BRENDA - Enzyme Database

Molecular basis of the general base catalysis of an alpha/beta-hydrolase catalytic triad

Sun, Y.; Yin, S.; Feng, Y.; Li, J.; Zhou, J.; Liu, C.; Zhu, G.; Guo, Z.; J. Biol. Chem. 289, 15867-15879 (2014)

Data extracted from this reference:

Cloned(Commentary)
EC Number
Cloned (Commentary)
Organism
4.2.99.20
-
Escherichia coli
Crystallization (Commentary)
EC Number
Crystallization (Commentary)
Organism
4.2.99.20
to 1.45 A resolution. The nucleophilicity of the catalytic serine-histidine-aspartate triad is shielded and its catalytic role is limited to being a specific general base by an open-closed conformational change
Escherichia coli
Engineering
EC Number
Protein Variants
Commentary
Organism
4.2.99.20
F153A
residue involved in open-closed transition, mutation leads to large decrease in enzymatic activity
Escherichia coli
4.2.99.20
V152A
residue involved in open-closed transition, mutation leads to large decrease in enzymatic activity
Escherichia coli
4.2.99.20
V152G
residue involved in open-closed transition, mutation leads to large decrease in enzymatic activity
Escherichia coli
4.2.99.20
V152G/F153A
inactive
Escherichia coli
4.2.99.20
W147A/Y148A
inactive
Escherichia coli
4.2.99.20
Y148A
residue involved in open-closed transition, mutation leads to large decrease in enzymatic activity
Escherichia coli
4.2.99.20
Y148F
residue involved in open-closed transition, mutation leads to large decrease in enzymatic activity
Escherichia coli
KM Value [mM]
EC Number
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
4.2.99.20
0.013
-
(1R,2S,5S,6S)-2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate
wild-type, pH 7.0, temperature not specified in the publication
Escherichia coli
4.2.99.20
0.036
-
(1R,2S,5S,6S)-2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate
mutant Y148F, pH 7.0, temperature not specified in the publication
Escherichia coli
4.2.99.20
0.05
-
(1R,2S,5S,6S)-2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate
mutant Y148A, pH 7.0, temperature not specified in the publication
Escherichia coli
4.2.99.20
0.07
-
(1R,2S,5S,6S)-2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate
mutant F153A, pH 7.0, temperature not specified in the publication
Escherichia coli
4.2.99.20
0.16
-
(1R,2S,5S,6S)-2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate
mutant V152G, pH 7.0, temperature not specified in the publication
Escherichia coli
4.2.99.20
0.3
-
(1R,2S,5S,6S)-2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate
mutant V152A, pH 7.0, temperature not specified in the publication
Escherichia coli
Organism
EC Number
Organism
UniProt
Commentary
Textmining
4.2.99.20
Escherichia coli
P37355
-
-
Reaction
EC Number
Reaction
Commentary
Organism
Reaction ID
4.2.99.20
5-enolpyruvoyl-6-hydroxy-2-succinylcyclohex-3-ene-1-carboxylate = (1R,6R)-6-hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate + pyruvate
the nucleophilicity of the catalyitc serine-histidine-aspartate triad is shielded and its catalytic role is limited to being a specific general base by an open-closed conformational change. The enzyme adopts an open conformation without a functional triad in its ligand-free form and a closed conformation with a fully functional catalytic triad in the presence of its reaction product. The open-to-closed conformational transition involves movement of half of the alpha-helical cap domain, which causes extensive structural changes in the apha/beta-domain and forces the side chainof the triad histidine to adopt an energetically disfavored gauche conformation to form the functional triad. The inactive open conformation without a triad prevails in ligand-free solution and is converted to the closed conformation with a properly formed triad by the reaction product
Escherichia coli
Substrates and Products (Substrate)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
Substrate Product ID
4.2.99.20
(1R,2S,5S,6S)-2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate
-
730042
Escherichia coli
(1R,6R)-2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate + pyruvate
-
-
-
?
Synonyms
EC Number
Synonyms
Commentary
Organism
4.2.99.20
MenH
-
Escherichia coli
Turnover Number [1/s]
EC Number
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
4.2.99.20
0.13
-
(1R,2S,5S,6S)-2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate
mutant V152A, pH 7.0, temperature not specified in the publication; mutant Y148A, pH 7.0, temperature not specified in the publication
Escherichia coli
4.2.99.20
0.2
-
(1R,2S,5S,6S)-2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate
mutant V152G, pH 7.0, temperature not specified in the publication
Escherichia coli
4.2.99.20
0.58
-
(1R,2S,5S,6S)-2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate
mutant Y148F, pH 7.0, temperature not specified in the publication
Escherichia coli
4.2.99.20
3.33
-
(1R,2S,5S,6S)-2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate
mutant F153A, pH 7.0, temperature not specified in the publication
Escherichia coli
4.2.99.20
8.5
-
(1R,2S,5S,6S)-2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate
wild-type, pH 7.0, temperature not specified in the publication
Escherichia coli
Cloned(Commentary) (protein specific)
EC Number
Commentary
Organism
4.2.99.20
-
Escherichia coli
Crystallization (Commentary) (protein specific)
EC Number
Crystallization
Organism
4.2.99.20
to 1.45 A resolution. The nucleophilicity of the catalytic serine-histidine-aspartate triad is shielded and its catalytic role is limited to being a specific general base by an open-closed conformational change
Escherichia coli
Engineering (protein specific)
EC Number
Protein Variants
Commentary
Organism
4.2.99.20
F153A
residue involved in open-closed transition, mutation leads to large decrease in enzymatic activity
Escherichia coli
4.2.99.20
V152A
residue involved in open-closed transition, mutation leads to large decrease in enzymatic activity
Escherichia coli
4.2.99.20
V152G
residue involved in open-closed transition, mutation leads to large decrease in enzymatic activity
Escherichia coli
4.2.99.20
V152G/F153A
inactive
Escherichia coli
4.2.99.20
W147A/Y148A
inactive
Escherichia coli
4.2.99.20
Y148A
residue involved in open-closed transition, mutation leads to large decrease in enzymatic activity
Escherichia coli
4.2.99.20
Y148F
residue involved in open-closed transition, mutation leads to large decrease in enzymatic activity
Escherichia coli
KM Value [mM] (protein specific)
EC Number
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
4.2.99.20
0.013
-
(1R,2S,5S,6S)-2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate
wild-type, pH 7.0, temperature not specified in the publication
Escherichia coli
4.2.99.20
0.036
-
(1R,2S,5S,6S)-2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate
mutant Y148F, pH 7.0, temperature not specified in the publication
Escherichia coli
4.2.99.20
0.05
-
(1R,2S,5S,6S)-2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate
mutant Y148A, pH 7.0, temperature not specified in the publication
Escherichia coli
4.2.99.20
0.07
-
(1R,2S,5S,6S)-2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate
mutant F153A, pH 7.0, temperature not specified in the publication
Escherichia coli
4.2.99.20
0.16
-
(1R,2S,5S,6S)-2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate
mutant V152G, pH 7.0, temperature not specified in the publication
Escherichia coli
4.2.99.20
0.3
-
(1R,2S,5S,6S)-2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate
mutant V152A, pH 7.0, temperature not specified in the publication
Escherichia coli
Substrates and Products (Substrate) (protein specific)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
ID
4.2.99.20
(1R,2S,5S,6S)-2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate
-
730042
Escherichia coli
(1R,6R)-2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate + pyruvate
-
-
-
?
Turnover Number [1/s] (protein specific)
EC Number
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
4.2.99.20
0.13
-
(1R,2S,5S,6S)-2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate
mutant V152A, pH 7.0, temperature not specified in the publication; mutant Y148A, pH 7.0, temperature not specified in the publication
Escherichia coli
4.2.99.20
0.2
-
(1R,2S,5S,6S)-2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate
mutant V152G, pH 7.0, temperature not specified in the publication
Escherichia coli
4.2.99.20
0.58
-
(1R,2S,5S,6S)-2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate
mutant Y148F, pH 7.0, temperature not specified in the publication
Escherichia coli
4.2.99.20
3.33
-
(1R,2S,5S,6S)-2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate
mutant F153A, pH 7.0, temperature not specified in the publication
Escherichia coli
4.2.99.20
8.5
-
(1R,2S,5S,6S)-2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate
wild-type, pH 7.0, temperature not specified in the publication
Escherichia coli
KCat/KM [mM/s]
EC Number
kcat/KM Value [1/mMs-1]
kcat/KM Value Maximum [1/mMs-1]
Substrate
Commentary
Organism
Structure
4.2.99.20
0.43
-
(1R,2S,5S,6S)-2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate
mutant V152A, pH 7.0, temperature not specified in the publication
Escherichia coli
4.2.99.20
1.2
-
(1R,2S,5S,6S)-2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate
mutant V152G, pH 7.0, temperature not specified in the publication
Escherichia coli
4.2.99.20
2.7
-
(1R,2S,5S,6S)-2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate
mutant Y148A, pH 7.0, temperature not specified in the publication
Escherichia coli
4.2.99.20
16.3
-
(1R,2S,5S,6S)-2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate
mutant Y148F, pH 7.0, temperature not specified in the publication
Escherichia coli
4.2.99.20
48
-
(1R,2S,5S,6S)-2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate
mutant F153A, pH 7.0, temperature not specified in the publication
Escherichia coli
4.2.99.20
533
-
(1R,2S,5S,6S)-2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate
wild-type, pH 7.0, temperature not specified in the publication
Escherichia coli
KCat/KM [mM/s] (protein specific)
EC Number
KCat/KM Value [1/mMs-1]
KCat/KM Value Maximum [1/mMs-1]
Substrate
Commentary
Organism
Structure
4.2.99.20
0.43
-
(1R,2S,5S,6S)-2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate
mutant V152A, pH 7.0, temperature not specified in the publication
Escherichia coli
4.2.99.20
1.2
-
(1R,2S,5S,6S)-2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate
mutant V152G, pH 7.0, temperature not specified in the publication
Escherichia coli
4.2.99.20
2.7
-
(1R,2S,5S,6S)-2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate
mutant Y148A, pH 7.0, temperature not specified in the publication
Escherichia coli
4.2.99.20
16.3
-
(1R,2S,5S,6S)-2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate
mutant Y148F, pH 7.0, temperature not specified in the publication
Escherichia coli
4.2.99.20
48
-
(1R,2S,5S,6S)-2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate
mutant F153A, pH 7.0, temperature not specified in the publication
Escherichia coli
4.2.99.20
533
-
(1R,2S,5S,6S)-2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate
wild-type, pH 7.0, temperature not specified in the publication
Escherichia coli