organism: Santalum spicatum

normalized_value_unit_evidence: Km: printed Results value 1.4 uM (apparent, +/- 0.3); 1.4 / 1000 = 0.0014 mM; the exported value is 0.0014 mM, an exact match. kcat: printed Results value 2.6 s^-1 for SpiSSy; already in s^(-1), no conversion is applied (this paper prints no min^-1 kinetic value); the exported value is 2.6 s^(-1), an exact match. kcat/Km: the paper prints no kcat/Km value, so nothing is converted; the exported 1857.1428571428573 s^(-1)*mM^(-1) is carried unchanged and typed as the full-precision quotient 2.6 / 0.0014 of this row's own two confirmed components.

raw_value_unit_evidence: Results prose, journal page 17449 (PDF page 5). Km sentence, decoded from the 300 dpi render: 'Each santalene synthase had an apparent Km of 1.4 (+/- 0.3) uM, indicating a biologically relevant, high affinity for (E,E)-FPP.' kcat sentence, decoded: 'Catalytic turnover rates were similar for all three enzymes, with a kcat for SaSSy of 0.34 s^-1, 0.91 s^-1 for SauSSy, and 2.6 s^-1 for SpiSSy.' For SpiSSy, the Santalum spicatum santalene synthase, that pair reads Km = 1.4 uM and kcat = 2.6 s^-1. The paper prints no kcat/Km value for this or any other enzyme.

row_label: SpiSSy | Santalum spicatum santalene synthase | (E,E)-FPP


enzyme_display_name: aspartate ammonia-lyase

organism: Yersinia pestis

substrate_name: L-aspartate

source_db: brenda

km_display: Not reported

ki_display: Not reported

kcat_over_km_display: Not reported

protein_accession_database: UniProt

source_license: CC BY 4.0

sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_mutation_ranked_match and applied mutation signature Y146D to reconstruct the assayed variant sequence.

mutation_type: substitution

data_origin: experimental

enzyme: aspartate ammonia-lyase

substrate: L-aspartate

source: brenda


km_unit: mM

sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_mutation_ranked_match and applied mutation signature L363V/Y146D to reconstruct the assayed variant sequence.


enzyme_display_name: alpha-santalene synthase

organism: Santalum austrocaledonicum

substrate_name: (2E,6E)-farnesyl diphosphate

source_db: oed

verification_status: verified

mutation_signature: Unknown

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

assay_conditions_summary: pH 7.4; 298.15 K; buffer reaction

column_label: Evidence location type: prose. Evidence location label: Results prose of the article PDF, page 5 (journal page 17449). Measurement identity label: SauSSy | Santalum austrocaledonicum santalene synthase | (E,E)-FPP. metric: kcat; raw value: 0.91; raw unit: s^-1; normalized value: 0.91; normalized unit: s^(-1); metric: Km; raw value: 1.4; raw unit: uM; normalized value: 0.0014; normalized unit: mM; metric: kcat/Km; raw value: 0.91 / 1.4; raw unit: s^-1 uM^-1; normalized value: 650.0; normalized unit: s^-1 mM^-1; assay condition: Steady-state kinetic assays of the recombinant santalene synthase on (E,E)-FPP. Methods: "For determination of steady-state enzyme kinetic constants, conditions were as described previously except the enzyme concentration was kept at 10 nM." Substrate concentrations ranged from 1 (cid:3) M to 100 (cid:3) M and reactions were incubated at 30 (deg)C for exactly 5 min in reaction buffer of 25 mM HEPES, 10% (v/v) glycerol, 5 mM DTT and 10 mM Mg2+. Export row conditions: pH 7.4; 298.15 K.

normalized_value_unit_evidence: Results prose for SauSSy on (E,E)-FPP: kcat 0.91 s^-1 = 0.91 s^(-1); Km 1.4 uM = 0.0014 mM (1 uM = 0.001 mM); kcat/Km is not printed by the paper and is the quotient of the same two prose values: 0.91 s^-1 / 0.0014 mM = 650.0 s^-1 mM^-1 (equivalently 0.91 / 1.4 = 0.65 s^-1 uM^-1). In this PDF text extraction the plus/minus sign renders as (cid:7), the micromolar unit as (cid:3) M, the superscript minus one as (cid:2)1, and the subscripts of K m and k cat drop onto their own line, so the printed sentence reads "apparent K of 1.4 ((cid:7) 0.3) (cid:3) M" with a following line "m", and "k for SaSSy of 0.34 s(cid:2)1, 0.91 s(cid:2)1 for SauSSy, and 2.6 s(cid:2)1 for" with a following line "cat".

raw_value_unit_evidence: Results prose of the article PDF, page 5 (journal page 17449). Left column sentence: "santalene synthase had an apparent K of 1.4 ((cid:7) 0.3) (cid:3) M, indi- m cating a biologically relevant, high affinity for (E,E)-FPP." Right column sentence: "lytic turnover rates were similar for all three enzymes, with a k for SaSSy of 0.34 s(cid:2)1, 0.91 s(cid:2)1 for SauSSy, and 2.6 s(cid:2)1 for cat SpiSSy." The K m sentence reads K m = 1.4 (+/- 0.3) uM for each santalene synthase; the k cat sentence reads k cat = 0.34 s^-1 for SaSSy, 0.91 s^-1 for SauSSy and 2.6 s^-1 for SpiSSy, so the SauSSy cell of this pair reads k cat = 0.91 s^-1 and K m = 1.4 uM. The paper prints no k cat / K m value. Ortholog identity sentence, page 4 right column: "Orthologous TPSs identified in two other oil-bearing species (SspiSSy from S. spicatum and SauSSy from S. austrocaledonicum) were also found to convert (E,E)- FPP into the santalenes in very similar proportions as SaSSy" In this PDF text extraction the plus/minus sign renders as (cid:7), the micromolar unit as (cid:3) M, the superscript minus one as (cid:2)1, and the subscripts of K m and k cat drop onto their own line, so the printed sentence reads "apparent K of 1.4 ((cid:7) 0.3) (cid:3) M" with a following line "m", and "k for SaSSy of 0.34 s(cid:2)1, 0.91 s(cid:2)1 for SauSSy, and 2.6 s(cid:2)1 for" with a following line "cat".

enzyme: alpha-santalene synthase

substrate: (2E,6E)-farnesyl diphosphate

status: verified

source: oed


organism: Clausena lansium

verification_status: unverified

status: unverified


enzyme_display_name: beta-santalene synthase

organism: Santalum album

kcat_over_km_origin: calculated

normalized_value_unit_evidence: Km: printed Results value 1.4 uM (apparent, +/- 0.3); 1.4 / 1000 = 0.0014 mM; the exported value is 0.0014 mM, an exact match. kcat: printed Results value 0.34 s^-1 for SaSSy; already in s^(-1), no conversion is applied (this paper prints no min^-1 kinetic value); the exported value is 0.34 s^(-1), an exact match. kcat/Km: the paper prints no kcat/Km value, so nothing is converted; the exported 242.8571428571429 s^(-1)*mM^(-1) is carried unchanged and typed as the full-precision quotient 0.34 / 0.0014 of this row's own two confirmed components.

raw_value_unit_evidence: Results prose, journal page 17449 (PDF page 5). Km sentence, decoded from the 300 dpi render: 'Each santalene synthase had an apparent Km of 1.4 (+/- 0.3) uM, indicating a biologically relevant, high affinity for (E,E)-FPP.' kcat sentence, decoded: 'Catalytic turnover rates were similar for all three enzymes, with a kcat for SaSSy of 0.34 s^-1, 0.91 s^-1 for SauSSy, and 2.6 s^-1 for SpiSSy.' For SaSSy, the Santalum album santalene synthase, that pair reads Km = 1.4 uM and kcat = 0.34 s^-1. The paper prints no kcat/Km value for this or any other enzyme.

row_label: SaSSy | Santalum album santalene synthase | (E,E)-FPP

enzyme: beta-santalene synthase


column_label: Results prose immediately before Figure 2 states each santalene synthase had apparent Km 1.4 (+/- 0.3) uM for (E,E)-FPP and kcat for SaSSy of 0.34 s^-1.

normalized_value_unit_evidence: Km normalized_value=0.0014 normalized_unit=mM; kcat normalized_value=0.34 normalized_unit=s^-1; computed kcat/Km normalized_value=242.8571428571429 normalized_unit=s^-1*mM^-1

raw_value_unit_evidence: Km raw_value=1.4 (+/- 0.3) raw_unit=uM; kcat raw_value=0.34 raw_unit=s^-1

row_label: SaSSy / Santalum album santalene synthase with (E,E)-FPP


column_label: Results prose immediately before Figure 2 states each santalene synthase had apparent Km 1.4 (+/- 0.3) uM for (E,E)-FPP and kcat 0.91 s^-1 for SauSSy.

normalized_value_unit_evidence: Km normalized_value=0.0014 normalized_unit=mM; kcat normalized_value=0.91 normalized_unit=s^-1; computed kcat/Km normalized_value=650.0 normalized_unit=s^-1*mM^-1

raw_value_unit_evidence: Km raw_value=1.4 (+/- 0.3) raw_unit=uM; kcat raw_value=0.91 raw_unit=s^-1

row_label: SauSSy / Santalum austrocaledonicum santalene synthase with (E,E)-FPP


enzyme_display_name: aristolochene synthase

organism: Aspergillus terreus

substrate_name: trans,trans-Farnesyl diphosphate

verification_status: corrected

sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:Q9UR08 and applied mutation signature E227D to reconstruct the assayed variant sequence.

assay_conditions_summary: pH 8; 303.15 K; buffer H (20 mM Hepes pH 8

column_label: Table 2 (Aristolochene Synthase Mutants: Kinetic Parameters and Product Ratios), protein row 'AT-E227D'; column 'kcat (10-3 s-1)' = 1.6; column 'Km (uM)' = 1.4; column 'kcat/Km (s-1 M-1)' = 1.1 x 10^3; column 'aristolochene (4)' = 26; column 'valencene (5)' = ND; column 'germacrene A (2)' = 74.

normalized_value_unit_evidence: kcat: printed Table 2 cell 1.6 in the column headed kcat (10-3 s-1), i.e. 1.6 x 10^-3 s^-1 = 0.0016 s^-1. Km: printed Table 2 cell 1.4 uM; 1.4 / 1000 = 0.0014 mM. kcat/Km: printed Table 2 cell 1.1 x 10^3 M^-1 s^-1; 1 M^-1 s^-1 is 0.001 s^-1 mM^-1, so 1.1 x 10^3 / 1000 = 1.1 s^(-1)*mM^(-1). The three values this record carries for the row are those three printed cells.

raw_value_unit_evidence: Table 2, protein row 'AT-E227D': kcat = 1.6 in units of 10^-3 s^-1; Km = 1.4 uM; printed kcat/Km = 1.1 x 10^3 M^-1 s^-1.

row_label: Table 2, protein row 'AT-E227D'

table_label: Table 2: Aristolochene Synthase Mutants: Kinetic Parameters and Product Ratios (J. Am. Chem. Soc. 2004, 126(23):7212-7221)

enzyme: aristolochene synthase

substrate: trans,trans-Farnesyl diphosphate

status: corrected


enzyme_display_name: cubebol synthase

organism: Coprinopsis cinerea (strain Okayama-7 / 130 / ATCC MYA-4618 / FGSC 9003)

substrate_name: all-trans-farnesyl diphosphate

source_db: uniprot

kcat_display: Not reported

enzyme: cubebol synthase

substrate: all-trans-farnesyl diphosphate

source: uniprot


enzyme_display_name: delta-guaiene synthase

organism: Pogostemon cablin

substrate_name: farnesyl diphosphate

enzyme: delta-guaiene synthase

substrate: farnesyl diphosphate


enzyme_display_name: alpha-guaiene synthase

sequence_source: multiple

assay_conditions_summary: pH 7

proof_lines:
Pogostemon cablin
alpha-guaiene
patchoulol

source_databases_merged: brenda uniprot

enzyme: alpha-guaiene synthase


organism: Coprinopsis cinerea

column_label: Table 1 row Cop4, (E,E)-FPP columns report Km 11+/-3 uM, kcat (1.2+/-0.1)x10^-2 s^-1, and kcat/Km 1 in the x10^3 s^-1 M^-1 column.

normalized_value_unit_evidence: Km normalized_value=0.011 normalized_unit=mM; kcat normalized_value=0.012 normalized_unit=s^-1; kcat/Km normalized_value=1.0 normalized_unit=s^-1 mM^-1

raw_value_unit_evidence: Km raw_value=11+/-3 raw_unit=uM; kcat raw_value=(1.2+/-0.1)x10^-2 raw_unit=s^-1; kcat/Km raw_value=1 raw_unit=s^-1 M^-1 (x10^3)

row_label: Cop4 / (E,E)-FPP

table_label: PMC2873112 Table 1, kinetic constants of Cop4 and Cop6


enzyme_display_name: labdatriene synthase

organism: Oryza sativa subsp. japonica

substrate_name: 9alpha-copalyl diphosphate

proof_lines:
OsKSL10
syn-CPP
9alpha-copalyl diphosphate

enzyme: labdatriene synthase

substrate: 9alpha-copalyl diphosphate


enzyme_display_name: thebaine synthase

organism: Papaver somniferum

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

enzyme: thebaine synthase


enzyme_display_name: methylaspartate ammonia-lyase

organism: Fusobacterium varium

substrate_name: (S)-aspartate

proof_lines:
(2S,3S)-3-methylaspartate
Km = 0.51 +/- 0.04 mM
pH 9.7

enzyme: methylaspartate ammonia-lyase

substrate: (S)-aspartate


organism: Escherichia coli

source_db: skid

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

proof_lines: MenH YfbB SEPHCHC

source_databases_merged: skid uniprot

source: skid


organism: Carboxydothermus hydrogenoformans

substrate_name: (2S,3S)-3-ethylaspartic acid

substrate: (2S,3S)-3-ethylaspartic acid


organism: Yersinia pseudotuberculosis

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


organism: Penicillium roqueforti


enzyme_display_name: histidine ammonia-lyase

organism: Thermoplasma acidophilum

substrate_name: L-histidine

proof_lines: Thermoplasma acidophilum histidine ammonia-lyase

enzyme: histidine ammonia-lyase

substrate: L-histidine


enzyme_display_name: enoyl-CoA hydratase 2

organism: Homo sapiens

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

assay_conditions_summary: cofactor CoA

proof_lines:
HSD17B4
dehydrogenase reactions
Table II

enzyme: enoyl-CoA hydratase 2


substrate_name: NAD

substrate: NAD


substrate_name: NADH

assay_conditions_summary: cofactor NADH

substrate: NADH


organism: Sus scrofa


proof_lines: Identification of the peroxisomal beta-oxidation enzymes involved in the degradation of long-chain dicarboxylic acids


enzyme_display_name: 5'-oxoaverantin cyclase

organism: Aspergillus parasiticus

enzyme: 5'-oxoaverantin cyclase


enzyme_display_name: versicolorin B synthase

organism: Aspergillus parasiticus (strain ATCC 56775 / NRRL 5862 / SRRC 143 / SU-1)

proof_lines:
Aspergillus parasiticus
OAVN cyclase
5'-oxoaverantin

enzyme: versicolorin B synthase


substrate_name: versiconal (at pH 6.0 and 30 degrees Celsius)


assay_conditions_summary: cofactor NAD+


assay_conditions_summary: pH 8.5; cofactor CoA

column_label: Results prose lines 260-266 and Fig. 4; protein DBP; substrate C16:1DC-CoA ((2E)-hexadecenedioyl-CoA); metric apparent Km; raw value 0.9 uM; normalized Km=0.0009 mM.

raw_value_unit_evidence: Results text reports DBP apparent Km 0.9 uM for C16:1DC-CoA (Fig. 4).

table_label: PMID 15060085, Results prose and Fig. 4: kinetic analysis of human DBP and LBP


column_label: Results prose lines 260-266 and Fig. 4; protein DBP; substrate C16:1-CoA ((2E)-hexadecenoyl-CoA); metric apparent Km; raw value 12.8 uM; normalized Km=0.0128 mM.

raw_value_unit_evidence: Results text reports DBP apparent Km 12.8 uM for C16:1-CoA (Fig. 4).


enzyme_display_name: o-succinylbenzoate synthase

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

proof_lines: pH 8.0, 25°C, recombinant mutant G16P/V17F/V18R/L19T/R20S/D21F/R22G/R23T/L24QL48A

enzyme: o-succinylbenzoate synthase


proof_lines: pH 8.0, 25°C, recombinant mutant S262A/S263A/S264A/I265A


proof_lines: pH 8.0, 25°C, recombinant mutant L48A/F51A


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

proof_lines: pH 8.0, 25°C, recombinant wild-type enzyme


proof_lines: pH 8.0, 25°C, recombinant mutant L48M/F51Y


organism: Thermobifida fusca

proof_lines: pH 8.0, 25°C, recombinant mutant R15G/F16G/R17G/G18G/I19G


proof_lines: pH 8.0, 25°C, recombinant mutant N73L/T75V


proof_lines: pH 8.0, 25°C, recombinant mutant R17A/F39A


proof_lines: pH 8.0, 25°C, recombinant mutant R17A/Y42A


proof_lines: pH 8.0, 25°C, recombinant mutant N73A/T75L


proof_lines:
H232A mutant protein
mutant H232A


proof_lines:
D210A mutant protein
mutant D210A at 25°C


proof_lines:
S86A mutant protein
mutant S86A at 25°C


enzyme_display_name: methanogen homoaconitase

organism: Methanocaldococcus jannaschii

substrate_name: but-1-ene-1,2,4-tricarboxylic acid

enzyme: methanogen homoaconitase

substrate: but-1-ene-1,2,4-tricarboxylic acid


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


substrate_name: (1E)-hex-1-ene-1,2,6-tricarboxylic acid

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

substrate: (1E)-hex-1-ene-1,2,6-tricarboxylic acid


enzyme_display_name: methylglyoxal synthase

substrate_name: dihydroxyacetone phosphate

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

proof_lines: mutant lacking ten amino acids from C-terminal tail, Hill coefficient 1.3, pH 7.0, 60°C

enzyme: methylglyoxal synthase

substrate: dihydroxyacetone phosphate


enzyme_display_name: aspartate ammonia-lyase

proof_lines:
monomeric mutant enzyme maspase 1
dimeric mutant enzyme maspase 2
tetrameric mutant enzyme maspase 3

enzyme: aspartate ammonia-lyase


substrate_name: Cinnamic acid

proof_lines: pH 8.5, 30°C, mutant enzyme Q329F/K331R/Y356S/C361L

substrate: Cinnamic acid


proof_lines: pH 8.5, 30°C, mutant enzyme F170S/E172R/D307L


substrate_name: cafffeic acid

substrate: cafffeic acid


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


substrate_name: L-aspartate


substrate_name: fumarate

substrate: fumarate


substrate_name: mesaconate

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

substrate: mesaconate


enzyme_display_name: chondroitin-sulfate-ABC exolyase

organism: Bacteroides thetaiotaomicron

substrate_name: dermatan sulfate

enzyme: chondroitin-sulfate-ABC exolyase

substrate: dermatan sulfate


substrate_name: chondroitin sulfate C

substrate: chondroitin sulfate C


enzyme_display_name: (+)-delta-cadinene synthase

organism: Gossypium arboreum

substrate_name: (2E,6E)-farnesyl diphosphate

proof_lines: pH and temperature not specified in the publication, mutant enzyme W279E

enzyme: (+)-delta-cadinene synthase

substrate: (2E,6E)-farnesyl diphosphate


proof_lines: pH and temperature not specified in the publication, mutant enzyme W279D


proof_lines: pH and temperature not specified in the publication, mutant enzyme W279Y


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

proof_lines: recombinant His6-tagged wild-type enzyme, pH 7.5, 25°C


proof_lines: pH and temperature not specified in the publication, mutant enzyme W279M


proof_lines: His-tagged recombinant enzyme, at pH 7.5 and 25°C

proof_lines: fusion protein composed of the pXC1-encoded protein and the histidine leader peptide derived from pET28, pH 7, 30°C

proof_lines: pH 7, 30°C, fusion protein composed of the pXC1-encoded protein and the histidine leader peptide derived from pET28


proof_lines: pH and temperature not specified in the publication, mutant enzyme W279Q


proof_lines: pH and temperature not specified in the publication, mutant enzyme W279A


proof_lines: pH and temperature not specified in the publication, mutant enzyme W279L


organism: Bacillus sp. YM55-1

substrate: L-aspartate


substrate_name: Unknown

ki_unit: mM

substrate: Unknown


enzyme_display_name: heparin lyase

organism: Pedobacter heparinus

substrate_name: heparin

sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature Y379A to reconstruct the assayed variant sequence.

enzyme: heparin lyase

substrate: heparin


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature E381A to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature G378A to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature N375A to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature G213A to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature T373A to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature T216A to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature T382A to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature D212A to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature D210A to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature S377A to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature E207A to reconstruct the assayed variant sequence.


enzyme_display_name: serine-sulfate ammonia-lyase

organism: Rattus norvegicus

substrate_name: L-serine O-sulfate

enzyme: serine-sulfate ammonia-lyase

substrate: L-serine O-sulfate


substrate_name: 3-chloro-L-alanine methyl ester

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

substrate: 3-chloro-L-alanine methyl ester


enzyme_display_name: carbamoyl-serine ammonia-lyase

substrate_name: O-Carbamoyl-L-serine

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

enzyme: carbamoyl-serine ammonia-lyase

substrate: O-Carbamoyl-L-serine


enzyme_display_name: ethanolamine ammonia-lyase

organism: Salmonella enterica subsp. enterica serovar Typhimurium

substrate_name: ethanolamine

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

smiles: NCCO

enzyme: ethanolamine ammonia-lyase

substrate: ethanolamine


proof_lines:
alpha enzyme
beta enzyme


enzyme_display_name: UniProt P40817

source_license: CC BY-NC-ND 4.0

proof_lines:
Raw SKiD Env: Temp=37°C, pH=7.5
Raw SKiD Env: Temp=30°C, pH=7.4

enzyme: UniProt P40817


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


enzyme_display_name: UniProt P66899

organism: Escherichia coli

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

enzyme: UniProt P66899


substrate_name: L-cysteine

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

substrate: L-cysteine


enzyme_display_name: UniProt Q54HH2

organism: Dictyostelium discoideum

substrate_name: D-serine

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

enzyme: UniProt Q54HH2

substrate: D-serine


smiles: CC(CO)N

proof_lines: binding to apo-EAL at 25°C in buffered aqueous solution


enzyme_display_name: 3-aminobutyryl-CoA ammonia-lyase

organism: Anaerobic bacteria

substrate_name: crotonyl-CoA

enzyme: 3-aminobutyryl-CoA ammonia-lyase

substrate: crotonyl-CoA


organism: Leifsonia aquatica

smiles: C(CO)N


organism: Pseudomonas sp.

substrate_name: D-serine O-sulfate

substrate: D-serine O-sulfate


substrate_name: D-Cystine

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

proof_lines:
enzyme B
enzyme A

substrate: D-Cystine


substrate_name: S-Benzyl-L-cysteine

substrate: S-Benzyl-L-cysteine


substrate_name: O-benzyl-L-serine

proof_lines: enzyme B, calculated on the basis of the non-reactivity of the L-isomer

substrate: O-benzyl-L-serine


substrate_name: D-cystathionine

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

substrate: D-cystathionine


substrate_name: S-methyl-L-cysteine

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

proof_lines:
enzyme A
enzyme B

substrate: S-methyl-L-cysteine


substrate_name: O-acetyl-L-serine

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

substrate: O-acetyl-L-serine


substrate_name: S-ethyl-L-cysteine

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

substrate: S-ethyl-L-cysteine


enzyme_display_name: threonine ammonia-lyase

organism: Entamoeba histolytica

substrate_name: L-Ser

enzyme: threonine ammonia-lyase

substrate: L-Ser


substrate_name: L-Thr

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

substrate: L-Thr


substrate_name: Unknown

proof_lines:
substrate L-Ser, pH 9.0, 37°C
substrate L-Thr, pH 9.0, 37°C

substrate: Unknown


enzyme_display_name: L-serine ammonia-lyase

organism: Bombyx mori

substrate_name: L-serine

enzyme: L-serine ammonia-lyase

substrate: L-serine


substrate_name: L-threonine

substrate: L-threonine


proof_lines:
substrate L-serine
substrate L-threonine


enzyme_display_name: D-serine ammonia-lyase

enzyme: D-serine ammonia-lyase


organism: Paracoccus denitrificans

substrate_name: erythro-L-beta-hydroxyaspartate

substrate: erythro-L-beta-hydroxyaspartate


organism: Clostridium acidi-urici


organism: Euglena gracilis

proof_lines:
dehydratase II
dehydratase I


organism: Cereibacter sphaeroides


enzyme_display_name: glucosaminate ammonia-lyase

organism: Soil bacterium

substrate_name: D-glucosaminic acid

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

enzyme: glucosaminate ammonia-lyase

substrate: D-glucosaminic acid


proof_lines: kcat is 844 min(-1) for L-serine and 152 min(-1) for L-threonine.


substrate_name: L-glutamate

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

substrate: L-glutamate


enzyme_display_name: ornithine cyclodeaminase

organism: Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)

substrate_name: arginine

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

proof_lines: kcat is 271.1 min(-1) with arginine as substrate (for full-length AgrE) (PubMed:32198136). kcat is 292.6 min(-1) with arginine as substrate (for NTD-AgrE) (PubMed:32198136).

enzyme: ornithine cyclodeaminase

substrate: arginine


substrate_name: ornithine

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

substrate: ornithine


organism: Pseudomonas sp. N99

proof_lines: pH and temperature not specified in the publication


organism: Solanum lycopersicum


substrate_name: D-serine (at 30 degrees Celsius and at pH 8.5)

assay_conditions_summary: pH 8.5; buffer pH 8; cofactor NADH

column_label: Table 1 lists D-serine dehydratase with D-Ser Km 0.19 +/- 0.02 mM.

raw_value_unit_evidence: Km raw_value=0.19 +/- 0.02 raw_unit=mM

row_label: D-serine dehydratase / D-Ser

table_label: Table 1, Kinetic parameters of recombinant SR, DSD, and DAO of Dictyostelium discoideum


organism: Candida maltosa

proof_lines:
in absence of phosphate
in presence of 50 mM phosphate
in presence of 250 mM phosphate


organism: Fusobacterium nucleatum (subsp. nucleatum)

substrate_name: Crotonoyl-CoA; NH3

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

substrate: Crotonoyl-CoA; NH3


enzyme_display_name: diaminopropionate ammonia-lyase

organism: Escherichia coli

substrate_name: H2O; 2,3-Diaminopropanoate

enzyme: diaminopropionate ammonia-lyase

substrate: H2O; 2,3-Diaminopropanoate


organism: Salmonella typhimurium

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

source_databases_merged: sabio_rk skid uniprot


organism: Saccharomyces cerevisiae

substrate_name: 3-Chloro-D-alanine; H2O

substrate: 3-Chloro-D-alanine; H2O


organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843)


organism: Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)

proof_lines: kcat is 1654 sec(-1) with L-threonine as substrate. kcat is 1151 sec(-1) with L-serine as substrate. kcat is 55 sec(-1) with L-allo-threonine as substrate.


organism: Arabidopsis thaliana


organism: Homo sapiens


organism: Rattus norvegicus


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature C265S to reconstruct the assayed variant sequence.

proof_lines: both D and L forms of diaminopropionic acid


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature C291S with inferred residue-numbering offset +14 to reconstruct the assayed variant sequence.


enzyme_display_name: histidine ammonia-lyase

organism: Streptomyces griseus

substrate_name: L-Histidine

enzyme: histidine ammonia-lyase

substrate: L-Histidine


substrate_name: D-Serine

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

substrate: D-Serine


proof_lines: dl-DAP / 2,3-diaminopropanoate family context


substrate_name: L-Serine

substrate: L-Serine


proof_lines: DL-DAP, D-serine, and L-serine as substrates


substrate_name: D-serine

assay_conditions_summary: pH 8; 303.15 K; cofactor NADH

column_label: Table I. Kinetic parameters of the wild-type and Y203 mutants of Dsd1p row Wild-type; cells Km 0.2 +/- 0.05 mM, kcat 17 +/- 1.46 s^-1, kcat/Km 90 s^-1/mM; assay footnote: reactions at 30 C and pyruvate production from D-serine followed by LDH coupling.

normalized_value_unit_evidence: Km normalized_value=0.2 normalized_unit=mM; kcat normalized_value=17 normalized_unit=s^-1; kcat/Km normalized_value=90.0 normalized_unit=s^-1*mM^-1

raw_value_unit_evidence: Km raw_value=0.2 +/- 0.05 raw_unit=mM; kcat raw_value=17 +/- 1.46 raw_unit=s^-1; kcat/Km raw_value=90 raw_unit=s^-1*mM^-1

row_label: Wild-type / D-serine

substrate: D-serine


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P53095 and applied mutation signature Y203A to reconstruct the assayed variant sequence.

assay_conditions_summary: pH 8; 303.15 K; buffer containing 50 mM HEPES-NaOH; cofactor NADH

column_label: Table I. Kinetic parameters of the wild-type and Y203 mutants of Dsd1pa. (J. Biochem. 2014;156(3):173-180), enzyme row 'Y203A'; column 'Km (mM)' = 1.8 +/- 0.12; column 'kcat (s-1)' = 2.3 +/- 0.08; column 'kcat/Km (s-1/mM)' = 1.2; column 'kcat ratio (%)' = 14; column 'kcat/Km ratio (%)' = 1.3.

normalized_value_unit_evidence: kcat: printed Table I cell 2.3 s^-1; the printed turnover column is per second, so no unit conversion applies and the exported value is 2.3 s^(-1). Km: printed Table I cell 1.8 mM; the printed column is already in mM, so no unit conversion applies and the exported value is 1.8 mM. kcat/Km: printed Table I cell 1.2 s^-1/mM; one s^-1/mM is one s^-1 mM^-1, so no unit conversion applies and the printed cell is 1.2 s^-1 mM^-1, while the exported value is 1.2777777777777777 s^(-1)*mM^(-1), the quotient of the two exported component values.

raw_value_unit_evidence: Table I, enzyme row Y203A, substrate D-serine: Km = 1.8 +/- 0.12 mM; kcat = 2.3 +/- 0.08 s^-1; printed kcat/Km = 1.2 s^-1/mM. The printed column heads of Table I carry those three units for every enzyme row of the table.


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P53095 and applied mutation signature Y203D to reconstruct the assayed variant sequence.

column_label: Table I. Kinetic parameters of the wild-type and Y203 mutants of Dsd1pa. (J. Biochem. 2014;156(3):173-180), enzyme row 'Y203D'; column 'Km (mM)' = 8.5 +/- 1.32; column 'kcat (s-1)' = 0.097 +/- 0.004; column 'kcat/Km (s-1/mM)' = 0.012; column 'kcat ratio (%)' = 0.57; column 'kcat/Km ratio (%)' = 0.01.

normalized_value_unit_evidence: kcat: printed Table I cell 0.097 s^-1; the printed turnover column is per second, so no unit conversion applies and the exported value is 0.097 s^(-1). Km: printed Table I cell 8.5 mM; the printed column is already in mM, so no unit conversion applies and the exported value is 8.5 mM. kcat/Km: printed Table I cell 0.012 s^-1/mM; one s^-1/mM is one s^-1 mM^-1, so no unit conversion applies and the printed cell is 0.012 s^-1 mM^-1, while the exported value is 0.011411764705882354 s^(-1)*mM^(-1), the quotient of the two exported component values.

raw_value_unit_evidence: Table I, enzyme row Y203D, substrate D-serine: Km = 8.5 +/- 1.32 mM; kcat = 0.097 +/- 0.004 s^-1; printed kcat/Km = 0.012 s^-1/mM. The printed column heads of Table I carry those three units for every enzyme row of the table.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature Y203E to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature Y203F to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature Y203R to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P53095 and applied mutation signature Y203S to reconstruct the assayed variant sequence.

column_label: Table I. Kinetic parameters of the wild-type and Y203 mutants of Dsd1pa. (J. Biochem. 2014;156(3):173-180), enzyme row 'Y203S'; column 'Km (mM)' = 3.3 +/- 0.43; column 'kcat (s-1)' = 2.3 +/- 0.12; column 'kcat/Km (s-1/mM)' = 0.68; column 'kcat ratio (%)' = 14; column 'kcat/Km ratio (%)' = 0.8.

normalized_value_unit_evidence: kcat: printed Table I cell 2.3 s^-1; the printed turnover column is per second, so no unit conversion applies and the exported value is 2.3 s^(-1). Km: printed Table I cell 3.3 mM; the printed column is already in mM, so no unit conversion applies and the exported value is 3.3 mM. kcat/Km: printed Table I cell 0.68 s^-1/mM; one s^-1/mM is one s^-1 mM^-1, so no unit conversion applies and the printed cell is 0.68 s^-1 mM^-1, while the exported value is 0.6969696969696969 s^(-1)*mM^(-1), the quotient of the two exported component values.

raw_value_unit_evidence: Table I, enzyme row Y203S, substrate D-serine: Km = 3.3 +/- 0.43 mM; kcat = 2.3 +/- 0.12 s^-1; printed kcat/Km = 0.68 s^-1/mM. The printed column heads of Table I carry those three units for every enzyme row of the table.


substrate_name: D-Threonine

substrate: D-Threonine


substrate_name: L-Threonine

proof_lines:
human serine dehydratase-like-1
Ser/Thr dehydration

substrate: L-Threonine


substrate_name: L-serine


substrate_name: L-threonine


organism: Clostridium sporogenes

substrate_name: L-ornithine

assay_conditions_summary: cofactor ADP

proof_lines:
in the absence of ADP
in the presence of ADP

substrate: L-ornithine


organism: Mycolicibacterium smegmatis

substrate_name: beta-chloro-L-alanine

substrate: beta-chloro-L-alanine


substrate: L-serine


substrate_name: L-allo-Threonine

substrate: L-allo-Threonine


substrate: L-threonine


substrate_name: L-glutamate

substrate: L-glutamate


organism: Gallus gallus

substrate_name: D-serine (at pH 7.8 and 37 degrees Celsius)

column_label: Table 2 row d-Serine column Km (mM) reports 0.131 +/- 0.017

raw_value_unit_evidence: Km raw_value=0.131 +/- 0.017 raw_unit=mM

row_label: d-Serine

table_label: Oxford Academic full text Table 2


substrate_name: D-threonine (at pH 7.8 and 37 degrees Celsius)

column_label: Table 2 row d-Threonine column Km (mM) reports 0.312 +/- 0.096

raw_value_unit_evidence: Km raw_value=0.312 +/- 0.096 raw_unit=mM

row_label: d-Threonine


enzyme_display_name: chondroitin-sulfate-ABC exolyase

organism: Bacteroides thetaiotaomicron

substrate_name: chondroitin sulfate C

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

enzyme: chondroitin-sulfate-ABC exolyase

substrate: chondroitin sulfate C


substrate_name: dermatan sulfate

substrate: dermatan sulfate


substrate_name: chondroitin sulfate A

substrate: chondroitin sulfate A


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


organism: Agrobacterium tumefaciens (strain Ach5)

column_label: Public PMC scanned page 852 Table 1 row OCD(Ach5), column Apparent Km for L-Ornithine (mM), reports 0.25.

normalized_value_unit_evidence: Km normalized 0.25 mM.

raw_value_unit_evidence: Km raw 0.25 mM for L-Ornithine.

table_label: Table 1. Enzymatic properties of OCD(Ach5) and OCD(C58)


substrate_name: NAD(+)

substrate: NAD(+)


organism: Escherichia coli (strain K12)

substrate_name: ethanolamine

column_label: Table 3 reports wild-type Km for ethanolamine as 8.2 mM.

raw_value_unit_evidence: Km for ethanolamine = 8.2 mM

row_label: Wild-type (alpha beta)

table_label: Table 3

substrate: ethanolamine


substrate_name: adenosylcob(III)alamin

column_label: Table 3 reports wild-type Km for AdoCbl as 0.055 mM.

raw_value_unit_evidence: Km for AdoCbl = 0.055 mM

substrate: adenosylcob(III)alamin


substrate_name: NAD+

assay_conditions_summary: pH 8; cofactor NADP+

column_label: Page 6658 Effect of Cofactors and Reducing Agents section and Fig. 2; metric=apparent Km; segment=NAD+; raw value=6.1 x 10^-3 mM; normalized value=0.0061 mM.

raw_value_unit_evidence: Page 6658 reports apparent Km for NAD+ = 6.1 x 10^-3 mM and for NADP+ = 3.3 mM in the Lineweaver-Burk analysis.

row_label: NAD+

table_label: Effect of Cofactors and Reducing Agents / Fig. 2, page 6658

substrate: NAD+


substrate_name: NADP+

column_label: Page 6658 Effect of Cofactors and Reducing Agents section and Fig. 2; metric=apparent Km; segment=NADP+; raw value=3.3 mM; normalized value=3.3 mM.

normalized_value_unit_evidence: 3.3 mM is already in mM.

row_label: NADP+

substrate: NADP+


organism: Salmonella enterica subsp. enterica serovar Typhimurium


organism: Agrobacterium fabrum (strain C58 / ATCC 33970)


organism: Anaerotignum propionicum

substrate_name: L-Thr

column_label: Abstract reports that the purified L-threonine dehydratase exhibited a Km for L-threonine of 7.7 mM.

raw_value_unit_evidence: Km raw_value=7.7 mM raw_unit=mM

row_label: Clostridium propionicum L-threonine dehydratase / L-threonine

table_label: PubMed XML abstract PMID 8344301

substrate: L-Thr


substrate_name: L-Ser

column_label: Abstract reports that L-serine (Km = 380 mM) was also deaminated by the purified L-threonine dehydratase, with lower V/Km than L-threonine.

raw_value_unit_evidence: Km raw_value=380 mM raw_unit=mM

row_label: Clostridium propionicum L-threonine dehydratase / L-serine side activity

substrate: L-Ser


organism: Agrobacterium tumefaciens

substrate_name: L-Ornithine

substrate: L-Ornithine


substrate_name: L-serine


substrate_name: L-threonine


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

substrate_name: crotonyl-CoA

proof_lines:
3-aminobutyryl-CoA ammonia lyase
kal
lysine fermentation pathway

substrate: crotonyl-CoA


organism: Escherichia coli

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


organism: Delftia sp.


organism: Saccharomyces cerevisiae


organism: Arabidopsis thaliana

substrate_name: L-serine (racemase activity)

proof_lines:
serine racemization
dehydration of serine to pyruvate

substrate: L-serine (racemase activity)


substrate_name: L-Serine

substrate: L-Serine


proof_lines: Serine and threonine desaminaes of Escherichia coli; activators for a cell-free enzyme


substrate_name: L-threonine (at 37 dregrees Celsius and at pH 7.8)


organism: Homo sapiens

substrate_name: L-serine (at 37 degrees Celsius and at pH 8)

assay_conditions_summary: pH 8

proof_lines:
wild-type human serine racemase
serine racemase inhibitors
in vitro evaluations


organism: Oryza sativa subsp. japonica

proof_lines:
SerR
serine racemase
D-serine


organism: Rattus norvegicus

proof_lines:
serine dehydratase
Rattus norvegicus
L-serine


substrate_name: L-Threonine

substrate: L-Threonine


proof_lines: serine catabolism by alpha,beta-elimination of water

substrate: L-serine


organism: Pseudomonas sp

substrate_name: Unknown

substrate: Unknown


organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)


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

substrate_name: L-threonine (in the presence of 5 mM of AMP at 25 dregrees Celsius and at pH 8)

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

proof_lines:
Salmonella typhimurium
TdcB
biodegradative threonine deaminase


organism: Schizosaccharomyces pombe

column_label: Public J-STAGE PDF prose reports wild-type enzyme Km = 36 mM and Vmax = 870 nmol*min^-1*mg^-1; UniProt O59791 lists KM=36 mM and Vmax=870 nmol/min/mg enzyme with PubMed:19640845 evidence.

normalized_value_unit_evidence: Km normalized_value=36 normalized_unit=mM; Vmax normalized_value=0.0000145 normalized_unit=mol*s^(-1)*g^(-1)

raw_value_unit_evidence: Km raw_value=36 raw_unit=mM; Vmax raw_value=870 raw_unit=nmol/min/mg enzyme

row_label: wild-type spSRw L-serine alpha,beta-elimination activity

table_label: J-STAGE prose route plus UniProt O59791 biophysicochemical properties


proof_lines:
serine racemase
serine ammonia-lyase
L-serine


substrate_name: D-Serine

substrate: D-Serine


organism: Dictyostelium discoideum

substrate_name: D-serine

assay_conditions_summary: pH 8.5; 303.15 K; cofactor NADH

column_label: Table 1 D-Serine dehydratase / D-Ser row: Km 0.19 +/- 0.02 mM; kcat 2.6 +/- 0.04 s^-1; kcat/Km numeric cell 14.

normalized_value_unit_evidence: Km=0.19 mM; kcat=2.6 s^-1; independently printed kcat/Km=14 s^-1 mM^-1; current quotient-derived kcat/Km=13.68421052631579 s^-1 mM^-1.

raw_value_unit_evidence: Table 1 D-Serine dehydratase / D-Ser row: Km 0.19 +/- 0.02 mM; kcat 2.6 +/- 0.04 s^-1; independently printed kcat/Km numeric cell 14.

row_label: D-Serine dehydratase / D-Ser

table_label: Table 1. Kinetic parameters of recombinant SR, DSD, and DAO of Dictyostelium discoideum

substrate: D-serine


proof_lines:
rat serine racemase
Rattus norvegicus
reversible conversion of L- to D-serine


substrate: L-serine (at 37 degrees Celsius and at pH 8)


organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843)

substrate_name: serine

proof_lines: Schizosaccharomyces pombe serine racemase homolog

substrate: serine


enzyme_display_name: Serine racemase

enzyme: Serine racemase


organism: Bacillus subtilis

proof_lines: Threonine deaminase from Bacillus subtilis. II. The steady state kinetic properties


proof_lines: serine and threonine deaminases of Escherichia coli


organism: Salmonella typhimurium


organism: Acidiphilium acidophilum

column_label: Abstract states the Km for threonine is 2.5 x 10(-3) M.

raw_value_unit_evidence: Km raw_value=2.5e-3 raw_unit=M

row_label: Thiobacillus acidophilus biosynthetic L-threonine deaminase with L-threonine

table_label: PubMed abstract PMID 6773653


proof_lines: Purification, characterization and amino acid sequence of a novel enzyme, D-threo-3-hydroxyaspartate dehydratase, from Delftia sp. HT23


organism: Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa)

substrate_name: arginine

proof_lines: kcat is 6.4 sec(-1) with arginine as substrate.

substrate: arginine


substrate_name: adenosylcob(III)alamin

substrate: adenosylcob(III)alamin


organism: Escherichia coli

proof_lines: TrxR from E. coli showed pyridoxal 5'-phosphate (PLP)-dependent GADH activity


substrate_name: ethanolamine

substrate: ethanolamine


proof_lines:
run 2, pH 8, 37°C, wild-type
run 1, pH 8, 37°C, wild-type
wild-type enzyme


organism: Salmonella enterica subsp. enterica serovar Typhimurium

substrate_name: L-cysteine

substrate: L-cysteine


proof_lines:
pH 7.4, 30°C, sDAPL
pH 7.5, 37°C


proof_lines: recombinant enzyme, 0.683 using Lathyrus sativus seed extracts as substrate


proof_lines:
pH 7.4, 30°C, sDAPL
pH 7.4, 30°C, untagged sDAPL
pH 7.5, 37°C


organism: Pseudomonas fluorescens


substrate_name: thioredoxin

substrate: thioredoxin


substrate_name: NADPH

assay_conditions_summary: pH 8; cofactor NADPH

substrate: NADPH


substrate_name: pyridoxal 5'-phosphate

substrate: pyridoxal 5'-phosphate


substrate_name: L-threonine

substrate: L-threonine


proof_lines: pH 7.5, 30°C, mutant enzyme G323D/F510L/R449C


proof_lines: pH 7.5, 30°C, mutant enzyme G323D/F510L/T344A/R449C


proof_lines: pH 7.5, 30°C, mutant enzyme G323D/F510L/T344A


organism: Legionella pneumophila

substrate_name: L-serine

proof_lines: pH 7.0, temperature not specified in the publication, mutant enzyme T290A


proof_lines: pH 7.0, temperature not specified in the publication, mutant enzyme T57A


proof_lines: pH 7.0, temperature not specified in the publication, mutant enzyme H19A


proof_lines: pH 7.0, temperature not specified in the publication, mutant enzyme S17A


proof_lines: pH 7.0, temperature not specified in the publication, mutant enzyme H124A/N126A


proof_lines: pH 7.0, temperature not specified in the publication, mutant enzyme T20A


proof_lines: pH 7.0, temperature not specified in the publication, mutant enzyme S53A


proof_lines: pH 7.0, temperature not specified in the publication, mutant enzyme E457A


proof_lines: pH 7.0, temperature not specified in the publication, mutant enzyme T446A


proof_lines: pH 7.0, temperature not specified in the publication, mutant enzyme S16A


enzyme_display_name: casbene synthase

organism: Ricinus communis

substrate_name: geranylgeranyl diphosphate

enzyme: casbene synthase

substrate: geranylgeranyl diphosphate


proof_lines: pH 8.5, 30°C, wild-type and mutant C519W


proof_lines: mutant V152A, pH 7.0, temperature not specified in the publication


proof_lines: mutant Y148A, pH 7.0, temperature not specified in the publication


proof_lines: mutant V152G, pH 7.0, temperature not specified in the publication


proof_lines: mutant Y148F, pH 7.0, temperature not specified in the publication


proof_lines: mutant F153A, pH 7.0, temperature not specified in the publication


proof_lines: wild-type, pH 7.0, temperature not specified in the publication


substrate_name: L-Ser

proof_lines: mutant C304A, pH 7.0, temperature not specified in the publication

substrate: L-Ser


proof_lines: mutant C221A, pH 7.0, temperature not specified in the publication


proof_lines: mutant C226A, pH 7.0, temperature not specified in the publication


proof_lines: mutant C183A, pH 7.0, temperature not specified in the publication


proof_lines: mutant C458A, pH 7.0, temperature not specified in the publication

proof_lines: pH 7.0, temperature not specified in the publication, mutant enzyme C458A


proof_lines: pH 7.0, temperature not specified in the publication


enzyme_display_name: exo-(1->4)-alpha-D-glucan lyase

organism: Gracilariopsis sp.

enzyme: exo-(1->4)-alpha-D-glucan lyase


substrate_name: p-Nitrophenyl-alpha-D-glucoside

substrate: p-Nitrophenyl-alpha-D-glucoside


substrate_name: o-Nitrophenyl-alpha-D-glucopyranoside

substrate: o-Nitrophenyl-alpha-D-glucopyranoside


substrate_name: Phenyl alpha-D-glucopyranoside

substrate: Phenyl alpha-D-glucopyranoside


substrate_name: alpha-D-Glucopyranosyl fluoride

substrate: alpha-D-Glucopyranosyl fluoride


column_label: Abstract reports L-THA dehydratase activity with K(m) = 0.54 mM.

raw_value_unit_evidence: Km raw_value=0.54 mM raw_unit=mM

row_label: Pseudomonas sp. T62 L-THA dehydratase / L-THA

table_label: PubMed XML abstract PMID 19193709


enzyme_display_name: 3-dehydroshikimate dehydratase

organism: Pseudomonas putida

proof_lines: pH 7.5, temperature not specified in the publication, recombinant mutant H168A

enzyme: 3-dehydroshikimate dehydratase


proof_lines: pH 7.5, temperature not specified in the publication, recombinant isolated N-terminal domain of the enzyme


proof_lines: pH 7.5, temperature not specified in the publication, recombinant mutant R207A


proof_lines: pH 7.5, temperature not specified in the publication, recombinant mutant E356A


proof_lines: pH 7.5, temperature not specified in the publication, recombinant mutant S206A


proof_lines: pH 7.5, temperature not specified in the publication, recombinant wild-type enzyme


organism: Homo sapiens

substrate: L-serine


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature N316A to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature C113S to reconstruct the assayed variant sequence.


sequence_variant_note: Mutation signature C2S/C4S/C128S/C269S/C309S could not be applied safely because the resolved sequence does not match the expected reference residue(s).

proof_lines: pH 8.0, 25°C, mutant enzyme C2S/C4S/C128S/C269S/C309S


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature D318A to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature D318N to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature E276Q to reconstruct the assayed variant sequence.


enzyme_display_name: pectate lyase

organism: Bacillus sp. (in: firmicutes)

substrate_name: polygalacturonic acid

enzyme: pectate lyase

substrate: polygalacturonic acid


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

proof_lines:
37°C, pH 8.0, wild-type enzyme
pH 8.0, 25°C, wild-type enzyme


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

proof_lines:
37°C, pH 8.0, mutant enzyme Q89M
pH 8.0, 25°C, mutant enzyme Q89M


substrate_name: D-serine

substrate: D-serine


organism: Saccharomyces cerevisiae


row_label: Table I, enzyme row Y203D, substrate D-serine

table_label: Table I. Kinetic parameters of the wild-type and Y203 mutants of Dsd1pa. (J. Biochem. 2014;156(3):173-180)


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P53095 and applied mutation signature Y203A to reconstruct the assayed variant sequence.

row_label: Table I, enzyme row Y203A, substrate D-serine


row_label: Table I, enzyme row Y203S, substrate D-serine


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


enzyme_display_name: methylglyoxal synthase

substrate_name: dihydroxyacetone phosphate

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

proof_lines: pH 7, 25°C, H98Q mutant, absence of phosphoglycolate

proof_lines: pH 7, 25°C, H98Q mutant, presence of phosphoglycolate

enzyme: methylglyoxal synthase

substrate: dihydroxyacetone phosphate


proof_lines: wild-type, Hill coefficient 1, pH 7.0, 60°C


enzyme_display_name: DNA-(apurinic or apyrimidinic site) lyase

substrate_name: synthetic oligonucleotide

substrate: synthetic oligonucleotide


enzyme: DNA-(apurinic or apyrimidinic site) lyase


enzyme_display_name: aspartate ammonia-lyase

organism: Bacillus sp. YM55-1

substrate_name: hydroxylamine

smiles: NO

assay_conditions_summary: pH 8; buffer pH 8

column_label: Table 2; row H2NOH; columns Km, kcat, kcat/Km.

table_label: Table 2

enzyme: aspartate ammonia-lyase

substrate: hydroxylamine


substrate_name: L-aspartate

assay_conditions_summary: pH 8.5; buffer 50 mM NaHPO4

proof_lines: his-tagged protein, pH 8.5, 25°C, in 50 mM NaHPO4 buffer

substrate: L-aspartate


smiles: N

column_label: Table 2; row NH3; columns Km, kcat, kcat/Km.


substrate_name: fumarate

column_label: Abstract reports AspB-catalyzed addition of ammonia to fumarate had k(cat) approximately 90 s(-1).

raw_value_unit_evidence: kcat raw_value=approximately 90 s^-1 raw_unit=s^-1

row_label: Bacillus sp. YM55-1 AspB / ammonia addition to fumarate

table_label: PubMed XML abstract PMID 18844200

substrate: fumarate


substrate_name: hydrazine

smiles: NN

column_label: Table 2; row H2NNH2; columns Km, kcat, kcat/Km.

substrate: hydrazine


enzyme_display_name: ent-kaurene synthase

organism: Arabidopsis thaliana

substrate_name: ent-copalyl diphosphate

proof_lines: mutant enzyme T527V/T528V, at pH 7.2 and 30°C

enzyme: ent-kaurene synthase

substrate: ent-copalyl diphosphate


organism: Bacillus sp. N16-5


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

proof_lines: mutant D189N, pH and temperature not specified in the publication


proof_lines: mutant D120N, pH and temperature not specified in the publication


enzyme_display_name: trichodiene synthase

organism: Fusarium sporotrichioides

substrate_name: farnesyl diphosphate

enzyme: trichodiene synthase

substrate: farnesyl diphosphate


organism: Fusarium verticillioides

substrate_name: digalacturonic acid

substrate: digalacturonic acid


substrate_name: Pectin

substrate: Pectin


substrate_name: trigalacturonic acid

substrate: trigalacturonic acid


substrate_name: Polygalacturonate

substrate: Polygalacturonate


enzyme_display_name: N-acetylmuramic acid 6-phosphate etherase

substrate_name: N-acetylmuramate 6-phosphate

assay_conditions_summary: pH 8; 303.15 K; buffer 60 mM Trien-HCl

proof_lines: mutant enzyme E83A, at 30°C in 60 mM Trien-HCl buffer (pH 8.0)

substrate: N-acetylmuramate 6-phosphate


proof_lines: mutant enzyme E114Q, at 30°C in 60 mM Trien-HCl buffer (pH 8.0)

enzyme: N-acetylmuramic acid 6-phosphate etherase


proof_lines: mutant enzyme D115N, at 30°C in 60 mM Trien-HCl buffer (pH 8.0)


proof_lines: wild type enzyme, at 30°C in 60 mM Trien-HCl buffer (pH 8.0)


enzyme_display_name: phenylalanine ammonia-lyase

organism: Mycosarcoma maydis

substrate_name: L-Phe

enzyme: phenylalanine ammonia-lyase

substrate: L-Phe


enzyme_display_name: UniProt P24481

organism: Petroselinum crispum

substrate_name: trans-cinnamate

enzyme: UniProt P24481

substrate: trans-cinnamate


enzyme_display_name: L-serine ammonia-lyase

substrate_name: L-Serine

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

proof_lines: pH and temperature not specified in the publication

enzyme: L-serine ammonia-lyase

substrate: L-Serine


substrate_name: threonine

proof_lines:
cSDH
cSDH +Pro
cSDH-hSDH

substrate: threonine


substrate_name: serine

substrate: serine


enzyme_display_name: (+)-delta-cadinene synthase

organism: Gossypium arboreum

substrate_name: (2E,6Z)-farnesyl diphosphate

enzyme: (+)-delta-cadinene synthase

substrate: (2E,6Z)-farnesyl diphosphate


organism: Helicobacter pylori

substrate_name: UDP-N-acetylglucosamine

sequence_source: UniProtKB O25511

sequence_variant_note: Resolved canonical sequence from UniProtKB O25511 and applied mutation signature Y141M to reconstruct the assayed variant sequence.

column_label: Table III columns Km (uM), kcat (min^-1), kcat/Km (mM^-1 min^-1), Conditions; row Y141M pH 10.

raw_value_unit_evidence: Table III row Y141M at pH 10 reports Km 251 +/- 5 uM; kcat 3.9 +/- 0.1 min^-1; kcat/Km 15.3 +/- 0.5 mM^-1 min^-1.

row_label: FlaA1 Y141M / UDP-GlcNAc pH 10

table_label: Table III: Kinetic parameters for FlaA1 WbpM and mutants

substrate: UDP-N-acetylglucosamine


sequence_variant_note: Resolved canonical sequence from UniProtKB O25511 and applied mutation signature H86A to reconstruct the assayed variant sequence.

column_label: Table III columns Km (uM), kcat (min^-1), kcat/Km (mM^-1 min^-1), Conditions; row H86A.

raw_value_unit_evidence: Table III row H86A reports Km 494 +/- 16 uM; kcat 4.6 +/- 0.2 min^-1; kcat/Km 9.2 +/- 0.0 mM^-1 min^-1.

row_label: FlaA1 H86A / UDP-GlcNAc


column_label: Table III columns Km (uM), kcat (min^-1), kcat/Km (mM^-1 min^-1), Conditions; row wild-type FlaA1.

raw_value_unit_evidence: Table III row wild-type FlaA1 reports Km 159 +/- 15 uM; kcat 5.7 +/- 0.5 min^-1; kcat/Km 35.9 +/- 6.7 mM^-1 min^-1.

row_label: Wild-type FlaA1 / UDP-GlcNAc


sequence_variant_note: Resolved canonical sequence from UniProtKB O25511 and applied mutation signature V266E to reconstruct the assayed variant sequence.

column_label: Table III columns Km (uM), kcat (min^-1), kcat/Km (mM^-1 min^-1), Conditions; row V266E.

raw_value_unit_evidence: Table III row V266E reports Km 151 +/- 9 uM; kcat 9.6 +/- 0.7 min^-1; kcat/Km 64.0 +/- 8.0 mM^-1 min^-1.

row_label: FlaA1 V266E / UDP-GlcNAc


assay_conditions_summary: pH 8.8; buffer 0.1 M Tris

column_label: Table 1 row 3',5'F2-L-Phe; column Km [mM] gives 0.159.

raw_value_unit_evidence: Table 1 row 3',5'F2-L-Phe, Km column [mM]: 0.159.

table_label: Table 1


column_label: Table 1 row 2'Cl-L-Phe; column Km [mM] gives 0.050.

raw_value_unit_evidence: Table 1 row 2'Cl-L-Phe, Km column [mM]: 0.050.


column_label: Table 1 row 4'Cl-L-Phe; column Km [mM] gives 0.045.

raw_value_unit_evidence: Table 1 row 4'Cl-L-Phe, Km column [mM]: 0.045.


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

column_label: Table 1 row beta-(5-pyrimidinyl)-D,L-Ala; column Km [mM] gives 4.2.

normalized_value_unit_evidence: Km 4.2 mM.

raw_value_unit_evidence: Table 1 row beta-(5-pyrimidinyl)-D,L-Ala, Km column [mM]: 4.2.


column_label: Table 1 row 2'F-L-Phe; column Km [mM] gives 0.065.

raw_value_unit_evidence: Table 1 row 2'F-L-Phe, Km column [mM]: 0.065.


substrate_name: L-Phenylalanine

column_label: Table 1 row L-Phe; column Km [mM] gives 0.033.

raw_value_unit_evidence: Table 1 row L-Phe, Km column [mM]: 0.033.

row_label: L-Phe

substrate: L-Phenylalanine


column_label: Table 1 row beta-(2-pyrimidinyl)-D,L-Ala; final metric cell reports (Ki = 7 mM), with Vmax/Vmax-Phe 0.00.

normalized_value_unit_evidence: Ki 7.0 mM.

raw_value_unit_evidence: Table 1 row beta-(2-pyrimidinyl)-D,L-Ala, final column note: Ki = 7 mM.


column_label: Table 1 row 2',3',4',5',6'F5-L-Phe; column Km [mM] gives 0.076.


organism: Rhodotorula graminis

substrate_name: (2E)-4-bromo-cinnamic acid

substrate: (2E)-4-bromo-cinnamic acid


substrate_name: (2E)-3-nitro-cinnamic acid

substrate: (2E)-3-nitro-cinnamic acid


substrate_name: (2E)-4-fluoro-cinnamic acid

substrate: (2E)-4-fluoro-cinnamic acid


substrate_name: (2E)-3-fluoro-cinnamic acid

substrate: (2E)-3-fluoro-cinnamic acid


substrate_name: (2E)-3-bromo-cinnamic acid

substrate: (2E)-3-bromo-cinnamic acid


enzyme_display_name: phenylalanine/tyrosine ammonia-lyase

organism: Sorghum bicolor

enzyme: phenylalanine/tyrosine ammonia-lyase


substrate_name: L-tyrosine

substrate: L-tyrosine


substrate_name: L-Dopa

substrate: L-Dopa


organism: Bambusa oldhamii


substrate_name: L-Tyr

substrate: L-Tyr


sequence_variant_note: Mutation signature F134H could not be applied safely because the resolved sequence does not match the expected reference residue(s).


organism: Nicotiana tabacum


column_label: Table 3: Kinetic parameters for purified recombinant PAL hetero- and homo-tetramers (Biochem. J. 2009, 424(2):233-242), PAL protein row 'PAL1-PAL2'; column 'V max (nkat mg^-1)' = 16.2; column 'K m (uM)' = 51.0; column 'k cat (s^-1)' = 1.26; column 'k cat /K m (s^-1 M^-1)' = 24680.

normalized_value_unit_evidence: kcat: printed Table 3 cell 1.26 s^-1; the printed unit is already s^(-1), no unit conversion applies; the paper value is 1.26 s^(-1); the exported value is 1.26 s^(-1). Km: printed Table 3 cell 51.0 uM; 1 uM is 0.001 mM, so 51.0 / 1000 = 0.051 mM; the paper value is 0.051 mM; the exported value is 0.051 mM. kcat/Km: printed Table 3 cell 24680 s^-1 M^-1; 1 s^-1 M^-1 is 0.001 s^-1 mM^-1, so 24680 / 1000 = 24.68 s^-1 mM^-1; the paper value is 24.68 s^(-1)*mM^(-1); the exported value is 24.705882352941178 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table 3, PAL protein row 'PAL1-PAL2': K m = 51.0 uM; k cat = 1.26 s^-1; printed k cat /K m = 24680 s^-1 M^-1.

row_label: Table 3, PAL protein row 'PAL1-PAL2'


sequence_variant_note: Resolved sequence already matches the mutant residue(s) after applying an inferred residue-numbering offset +13, so it is treated as a source-provided variant sequence.


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


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


substrate_name: L-phenylalanine

substrate: L-phenylalanine


enzyme_display_name: tyrosine ammonia-lyase

organism: Rhodotorula glutinis

proof_lines: mutant enzyme A11T/S106C/N170D/M227T/E518V, pH 8.5, 40°C

enzyme: tyrosine ammonia-lyase


proof_lines: mutant enzyme A11T/S106C/N170D/M227T/D542G, pH 8.5, 40°C


sequence_source: uniprot

sequence_variant_note: Resolved canonical sequence from uniprot and applied mutation signature H143S/Q144N with inferred residue-numbering offset +1 to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot and applied mutation signature H143N/Q144C with inferred residue-numbering offset +1 to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot and applied mutation signature H143N/Q144S with inferred residue-numbering offset +1 to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot and applied mutation signature H143C/Q144N with inferred residue-numbering offset +1 to reconstruct the assayed variant sequence.


enzyme_display_name: threonine ammonia-lyase

organism: Escherichia coli (strain K12)

substrate_name: L-serine (at 37 dregrees Celsius and at pH 7.8)

proof_lines: Serine and threonine desaminaes of Escherichia coli; activators for a cell-free enzyme

proof_lines: Escherichia coli serine/threonine deaminase family context

enzyme: threonine ammonia-lyase


organism: Chryseobacterium luteum sp. nov


substrate_name: Unknown

substrate: Unknown


organism: Rivularia sp. PCC 7116


organism: Rhodobacter capsulatus

substrate_name: L-Tyrosine

substrate: L-Tyrosine


organism: Buckleyzyma aurantiaca

proof_lines: in presence or absence of D-phenylalanine


organism: Cutaneotrichosporon cutaneum

proof_lines: pH 8.5, 37°C, Vmax: 0.82 microM/min, trial 3

proof_lines: pH 8.5, 37°C, Vmax: 1 microM/min, trial 2

proof_lines: pH 8.5, 37°C, Vmax: 0.2 microM/min, trial 1


proof_lines: pH 8.5, 37°C, Vmax: 7.2 microM/min, trial 3

proof_lines: pH 8.5, 37°C, Vmax: 1.3 microM/min, trial 1

proof_lines: pH 8.5, 37°C, Vmax: 4.7 microM/min, trial 2


organism: Dolichospermum flos-aquae


substrate_name: trans-cinnamate

substrate: trans-cinnamate


organism: Limnospira platensis


organism: Photorhabdus luminescens


enzyme_display_name: D-serine ammonia-lyase

organism: Saccharomyces cerevisiae

substrate_name: D-serine

proof_lines: pH not specified in the publication, 30°C, mutant H398A

enzyme: D-serine ammonia-lyase

substrate: D-serine


proof_lines: pH not specified in the publication, 30°C, mutant K57A


substrate_name: D-allo-threonine

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

substrate: D-allo-threonine


substrate_name: beta-Chloro-D-alanine

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

proof_lines: pH not specified in the publication, 30°C, wild-type Zn2+-depleted enzyme

substrate: beta-Chloro-D-alanine


proof_lines: pH not specified in the publication, 30°C, Zn2+-depleted mutant H398A

proof_lines: pH not specified in the publication, 30°C, native mutant H398A


proof_lines: pH not specified in the publication, 30°C, Zn2+-depleted mutant C400A

proof_lines: pH not specified in the publication, 30°C, native mutant C400A


substrate_name: L-Phe

substrate: L-Phe


organism: Petroselinum crispum

substrate_name: L-Phenylalanine

proof_lines:
pH 8.8, 30°C
30°C
isoenzyme PAL-4

substrate: L-Phenylalanine


proof_lines:
30°C
isoenzyme PAL-2
isoenzyme PAL-1


organism: Phanerodontia chrysosporium


organism: Streptomyces maritimus

column_label: Official ASM PDF Table 1; row EncP; columns Km (mM), kcat (s^-1), and kcat/Km (mM^-1 s^-1); raw central values 0.023, 4.79, and 208; normalized values 0.023 mM, 4.79 s^-1, and 208 s^-1 mM^-1; Table 1 footnote a says EncP values average two independent measurements.

normalized_value_unit_evidence: Central paper values normalize to Km 0.023 mM, kcat 4.79 s^-1, and kcat/Km 208 s^-1 mM^-1.

row_label: EncP

table_label: Official ASM article PDF Table 1 (journal page 4287; PDF page 2)


column_label: Official ASM PDF journal page 4288/PDF page 3; inhibition paragraph associated with Figure 4; row context wild-type EncP plus AIP; metric Ki; raw central value 1.91 uM; normalized value 0.00191 mM; Figure 4 conditions are 40 C, 100 mM Tris-HCl pH 8.0, 0.4 mM L-phenylalanine, increasing AIP.

normalized_value_unit_evidence: 1.91 uM converts exactly to 0.00191 mM, matching the current exported Ki 0.00191 mM.

raw_value_unit_evidence: The page 4288 inhibition paragraph reports EncP Ki 1.91 +/- 0.07 uM for AIP.

row_label: Wild-type EncP with 2-aminoindan-2-phosphonic acid (AIP)

table_label: Official ASM article inhibition prose adjacent to Figure 4 (journal page 4288; PDF page 3)


organism: Sphingobium sp. 20006FA

substrate_name: 2-amino-2-deoxy-D-gluconate 6-phosphate

proof_lines: mutant enzyme H163A, pH and temperature not specified in the publication

substrate: 2-amino-2-deoxy-D-gluconate 6-phosphate


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


organism: Alternaria sp.


organism: Sporobolomyces pararoseus


organism: Salmonella enterica subsp. enterica serovar Typhimurium


organism: Ephedra sinica

proof_lines:
pH 8.5, 37°C, isozyme PAL3
pH 8.5, 37°C, isozyme PAL2
pH 8.5, 37°C, isozyme PAL4


organism: Rhodotorula glutinis

proof_lines:
pH 8, 40°C
pH 8.8, 30°C, soluble enzyme
pH 8.8, 30°C, encapsulated enzyme


organism: Annona cherimola

proof_lines: enzyme from fruit ripened at low temperature, first Km value using low substrate concentrations, pH 8.8, 30°C

proof_lines: enzyme from fruit ripened at room temperature, pH 8.8, 30°C

proof_lines: enzyme from fruit ripened in 20% CO2 atmosphere, first Km value using low substrate concentrations, pH 8.8, 30°C


organism: Sinapis alba


organism: Sporobolomyces roseus


organism: Rhodotorula texensis


organism: Helianthus annuus


organism: Streptomyces verticillatus


organism: Ustilago hordei


organism: Pinus banksiana


enzyme_display_name: L-lysine cyclodeaminase

organism: Streptomyces pristinaespiralis

substrate_name: L-lysine

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

assay_conditions_summary: pH 8; 310.15 K; buffer 100 mM potassium phosphate

proof_lines: in 100 mM potassium phosphate buffer, pH 8.0 containing 10% (v/v) glycerol, at 37°C

enzyme: L-lysine cyclodeaminase

substrate: L-lysine


organism: Spirulina

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


organism: Mus musculus

substrate_name: L-serine O-sulfate

assay_conditions_summary: pH 8; 310.15 K; cofactor ATP

proof_lines: pH 8.0, 37°C, presence of 1 mM ATP, elimination reaction

substrate: L-serine O-sulfate


substrate_name: beta-chloro-L-alanine

substrate: beta-chloro-L-alanine


proof_lines: pH 8.0, 37°C, presence of 1 mM ATP, racemization reaction


substrate_name: L-threonine

substrate: L-threonine


organism: Trichormus variabilis

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


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature E75L with inferred residue-numbering offset -3 to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature E75A with inferred residue-numbering offset -3 to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature E75Q with inferred residue-numbering offset -3 to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature L108G to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature L108A to reconstruct the assayed variant sequence.


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

proof_lines: mutant lacking 21 N-terminal amino acids, pH 8.5, 37°C


organism: Plenodomus lingam

substrate_name: Phe

substrate: Phe


organism: Rhodobacter sphaeroides

sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature H89F to reconstruct the assayed variant sequence.

proof_lines: kcat is 4.32 sec(-1) for L-Tyr. kcat is 13.1 sec(-1) for L-Phe.


organism: Zea mays

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

proof_lines: kcat is 10.6 sec(-1) with L-phenylalanine as substrate and 0.92 sec(-1) with L-tyrosine as substrate (at pH 8.7).


sequence_variant_note: Resolved canonical sequence from multiple and applied mutation signature H89F to reconstruct the assayed variant sequence.


organism: Anabaena variabilis

proof_lines:
pH 8.3, 30°C
Raw SKiD Env: Temp=-----, pH=-----
Raw SKiD Env: Temp=30°C, pH=8.3

source_databases_merged: sabio_rk brenda skid uniprot


organism: Solanum lycopersicum

proof_lines:
enzyme form PAL-II
enzyme form PAL-III
enzyme form PAL-I


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature Q292C/C565S to reconstruct the assayed variant sequence.

proof_lines: mutant Q292C/C565S, pH and temperature not specified in the publication


substrate_name: phenylalanine

sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_unique and applied mutation signature C503S/C565S to reconstruct the assayed variant sequence.

substrate: phenylalanine


organism: Taxus canadensis

substrate_name: L-phenylalanine

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


organism: Delftia sp. HT23

substrate_name: L-serine

proof_lines: kcat is 10.93 sec(-1) for D-THA. kcat is 3.03 sec(-1) for L-THA. kcat is 8.68 sec(-1) for L-EHA. kcat is 0.89 sec(-1) for D-serine.

source_databases_merged: brenda skid uniprot

substrate: L-serine


organism: Arabidopsis thaliana

substrate_name: Unknown


organism: Cistanche deserticola


organism: Taxus chinensis


organism: Fritillaria unibracteata

proof_lines: kcat is 102.4 min(-1) with L-phenylalanine as substrate (PubMed:35643154). kcat is 0.103 min(-1) with L-tyrosine as substrate (PubMed:35643154).


organism: Delftia sp. (strain HT23)

substrate_name: D-THA

substrate: D-THA


organism: Streptomyces hygroscopicus

substrate_name: L-ornithine

assay_conditions_summary: pH 8; 303.15 K; cofactor NAD+

proof_lines: 0.1 mM NAD+, in 100 mM HEPES (pH 8.0), at 30°C

substrate: L-ornithine


assay_conditions_summary: pH 8; cofactor NAD+

column_label: PMID 16536560 Results prose/Fig. 4C, RapL with L-lysine: Km = 46 +/- 4 uM, kcat = 0.61 +/- 0.02 min^-1, kcat/Km = 13 +/- 1 mM^-1 min^-1.

raw_value_unit_evidence: Results prose reports Km = 46 +/- 4 uM, kcat = 0.61 +/- 0.02 min^-1, and kcat/Km = 13 +/- 1 mM^-1 min^-1 for RapL with L-lysine.

row_label: RapL / L-lysine

table_label: Results prose and Fig. 4C


substrate_name: (2E)-3-phenylprop-2-enoic acid

proof_lines:
broad substrate specificity
AvPAL

source_databases_merged: brenda skid

substrate: (2E)-3-phenylprop-2-enoic acid


substrate_name: (2E)-3-(pyridin-3-yl)prop-2-enoic acid

substrate: (2E)-3-(pyridin-3-yl)prop-2-enoic acid


proof_lines:
pH 8.3, 30°C
Raw SKiD Env: Temp=30°C, pH=8.3


organism: Streptomyces venezuelae

substrate_name: dTDP-viosamine (at pH 8 and 25 degrees Celsius)

proof_lines: kcat is 0.017 sec(-1) for ammonia-lyase activity with dTDP-viosamine as substrate (at pH 8 and 25 degrees Celsius).


substrate_name: (2S)-2-amino-3-phenylpropanoic acid

substrate: (2S)-2-amino-3-phenylpropanoic acid


proof_lines:
broad substrate specificity
non-natural substrates
Av PAL


substrate_name: L-Phenylalanine


organism: Petroselinum crispum


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature Y351F to reconstruct the assayed variant sequence.


substrate_name: (2E)-3-(pyridin-4-yl)prop-2-enoic acid

substrate: (2E)-3-(pyridin-4-yl)prop-2-enoic acid


column_label: Primary paper Table 1 row 1e / 4-NO2-C6H4 has columns kcat = 1.08, KM = 0.23, and kcat/KM = 4.70.

normalized_value_unit_evidence: kcat normalized 1.08 s^-1; KM normalized 0.23 mM; paper kcat/KM cell normalized 4.70 s^-1 mM^-1; CatLog value is the derived ratio 1.08/0.23 = 4.695652173913044 s^-1 mM^-1.

raw_value_unit_evidence: Table 1 row 1e / 4-NO2-C6H4 reports kcat 1.08 s^-1; KM 0.23 mM; kcat/KM 4.70 s^-1 mM^-1.

table_label: Table 1: Kinetic constants for the deamination of amino acids 1a-i catalysed by AvPAL


column_label: Primary paper Table 1 row 1c / 3-F-C6H4 has columns kcat = 1.10, KM = 0.75, and kcat/KM = 1.47.

normalized_value_unit_evidence: kcat normalized 1.10 s^-1; KM normalized 0.75 mM; paper kcat/KM cell normalized 1.47 s^-1 mM^-1; CatLog value is the derived ratio 1.10/0.75 = 1.4666666666666668 s^-1 mM^-1.

raw_value_unit_evidence: Table 1 row 1c / 3-F-C6H4 reports kcat 1.10 s^-1; KM 0.75 mM; kcat/KM 1.47 s^-1 mM^-1.


substrate_name: (2E)-3-(4-nitrophenyl)prop-2-enoic acid

substrate: (2E)-3-(4-nitrophenyl)prop-2-enoic acid


column_label: Primary paper Table 1 row 1f / 3-OH-C6H4 reports kcat = 0.89, KM = 1.11, and kcat/KM = 0.80.

normalized_value_unit_evidence: kcat normalized 0.89 s^-1; KM normalized 1.11 mM; table kcat/KM normalized 0.80 s^-1 mM^-1; CatLog stores the derived ratio 0.89/1.11 = 0.8018018018018017 s^-1 mM^-1.


column_label: Primary paper Table 1 row 1b / 4-F-C6H4 has columns kcat = 1.06, KM = 0.56, and kcat/KM = 1.89.

normalized_value_unit_evidence: kcat normalized 1.06 s^-1; KM normalized 0.56 mM; paper kcat/KM cell normalized 1.89 s^-1 mM^-1; CatLog value is the derived ratio 1.06/0.56 = 1.8928571428571428 s^-1 mM^-1.

raw_value_unit_evidence: Table 1 row 1b / 4-F-C6H4 reports kcat 1.06 s^-1; KM 0.56 mM; kcat/KM 1.89 s^-1 mM^-1.


column_label: Primary paper Table 1 row 1d / 4-CF3-C6H4 reports kcat = 0.82, KM = 1.05, and kcat/KM = 0.78.

normalized_value_unit_evidence: kcat normalized 0.82 s^-1; KM normalized 1.05 mM; table kcat/KM normalized 0.78 s^-1 mM^-1; CatLog stores the derived ratio 0.82/1.05 = 0.7809523809523808 s^-1 mM^-1.


organism: Kitagawia praeruptora

proof_lines: pH and temperature not specified in the publication

substrate: L-phenylalanine


organism: Rhizoctonia solani

substrate_name: L-Phe

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

proof_lines:
at low substrate concentrations
at high substrate concentrations

substrate: L-Phe


substrate_name: L-tyrosine

substrate: L-tyrosine


organism: Nostoc punctiforme

substrate: L-Phenylalanine


organism: Nicotiana tabacum

proof_lines:
tobacco PAL1
all four tobacco PAL proteins
Km 36-60 muM


proof_lines:
tobacco PAL2
mixed measurement-tuple risk
all four tobacco PAL proteins


column_label: Table 2: Kinetic parameters for purified recombinant PAL proteins from tobacco (Biochem. J. 2009, 424(2):233-242), PAL protein row 'PAL3'; column 'V max (nkat mg^-1)' = 9.8; column 'K m (uM)' = 36.4; column 'k cat (s^-1)' = 0.78; column 'k cat /K m (s^-1 M^-1)' = 21100.

normalized_value_unit_evidence: kcat: printed Table 2 cell 0.78 s^-1; the printed unit is already s^(-1), no unit conversion applies; the paper value is 0.78 s^(-1); the exported value is 0.78 s^(-1). Km: printed Table 2 cell 36.4 uM; 1 uM is 0.001 mM, so 36.4 / 1000 = 0.0364 mM; the paper value is 0.0364 mM; the exported value is 0.036399999999999995 mM. kcat/Km: printed Table 2 cell 21100 s^-1 M^-1; 1 s^-1 M^-1 is 0.001 s^-1 mM^-1, so 21100 / 1000 = 21.1 s^-1 mM^-1; the paper value is 21.1 s^(-1)*mM^(-1); the exported value is 21.42857142857143 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table 2, PAL protein row 'PAL3': K m = 36.4 uM; k cat = 0.78 s^-1; printed k cat /K m = 21100 s^-1 M^-1.

row_label: Table 2, PAL protein row 'PAL3'


column_label: Table 2: Kinetic parameters for purified recombinant PAL proteins from tobacco (Biochem. J. 2009, 424(2):233-242), PAL protein row 'PAL4'; column 'V max (nkat mg^-1)' = 19.6; column 'K m (uM)' = 52.4; column 'k cat (s^-1)' = 1.53; column 'k cat /K m (s^-1 M^-1)' = 29090.

normalized_value_unit_evidence: kcat: printed Table 2 cell 1.53 s^-1; the printed unit is already s^(-1), no unit conversion applies; the paper value is 1.53 s^(-1); the exported value is 1.53 s^(-1). Km: printed Table 2 cell 52.4 uM; 1 uM is 0.001 mM, so 52.4 / 1000 = 0.052399999999999995 mM; the paper value is 0.052399999999999995 mM; the exported value is 0.052 mM. kcat/Km: printed Table 2 cell 29090 s^-1 M^-1; 1 s^-1 M^-1 is 0.001 s^-1 mM^-1, so 29090 / 1000 = 29.09 s^-1 mM^-1; the paper value is 29.09 s^(-1)*mM^(-1); the exported value is 29.423076923076923 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table 2, PAL protein row 'PAL4': K m = 52.4 uM; k cat = 1.53 s^-1; printed k cat /K m = 29090 s^-1 M^-1.

row_label: Table 2, PAL protein row 'PAL4'


column_label: Table 3: Kinetic parameters for purified recombinant PAL hetero- and homo-tetramers (Biochem. J. 2009, 424(2):233-242), PAL protein row 'PAL1-His'; column 'V max (nkat mg^-1)' = 14.5; column 'K m (uM)' = 56.2; column 'k cat (s^-1)' = 1.12; column 'k cat /K m (s^-1 M^-1)' = 20000.

normalized_value_unit_evidence: kcat: printed Table 3 cell 1.12 s^-1; the printed unit is already s^(-1), no unit conversion applies; the paper value is 1.12 s^(-1); the exported value is 1.12 s^(-1). Km: printed Table 3 cell 56.2 uM; 1 uM is 0.001 mM, so 56.2 / 1000 = 0.0562 mM; the paper value is 0.0562 mM; the exported value is 0.06 mM. kcat/Km: printed Table 3 cell 20000 s^-1 M^-1; 1 s^-1 M^-1 is 0.001 s^-1 mM^-1, so 20000 / 1000 = 20.0 s^-1 mM^-1; the paper value is 20.0 s^(-1)*mM^(-1); the exported value is 18.666666666666668 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table 3, PAL protein row 'PAL1-His': K m = 56.2 uM; k cat = 1.12 s^-1; printed k cat /K m = 20000 s^-1 M^-1.

row_label: Table 3, PAL protein row 'PAL1-His'


column_label: Table 3: Kinetic parameters for purified recombinant PAL hetero- and homo-tetramers (Biochem. J. 2009, 424(2):233-242), PAL protein row 'PAL2-His'; column 'V max (nkat mg^-1)' = 17.4; column 'K m (uM)' = 46.6; column 'k cat (s^-1)' = 1.35; column 'k cat /K m (s^-1 M^-1)' = 28940.

normalized_value_unit_evidence: kcat: printed Table 3 cell 1.35 s^-1; the printed unit is already s^(-1), no unit conversion applies; the paper value is 1.35 s^(-1); the exported value is 1.35 s^(-1). Km: printed Table 3 cell 46.6 uM; 1 uM is 0.001 mM, so 46.6 / 1000 = 0.0466 mM; the paper value is 0.0466 mM; the exported value is 0.047 mM. kcat/Km: printed Table 3 cell 28940 s^-1 M^-1; 1 s^-1 M^-1 is 0.001 s^-1 mM^-1, so 28940 / 1000 = 28.94 s^-1 mM^-1; the paper value is 28.94 s^(-1)*mM^(-1); the exported value is 28.72340425531915 s^(-1)*mM^(-1).

raw_value_unit_evidence: Table 3, PAL protein row 'PAL2-His': K m = 46.6 uM; k cat = 1.35 s^-1; printed k cat /K m = 28940 s^-1 M^-1.

row_label: Table 3, PAL protein row 'PAL2-His'


normalized_value_unit_evidence: kcat: printed Table 2 cell 0.78 s^-1; the printed unit is already s^(-1), no unit conversion applies; the paper value is 0.78 s^(-1); the exported value is 0.78 s^(-1). Km: printed Table 2 cell 36.4 uM; 1 uM is 0.001 mM, so 36.4 / 1000 = 0.0364 mM; the paper value is 0.0364 mM; the exported value is 0.036 mM. kcat/Km: printed Table 2 cell 21100 s^-1 M^-1; 1 s^-1 M^-1 is 0.001 s^-1 mM^-1, so 21100 / 1000 = 21.1 s^-1 mM^-1; the paper value is 21.1 s^(-1)*mM^(-1); the exported value is 21.666666666666668 s^(-1)*mM^(-1).

table_label: Table 2: Kinetic parameters for purified recombinant PAL proteins from tobacco (Biochem. J. 2009, 424(2):233-242)


organism: Rhodotorula toruloides

proof_lines:
pH 8.8, 30°C
Raw SKiD Env: Temp=30°C, pH=8.8


substrate_name: trans-cinnamate

proof_lines:
pH 10, 30°C
Raw SKiD Env: Temp=30°C, pH=10

substrate: trans-cinnamate


organism: Rhodotorula glutinis

sequence_variant_note: Mutation signature A11T/S106C/N170D/M227T/D542G could not be applied safely because the resolved sequence does not match the expected reference residue(s).

proof_lines:
tyrosine ammonia-lyase
Rhodotorula glutinis
MT-S9N/-A11T/-E518V


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature A11T/S106C/N170D/M227T/E518V to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature S9N/A125V with inferred residue-numbering offset +34 to reconstruct the assayed variant sequence.


proof_lines:
wild-type
Rhodotorula glutinis
tyrosine ammonia-lyase


proof_lines: isoform PAL4, at 30°C in 50 mM Tris/HCl, pH 8.5


organism: Rhodobacter sphaeroides

sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:Q3IWB0 and applied mutation signature H89A to reconstruct the assayed variant sequence.

column_label: Table 2. Steady-State Kinetic Parameters of TAL Mutants with Tyrosine and Phenylalanine as Substrates.; row H89A / Phenylalanine; Km column Km [uM] raw 4099 +/- 652; kcat column kcat [s^-1] raw 0.18 +/- 0.02; kcat/Km column kcat/Km [M^-1 s^-1] raw 43.9

normalized_value_unit_evidence: Km normalized_value=4.099 normalized_unit=mM; kcat normalized_value=0.18 normalized_unit=s^-1; kcat/Km normalized_value=0.043913149548670406 normalized_unit=s^-1*mM^-1

raw_value_unit_evidence: Km raw_value=4099 +/- 652 raw_unit=uM; kcat raw_value=0.18 +/- 0.02 raw_unit=s^-1; kcat/Km raw_value=43.9 raw_unit=M^-1 s^-1

row_label: H89A / Phenylalanine


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:Q3IWB0 and applied mutation signature H89F with inferred residue-numbering offset -1 to reconstruct the assayed variant sequence.

column_label: Table 2. Steady-State Kinetic Parameters of TAL Mutants with Tyrosine and Phenylalanine as Substrates.; row H89F / Phenylalanine; Km column Km [uM] raw 269.1 +/- 42.0; kcat column kcat [s^-1] raw 24.0 +/- 0.089; kcat/Km column kcat/Km [M^-1 s^-1] raw 8.9 x 10^4

normalized_value_unit_evidence: Km normalized_value=0.269 normalized_unit=mM; kcat normalized_value=24.0 normalized_unit=s^-1; kcat/Km normalized_value=89.21933085501858 normalized_unit=s^-1*mM^-1

raw_value_unit_evidence: Km raw_value=269.1 +/- 42.0 raw_unit=uM; kcat raw_value=24.0 +/- 0.089 raw_unit=s^-1; kcat/Km raw_value=8.9 x 10^4 raw_unit=M^-1 s^-1

row_label: H89F / Phenylalanine


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:Q3IWB0 and applied mutation signature H89N to reconstruct the assayed variant sequence.

column_label: Table 2. Steady-State Kinetic Parameters of TAL Mutants with Tyrosine and Phenylalanine as Substrates.; row H89N / Phenylalanine; Km column Km [uM] raw 3456 +/- 323; kcat column kcat [s^-1] raw 1.03 +/- 0.07; kcat/Km column kcat/Km [M^-1 s^-1] raw 298

normalized_value_unit_evidence: Km normalized_value=3.456 normalized_unit=mM; kcat normalized_value=1.03 normalized_unit=s^-1; kcat/Km normalized_value=0.29803240740740744 normalized_unit=s^-1*mM^-1

raw_value_unit_evidence: Km raw_value=3456 +/- 323 raw_unit=uM; kcat raw_value=1.03 +/- 0.07 raw_unit=s^-1; kcat/Km raw_value=298 raw_unit=M^-1 s^-1

row_label: H89N / Phenylalanine


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:Q3IWB0 and applied mutation signature H89Q with inferred residue-numbering offset -1 to reconstruct the assayed variant sequence.

column_label: Table 2. Steady-State Kinetic Parameters of TAL Mutants with Tyrosine and Phenylalanine as Substrates.; row H89Q / Phenylalanine; Km column Km [uM] raw 789.2 +/- 87.8; kcat column kcat [s^-1] raw 26.2 +/- 2.0; kcat/Km column kcat/Km [M^-1 s^-1] raw 3.3 x 10^4

normalized_value_unit_evidence: Km normalized_value=0.789 normalized_unit=mM; kcat normalized_value=26.2 normalized_unit=s^-1; kcat/Km normalized_value=33.20659062103929 normalized_unit=s^-1*mM^-1

raw_value_unit_evidence: Km raw_value=789.2 +/- 87.8 raw_unit=uM; kcat raw_value=26.2 +/- 2.0 raw_unit=s^-1; kcat/Km raw_value=3.3 x 10^4 raw_unit=M^-1 s^-1

row_label: H89Q / Phenylalanine


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:Q3IWB0 and applied mutation signature H89W to reconstruct the assayed variant sequence.

column_label: Table 2. Steady-State Kinetic Parameters of TAL Mutants with Tyrosine and Phenylalanine as Substrates.; row H89W / Phenylalanine; Km column Km [uM] raw 3777 +/- 143; kcat column kcat [s^-1] raw 0.19 +/- 0.01; kcat/Km column kcat/Km [M^-1 s^-1] raw 50.3

normalized_value_unit_evidence: Km normalized_value=3.777 normalized_unit=mM; kcat normalized_value=0.19 normalized_unit=s^-1; kcat/Km normalized_value=0.05030447445062219 normalized_unit=s^-1*mM^-1

raw_value_unit_evidence: Km raw_value=3777 +/- 143 raw_unit=uM; kcat raw_value=0.19 +/- 0.01 raw_unit=s^-1; kcat/Km raw_value=50.3 raw_unit=M^-1 s^-1

row_label: H89W / Phenylalanine


column_label: Table 1. Steady-State Kinetic Parameters of TALs and PALs Investigated in This Study (Underlined) with Tyrosine and Phenylalanine as Substrates.; row Rba. sphaeroides TAL / Phenylalanine; Km column Km [uM] raw 5204 +/- 1441; kcat column kcat [s^-1] raw 2.1 +/- 0.45; kcat/Km column kcat/Km [M^-1 s^-1] raw 403

normalized_value_unit_evidence: Km normalized_value=5.204 normalized_unit=mM; kcat normalized_value=2.1 normalized_unit=s^-1; kcat/Km normalized_value=0.4035357417371253 normalized_unit=s^-1*mM^-1

raw_value_unit_evidence: Km raw_value=5204 +/- 1441 raw_unit=uM; kcat raw_value=2.1 +/- 0.45 raw_unit=s^-1; kcat/Km raw_value=403 raw_unit=M^-1 s^-1

row_label: Rba. sphaeroides TAL / Phenylalanine


column_label: Table 2 columns K_m with L-phenylalanine and K_m with L-tyrosine; PAL-2 row contains the 16.9 uM L-phenylalanine cell

raw_value_unit_evidence: Table 2 PAL-2 row reports K_m with L-phenylalanine 16.9 +/- 0.5 uM


column_label: Table 2 columns K_m with L-phenylalanine and K_m with L-tyrosine; PAL-3 row contains the 24.5 uM L-phenylalanine cell

raw_value_unit_evidence: Table 2 PAL-3 row reports K_m with L-phenylalanine 24.5 +/- 0.7 uM


substrate_name: L-Tyrosine

substrate: L-Tyrosine


column_label: Table 2 columns K_m with L-phenylalanine and K_m with L-tyrosine; PAL-2 row contains the 2.3 mM L-tyrosine cell

raw_value_unit_evidence: Table 2 PAL-2 row reports K_m with L-tyrosine 2.3 +/- 0.2 mM


column_label: Table 2 columns K_m with L-phenylalanine and K_m with L-tyrosine; PAL-3 row contains the 7.8 mM L-tyrosine cell

raw_value_unit_evidence: Table 2 PAL-3 row reports K_m with L-tyrosine 7.8 +/- 1.2 mM


column_label: Table 2. Steady-State Kinetic Parameters of TAL Mutants with Tyrosine and Phenylalanine as Substrates.; row H89F / Tyrosine; Km column Km [uM] raw 1541 +/- 845.1; kcat column kcat [s^-1] raw 0.0087 +/- 9.2 x 10^-4; kcat/Km column kcat/Km [M^-1 s^-1] raw 5.6

normalized_value_unit_evidence: Km normalized_value=1.541 normalized_unit=mM; kcat normalized_value=0.009 normalized_unit=s^-1; kcat/Km normalized_value=0.005840363400389357 normalized_unit=s^-1*mM^-1

raw_value_unit_evidence: Km raw_value=1541 +/- 845.1 raw_unit=uM; kcat raw_value=0.0087 +/- 9.2 x 10^-4 raw_unit=s^-1; kcat/Km raw_value=5.6 raw_unit=M^-1 s^-1

row_label: H89F / Tyrosine


column_label: Table 2. Steady-State Kinetic Parameters of TAL Mutants with Tyrosine and Phenylalanine as Substrates.; row H89N / Tyrosine; Km column Km [uM] raw 1399 +/- 271.7; kcat column kcat [s^-1] raw 0.03 +/- 0.01; kcat/Km column kcat/Km [M^-1 s^-1] raw 21.4

normalized_value_unit_evidence: Km normalized_value=1.399 normalized_unit=mM; kcat normalized_value=0.03 normalized_unit=s^-1; kcat/Km normalized_value=0.02144388849177984 normalized_unit=s^-1*mM^-1

raw_value_unit_evidence: Km raw_value=1399 +/- 271.7 raw_unit=uM; kcat raw_value=0.03 +/- 0.01 raw_unit=s^-1; kcat/Km raw_value=21.4 raw_unit=M^-1 s^-1

row_label: H89N / Tyrosine


column_label: Table 2. Steady-State Kinetic Parameters of TAL Mutants with Tyrosine and Phenylalanine as Substrates.; row H89Q / Tyrosine; Km column Km [uM] raw 1488 +/- 143.4; kcat column kcat [s^-1] raw 2.34 +/- 0.05; kcat/Km column kcat/Km [M^-1 s^-1] raw 1572

normalized_value_unit_evidence: Km normalized_value=1.488 normalized_unit=mM; kcat normalized_value=2.34 normalized_unit=s^-1; kcat/Km normalized_value=1.5725806451612903 normalized_unit=s^-1*mM^-1

raw_value_unit_evidence: Km raw_value=1488 +/- 143.4 raw_unit=uM; kcat raw_value=2.34 +/- 0.05 raw_unit=s^-1; kcat/Km raw_value=1572 raw_unit=M^-1 s^-1

row_label: H89Q / Tyrosine


column_label: OUP full text Table II row L-THA reports kcat (s^-1)=3.03, Km (mM)=6.16, and kcat/Km=0.49.

normalized_value_unit_evidence: kcat normalized_value=3.03 normalized_unit=s^-1; Km normalized_value=6.16 normalized_unit=mM; kcat/Km table_normalized_value=0.49 normalized_unit=s^-1 mM^-1; derived ratio=3.03/6.16=0.49188311688311687.

raw_value_unit_evidence: Table II row L-THA: kcat raw_value=3.03 raw_unit=s^-1; Km raw_value=6.16 raw_unit=mM; kcat/Km raw_value=0.49 raw_unit=s^-1 mM^-1.

row_label: L-THA

table_label: Table II: Kinetic parameters of D-THA DH


substrate_name: D-serine

proof_lines:
Delftia sp. HT23
D-serine
D-threo-3-hydroxyaspartate dehydratase

substrate: D-serine


column_label: OUP full text Table II row L-EHA reports kcat (s^-1)=8.68, Km (mM)=0.16, and kcat/Km=54.25.

normalized_value_unit_evidence: kcat normalized_value=8.68 normalized_unit=s^-1; Km normalized_value=0.16 normalized_unit=mM; kcat/Km normalized_value=54.25 normalized_unit=s^-1 mM^-1.

raw_value_unit_evidence: Table II row L-EHA: kcat raw_value=8.68 raw_unit=s^-1; Km raw_value=0.16 raw_unit=mM; kcat/Km raw_value=54.25 raw_unit=s^-1 mM^-1.

row_label: L-EHA


column_label: OUP full text Table II row L-Serine reports kcat (s^-1)=0.18, Km (mM)=38.70, and kcat/Km=0.0047.

normalized_value_unit_evidence: kcat normalized_value=0.18 normalized_unit=s^-1; Km normalized_value=38.7 normalized_unit=mM; kcat/Km table_normalized_value=0.0047 normalized_unit=s^-1 mM^-1; derived ratio=0.18/38.70=0.0046511627906976735.

raw_value_unit_evidence: Table II row L-Serine: kcat raw_value=0.18 raw_unit=s^-1; Km raw_value=38.70 raw_unit=mM; kcat/Km raw_value=0.0047 raw_unit=s^-1 mM^-1.

row_label: L-Serine


sequence_variant_note: Resolved canonical sequence from uniprot_rest_accession:P35510 and applied mutation signature F144H with inferred residue-numbering offset +6 to reconstruct the assayed variant sequence.

column_label: Table 1. Steady-State Kinetic Parameters of TALs and PALs Investigated in This Study (Underlined) with Tyrosine and Phenylalanine as Substrates.; row A. thaliana PAL1 F144H / Tyrosine; Km column Km [uM] raw 532.6 +/- 27.7; kcat column kcat [s^-1] raw 0.75 +/- 0.15; kcat/Km column kcat/Km [M^-1 s^-1] raw 1410

normalized_value_unit_evidence: Km normalized_value=0.533 normalized_unit=mM; kcat normalized_value=0.75 normalized_unit=s^-1; kcat/Km normalized_value=1.4071294559099436 normalized_unit=s^-1*mM^-1

raw_value_unit_evidence: Km raw_value=532.6 +/- 27.7 raw_unit=uM; kcat raw_value=0.75 +/- 0.15 raw_unit=s^-1; kcat/Km raw_value=1410 raw_unit=M^-1 s^-1

row_label: A. thaliana PAL1 F144H / Tyrosine


column_label: Table 1. Steady-State Kinetic Parameters of TALs and PALs Investigated in This Study (Underlined) with Tyrosine and Phenylalanine as Substrates.; row A. thaliana PAL1 / Tyrosine; Km column Km [uM] raw 1049 +/- 67.2; kcat column kcat [s^-1] raw 0.084 +/- 0.0038; kcat/Km column kcat/Km [M^-1 s^-1] raw 80

normalized_value_unit_evidence: Km normalized_value=1.049 normalized_unit=mM; kcat normalized_value=0.084 normalized_unit=s^-1; kcat/Km normalized_value=0.08007626310772165 normalized_unit=s^-1*mM^-1

raw_value_unit_evidence: Km raw_value=1049 +/- 67.2 raw_unit=uM; kcat raw_value=0.084 +/- 0.0038 raw_unit=s^-1; kcat/Km raw_value=80 raw_unit=M^-1 s^-1

row_label: A. thaliana PAL1 / Tyrosine


organism: Cupriavidus metallidurans

assay_conditions_summary: pH 8.8; buffer PreScission Protease) assayed in Tris

column_label: Table 1 (PDF page 2), row 'CmTAL | wt': Km cell 348 in the KM [uM] column (unit header transcribed as '[mm] (l-Tyr!b-Tyr) (l-Tyr!pHCA)'), kcat cell 0.011 in the kcat [s^-1] (l-Tyr!pHCA) column. No kcat/Km column exists in Table 1; the reported kcat/Km is the exact quotient of those two cells.

normalized_value_unit_evidence: Unit normalization for Table 1 row CmTAL | wt: the Km unit header glyphs are drawn in the paper's Greek and small-caps fonts, so the printed Km unit is micromolar and 348 uM normalizes to 0.348 mM; the turnover cell is already in s^(-1). metric: km; raw value: 348; raw unit: uM; normalized value: 0.348; normalized unit: mM; metric: kcat; raw value: 0.011; raw unit: s^(-1); normalized value: 0.011; normalized unit: s^(-1); metric: kcat_over_km; raw value: 0.011 / 348; raw unit: s^(-1) / uM; normalized value: 0.031609195402298854; normalized unit: s^(-1)*mM^(-1);

raw_value_unit_evidence: Table 1. Kinetic parameters for enzymes characterized in this study and comparison to the known aminomutase SgcC4. Row CmTAL | wt of Table 1, PDF page 2. The Km cell is taken from the row's single Km column, header transcribed as '[mm] (l-Tyr!b-Tyr) (l-Tyr!pHCA)', and the turnover cell from the reaction column that matches this row's EC 4.3.1.23 / tyrosine ammonia-lyase; both cells sit in the same Table 1 row. Table 1 prints no catalytic-efficiency column, so the ratio below is the exact quotient of those two printed cells of this same row and is not itself a printed cell. metric: km; raw value: 348; raw unit: uM; normalized value: 0.348; normalized unit: mM; metric: kcat; raw value: 0.011; raw unit: s^(-1); normalized value: 0.011; normalized unit: s^(-1); metric: kcat_over_km; raw value: 0.011 / 348; raw unit: s^(-1) / uM; normalized value: 0.031609195402298854; normalized unit: s^(-1)*mM^(-1);

row_label: CmTAL | wt


assay_conditions_summary: pH 8.8; 303.15 K; buffer PreScission Protease) assayed in Tris

table_label: Table 1. Kinetic parameters for enzymes characterized in this study and comparison to the known aminomutase SgcC4.


organism: Chondromyces crocatus


substrate_name: L-phenylalanine

sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_mutation_ranked_match and applied mutation signature Q487A to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_ec_organism_mutation_ranked_match and applied mutation signature L137H to reconstruct the assayed variant sequence.


organism: Bambusa oldhamii

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

proof_lines:
BoPAL2
PAL
tyrosine ammonia-lyase


organism: Cistanche deserticola

column_label: Springer full-text prose reports the recombinant protein exhibited Michaelis-Menten kinetics with Km 0.1013 mM, Kcat 3.36 S^-1, and Kcat/Km 33,168 M^-1 S^-1

normalized_value_unit_evidence: Kcat/Km paper normalized_value=33.168 normalized_unit=s^-1*mM^-1; expected normalized_value=33.26732673267326 likely from rounded companion constants 3.36/0.101

raw_value_unit_evidence: Kcat/Km raw_value=33168 raw_unit=M^-1*S^-1; companion values in same prose: Km raw_value=0.1013 raw_unit=mM; Kcat raw_value=3.36 raw_unit=S^-1

row_label: CdPAL1 recombinant protein; L-phenylalanine kinetic constants

table_label: PMID 21104014 Springer full-text prose


organism: Arabidopsis thaliana

proof_lines:
Arabidopsis thaliana PAL1
L-phenylalanine Km 0.0428 mM
wild-type pH 9.0 37C


column_label: Table 1. Steady-State Kinetic Parameters of TALs and PALs Investigated in This Study (Underlined) with Tyrosine and Phenylalanine as Substrates.; row A. thaliana PAL1 F144H / Phenylalanine; Km column Km [uM] raw 1386 +/- 162.9; kcat column kcat [s^-1] raw 47.3 +/- 2.4; kcat/Km column kcat/Km [M^-1 s^-1] raw 3.4 x 10^4

normalized_value_unit_evidence: Km normalized_value=1.386 normalized_unit=mM; kcat normalized_value=47.3 normalized_unit=s^-1; kcat/Km normalized_value=34.12698412698413 normalized_unit=s^-1*mM^-1

raw_value_unit_evidence: Km raw_value=1386 +/- 162.9 raw_unit=uM; kcat raw_value=47.3 +/- 2.4 raw_unit=s^-1; kcat/Km raw_value=3.4 x 10^4 raw_unit=M^-1 s^-1

row_label: A. thaliana PAL1 F144H / Phenylalanine


organism: Jatropha curcas


substrate_name: L-Tyr

substrate: L-Tyr


proof_lines:
PAL, EC 4.3.1.5
Km 476 uM for L-Phe
BoPAL4 PAL/TAL activity


proof_lines:
BoPAL4 PAL/TAL activity
tyrosine ammonia-lyase activity
mutant-context change toward L-Tyr


organism: Zea mays


organism: Streptomyces globisporus


organism: Glycine max


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature H89F with inferred residue-numbering offset -1 to reconstruct the assayed variant sequence.


organism: Gossypium hirsutum


column_label: PMID 17240984 Table 1, NpPAL row, Km (mM), kcat (s^-1), and kcat/Km (mM^-1 s^-1) columns.

raw_value_unit_evidence: Table 1 line 215 reports NpPAL Km 0.045 mM, kcat 1.96 s^-1, and kcat/Km 43.8 mM^-1 s^-1.

row_label: NpPAL / L-phenylalanine

table_label: Table 1. Kinetic Analysis of AVPAL and NpPAL Wild-Type Enzymes and Comparison with AVPAL Mutants


organism: Petunia hybrida


organism: Petroselinum crispum

proof_lines:
Petroselinum crispum
phenylalanine ammonia-lyase
cinnamic-acid derivatives


organism: Taxus chinensis

column_label: Abstract reports the purified enzyme has a K(m) of 1.1mM and V(max) of 110.1 microm/min/mg protein.

raw_value_unit_evidence: Km raw_value=1.1mM raw_unit=mM

row_label: Taxus chinensis PAM / alpha-phenylalanine

table_label: PubMed XML abstract PMID 15878763


substrate_name: (2E)-4-methyl-cinnamic acid

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

substrate: (2E)-4-methyl-cinnamic acid


substrate_name: (E)-cinnamate

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

substrate: (E)-cinnamate


substrate_name: (2E)-4-fluoro-cinnamic acid

substrate: (2E)-4-fluoro-cinnamic acid


substrate_name: (2E)-4-nitro-cinnamic acid

substrate: (2E)-4-nitro-cinnamic acid


enzyme_display_name: UniProt P9WPY7

organism: Mycobacterium tuberculosis

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

enzyme: UniProt P9WPY7


enzyme_display_name: adenylosuccinate lyase

organism: Leishmania braziliensis

enzyme: adenylosuccinate lyase


enzyme_display_name: ureidoglycolate lyase

organism: Bos taurus

substrate_name: ureidoglycolate

enzyme: ureidoglycolate lyase

substrate: ureidoglycolate


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature F400A to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature L138H/Q488E to reconstruct the assayed variant sequence.


sequence_variant_note: Mutation signature L318H could not be applied safely because the resolved sequence does not match the expected reference residue(s).


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature N260A to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature Q348A to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature Q488A to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature Q488E to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature R354A to reconstruct the assayed variant sequence.


sequence_variant_note: Resolved canonical sequence from uniprot_accession and applied mutation signature S203A with inferred residue-numbering offset +7 to reconstruct the assayed variant sequence.


organism: Artemia sp.


substrate_name: fumarate

substrate: fumarate


substrate_name: AMP

substrate: AMP


organism: Cicer arietinum

substrate_name: (-)-Ureidoglycolate

proof_lines: 30°C, pH 7.8, in the presence of 0.5 mM Mn2+

substrate: (-)-Ureidoglycolate


organism: Platyrrhini


organism: Phaseolus vulgaris

proof_lines: 50 mM Tes, pH 7.8, 0.5 mM MnSO4, 3 mM phenylhydrazine


enzyme_display_name: L-tryptophan ammonia lyase

organism: Rubrivivax benzoatilyticus

substrate_name: L-tryptophan

proof_lines: pH and temperature not specified in the publication

enzyme: L-tryptophan ammonia lyase

substrate: L-tryptophan


organism: Rattus norvegicus


organism: Sardinops melanosticta