA1

sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature Y61F to reconstruct the assayed variant sequence.


organism: Pseudomonas protegens (strain DSM 19095 / LMG 27888 / CFBP 6595 / CHA0)


organism: Pseudomonas sp.

proof_lines:
recombinant enzyme, pH 7.0, 25°C
kcat is 5.8 sec(-1).

source_databases_merged: brenda uniprot


organism: Sphingomonas sp. SKA58

substrate_name: Acetylpyruvate

proof_lines: kcat is 14.2 min(-1) with acetylpyruvate as substrate. kcat is 34.8 min(-1) with trimethylacetopyruvate as substrate.

substrate: Acetylpyruvate


organism: Rhodobacteraceae bacterium UDC319

substrate_name: 2-bromoacetic acid

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

substrate: 2-bromoacetic acid


organism: Sulfurisphaera tokodaii

substrate_name: (S)-2-chloropropionic acid

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

assay_conditions_summary: pH 9

proof_lines:
pH 9.0, 50°C, soluble enzyme
pH 9.0, 22°C, immobilized enzyme
pH 9.0, 37°C, immobilized enzyme

substrate: (S)-2-chloropropionic acid


organism: Pseudomonas sp. (strain YL)

substrate_name: (2S)-2-chloropropanoic acid

proof_lines: kcat is 47 sec(-1) for (2S)-2-chloropropanoic acid as substrate.

substrate: (2S)-2-chloropropanoic acid


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


proof_lines:
pH 9.5, 70°C
Raw SKiD Env: Temp=70°C, pH=9.5

source_databases_merged: brenda skid


organism: Pseudomonas fluorescens


substrate_name: Unknown

substrate: Unknown


substrate_name: trimethylacetopyruvate

substrate: trimethylacetopyruvate


organism: Burkholderia sp


organism: Polaromonas sp. JS666


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature H214Q with inferred residue-numbering offset -10 to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature N132A to reconstruct the assayed variant sequence.


column_label: Table 2 'Table 2: Kinetic parameters of PhlG wild type and active-site mutants'; row Wild type; Km, kcat, and kcat/Km cells.

normalized_value_unit_evidence: Table 2 row Wild type, normalized where unambiguous: kcat 4.7 s^-1; Km 0.272 mM; kcat/Km 17 s^-1 mM^-1.

raw_value_unit_evidence: Table 2 row Wild type: Km 272 ± 42 uM; kcat 4.7 ± 0.1 s^-1; kcat/Km 17000.

row_label: Wild type


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature Y121A with inferred residue-numbering offset +6 to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature Y229A 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:
Burkholderia sp
fluoroacetate
fluoroacetate dehalogenase


organism: Rhodopseudomonas palustris

substrate_name: 2-fluoropropionic acid

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

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

substrate: 2-fluoropropionic acid


column_label: Table 2 reports ST2570 defluorination kcat 7.0 +/- 0.4 min^-1, KM 2.4 +/- 0.7 mM, Kcat/KM 49 +/- 15 s^-1 M^-1; paper-unit values convert to slightly different normalized values than current export

normalized_value_unit_evidence: KM normalized_value=2.4 normalized_unit=mM; kcat normalized_value=0.1166666667 normalized_unit=s^-1; kcat_over_km normalized_value=0.049 normalized_unit=s^-1*mM^-1; current_export_kcat=0.12 s^-1; current_export_kcat_over_km=0.05 s^-1*mM^-1

raw_value_unit_evidence: KM raw_value=2.4 +/- 0.7 raw_unit=mM; kcat raw_value=7.0 +/- 0.4 raw_unit=min^-1; kcat_over_km raw_value=49 +/- 15 raw_unit=s^-1*M^-1 for ST2570 defluorination

row_label: Table 2 steady-state defluorination ST2570 row; kcat, KM, and Kcat/KM columns

table_label: PMID 34643018 PMC HTML Table 2


column_label: Table 2 reports ST2570 dechlorination kcat 15.4 +/- 0.2 min^-1, KM 3.53 x 10^-3 +/- 3 x 10^-5 mM, Kcat/KM 7.3 x 10^4 +/- 1.1 x 10^3 s^-1 M^-1; paper-unit values convert to slightly different normalized values than current export

normalized_value_unit_evidence: KM normalized_value=0.00353 normalized_unit=mM; kcat normalized_value=0.2566666667 normalized_unit=s^-1; kcat_over_km normalized_value=73 normalized_unit=s^-1*mM^-1; current_export_kcat=0.26 s^-1; current_export_km=0.0035 mM; current_export_kcat_over_km=74.28571428571429 s^-1*mM^-1

raw_value_unit_evidence: KM raw_value=3.53 x 10^-3 +/- 3 x 10^-5 raw_unit=mM; kcat raw_value=15.4 +/- 0.2 raw_unit=min^-1; kcat_over_km raw_value=7.3 x 10^4 +/- 1.1 x 10^3 raw_unit=s^-1*M^-1 for ST2570 dechlorination

row_label: Table 2 steady-state dechlorination ST2570 row; kcat, KM, and Kcat/KM columns


substrate_name: monoiodoacetate

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

substrate: monoiodoacetate


organism: Agrobacterium sp.


organism: Burkholderia cepacia


substrate_name: Dichloroacetate

substrate: Dichloroacetate


substrate_name: Chloroacetate

substrate: Chloroacetate


organism: Ralstonia solanacearum


enzyme_display_name: D-amino-acid oxidase

organism: Rhodotorula toruloides

substrate_name: D-alanine

sequence_variant_note: Resolved canonical sequence from multiple and applied mutation signature S335G to reconstruct the assayed variant sequence.

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

proof_lines: mutant enzyme S335G, in 50 mM sodium diphosphate, pH 8.5, at air (21%) oxygen saturation, at 25°C, apparent value

enzyme: D-amino-acid oxidase

substrate: D-alanine


substrate_name: cephalosporin C

substrate: cephalosporin C


sequence_variant_note: Resolved canonical sequence from multiple and applied mutation signature Y223F to reconstruct the assayed variant sequence.

proof_lines: mutant enzyme Y223F, in 50 mM sodium diphosphate, pH 8.5, at air (21%) oxygen saturation, at 25°C, apparent value


proof_lines: wild type enzyme, in 50 mM sodium diphosphate, pH 8.5, at air (21%) oxygen saturation, at 25°C, apparent value


sequence_variant_note: Resolved canonical sequence from multiple and applied mutation signature S335H to reconstruct the assayed variant sequence.

proof_lines: mutant enzyme S335H, in 50 mM sodium diphosphate, pH 8.5, at air (21%) oxygen saturation, at 25°C, apparent value


substrate_name: D-Aspartate

substrate: D-Aspartate


substrate_name: D-arginine

sequence_variant_note: Resolved canonical sequence from multiple and applied mutation signature Q339E to reconstruct the assayed variant sequence.

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

proof_lines: kcat less than 0.2/s, mutant enzyme Q339E, in 50 mM sodium diphosphate, pH 8.5, at air (21%) oxygen saturation, at 25°C, apparent value

substrate: D-arginine


sequence_variant_note: Mutation signature Y228F could not be applied safely because the resolved sequence does not match the expected reference residue(s).

proof_lines: mutant enzyme Y228F, in 50 mM sodium diphosphate, pH 8.5, at air (21%) oxygen saturation, at 25°C, apparent value


proof_lines: mutant enzyme Q339E, in 50 mM sodium diphosphate, pH 8.5, at air (21%) oxygen saturation, at 25°C, apparent value


sequence_variant_note: Resolved canonical sequence from multiple and applied mutation signature Y223S to reconstruct the assayed variant sequence.

proof_lines: mutant enzyme Y223S, in 50 mM sodium diphosphate, pH 8.5, at air (21%) oxygen saturation, at 25°C, apparent value


sequence_variant_note: Resolved canonical sequence from multiple and applied mutation signature Y238S to reconstruct the assayed variant sequence.

proof_lines: mutant enzyme Y238S, in 50 mM sodium diphosphate, pH 8.5, at air (21%) oxygen saturation, at 25°C, apparent value


sequence_variant_note: Resolved canonical sequence from multiple and applied mutation signature S335R to reconstruct the assayed variant sequence.

proof_lines: mutant enzyme S335R, in 50 mM sodium diphosphate, pH 8.5, at air (21%) oxygen saturation, at 25°C, apparent value


sequence_variant_note: Resolved canonical sequence from multiple and applied mutation signature Q339N to reconstruct the assayed variant sequence.

proof_lines: mutant enzyme Q339N, in 50 mM sodium diphosphate, pH 8.5, at air (21%) oxygen saturation, at 25°C, apparent value


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature Y238R to reconstruct the assayed variant sequence.

proof_lines: mutant enzyme Y238R, in 50 mM sodium diphosphate, pH 8.5, at air (21%) oxygen saturation, at 25°C, apparent value


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature M213E to reconstruct the assayed variant sequence.

proof_lines: mutant enzyme M213E, in 50 mM sodium diphosphate, pH 8.5, at air (21%) oxygen saturation, at 25°C, apparent value


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature S335R to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature M213R to reconstruct the assayed variant sequence.

proof_lines: mutant enzyme M213R, in 50 mM sodium diphosphate, pH 8.5, at air (21%) oxygen saturation, at 25°C, apparent value


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature Q339E to reconstruct the assayed variant sequence.


enzyme_display_name: deacetoxycephalosporin-C synthase

organism: Streptomyces clavuligerus

substrate_name: ampicillin

sequence_variant_note: Resolved canonical sequence from uniprot:P18548 and applied mutation signature C281Y/N304K to reconstruct the assayed variant sequence.

enzyme: deacetoxycephalosporin-C synthase

substrate: ampicillin


sequence_variant_note: Resolved canonical sequence from uniprot:P18548 and applied mutation signature C281Y/R307L to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot:P18548 and applied mutation signature C281Y/N304M to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot:P18548 and applied mutation signature V275I/N304M to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot:P18548 and applied mutation signature V275I/R307L to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot:P18548 and applied mutation signature R306L to reconstruct the assayed variant sequence.

proof_lines:
mutant R306L, pH 7.4, 30°C
mutant R306L, 30°C


sequence_variant_note: Resolved canonical sequence from uniprot:P18548 and applied mutation signature R307L to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot:P18548 and applied mutation signature N304R to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot:P18548 and applied mutation signature C281Y/N304A to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot:P18548 and applied mutation signature N304M to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot:P18548 and applied mutation signature I305M to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot:P18548 and applied mutation signature V275I/I305M to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot:P18548 and applied mutation signature C281Y/I305M to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot:P18548 and applied mutation signature N304M/R306L to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot:P18548 and applied mutation signature N304L/R306L to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot:P18548 and applied mutation signature N304R/R306L to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot:P18548 and applied mutation signature V275L to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot:P18548 and applied mutation signature N304K/R306L to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot:P18548 and applied mutation signature N304A/R306L to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot:P18548 and applied mutation signature V275I/R306L to reconstruct the assayed variant sequence.


enzyme_display_name: methylamine dehydrogenase (amicyanin)

organism: Paracoccus denitrificans

substrate_name: methylamine

sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_candidate and applied mutation signature I107V with inferred residue-numbering offset -15 to reconstruct the assayed variant sequence.

smiles: CN

enzyme: methylamine dehydrogenase (amicyanin)

substrate: methylamine


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

smiles: CCCCCN


substrate_name: Butylamine

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

smiles: CCCCN

substrate: Butylamine


substrate_name: ethylamine

smiles: CCN

substrate: ethylamine


substrate_name: Propylamine

smiles: CCCN

substrate: Propylamine


smiles: C(CCCN)CCCN