BRENDA - Enzyme Database
show all sequences of 3.3.2.13

Comparative studies of the catalytic mechanisms of two chorismatases CH-fkbo and CH-Hyg5

Dong, L.; Liu, Y.; Proteins 85, 1146-1158 (2017)

Data extracted from this reference:

Inhibitors
Inhibitors
Commentary
Organism
Structure
3-(2-carboxyethyl)benzoate
-
Streptomyces hygroscopicus
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
ID
chorismate + H2O
Streptomyces hygroscopicus
-
(4R,5R)-4,5-dihydroxycyclohexa-1(6),2-diene-1-carboxylate + pyruvate
-
-
?
Organism
Organism
UniProt
Commentary
Textmining
Streptomyces hygroscopicus
Q9KID9
-
-
Reaction
Reaction
Commentary
Organism
Reaction ID
chorismate + H2O = (4R,5R)-4,5-dihydroxycyclohexa-1(6),2-diene-1-carboxylate + pyruvate
catalytic mechanism, the two carboxyl groups of chorismate form a H-bond network with residues R228, Y215, Y155, and R162. These H-bonds are maintained during the whole catalytic process, which may play a role in stabilizing the negative charged substrate. The protonated E338 builds a strong H-bond with the 4-OH of chorismate. The distance between HA of E338 and C3' of chorismate is 4.00 A. Two water molecules enter the reactive center, which may function as mediators in the catalytic reaction. The reaction steps are protonation of methylene group, followed by nucleophilic attack of carbocation by (activated) water molecule W1, and cleavage of C2'-O8 bond
Streptomyces hygroscopicus
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
Substrate Product ID
chorismate + H2O
-
755348
Streptomyces hygroscopicus
(4R,5R)-4,5-dihydroxycyclohexa-1(6),2-diene-1-carboxylate + pyruvate
-
-
-
?
Synonyms
Synonyms
Commentary
Organism
CH-fkbo
-
Streptomyces hygroscopicus
fkbO
-
Streptomyces hygroscopicus
Inhibitors (protein specific)
Inhibitors
Commentary
Organism
Structure
3-(2-carboxyethyl)benzoate
-
Streptomyces hygroscopicus
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
ID
chorismate + H2O
Streptomyces hygroscopicus
-
(4R,5R)-4,5-dihydroxycyclohexa-1(6),2-diene-1-carboxylate + pyruvate
-
-
?
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
ID
chorismate + H2O
-
755348
Streptomyces hygroscopicus
(4R,5R)-4,5-dihydroxycyclohexa-1(6),2-diene-1-carboxylate + pyruvate
-
-
-
?
General Information
General Information
Commentary
Organism
additional information
structure of Fkbo-substrate complex, the solvated model of CH-Fkbo is optimized to calculate the catalytic mechanism. In the reactant structure, the substrate chorismate takes the similar binding model as inhibitor 3-(2-carboxyethyl)benzoate in crystal structure and adopts a trans-pseudodiaxial conformation. The structure of Streptomyces hygroscopicus chorismatase CH-Hyg5 is very similar to that of Streptomyces hygroscopicus chorismatase CH-Fkbo, all amino acid residues in the active site are the same except residues G240Hyg5 (A244Fkb8) and C327Hyg5 (A331Fkb8) are the same. The optimized active site structure of Hyg5 complex is superpositioned with that of Fkbo, overview. Two nonconserved active site residues are responsible for the different reaction mechanism of CH-Fkbo and CH-Hyg5. In CH-Hyg5, the lack of methyl in G240Hyg5 leads to the different conformation of the side chain of E334 (or E338) in Hyg5 and Fkbo. This small change eventually decreases the ESP charge of C3 atom of the substrate, which facilitates the cleavage of C3-O8 bond in Hyg5. Furthermore, C327Hyg5 is involved in the selective product formation in Hyg5 enzyme
Streptomyces hygroscopicus
General Information (protein specific)
General Information
Commentary
Organism
additional information
structure of Fkbo-substrate complex, the solvated model of CH-Fkbo is optimized to calculate the catalytic mechanism. In the reactant structure, the substrate chorismate takes the similar binding model as inhibitor 3-(2-carboxyethyl)benzoate in crystal structure and adopts a trans-pseudodiaxial conformation. The structure of Streptomyces hygroscopicus chorismatase CH-Hyg5 is very similar to that of Streptomyces hygroscopicus chorismatase CH-Fkbo, all amino acid residues in the active site are the same except residues G240Hyg5 (A244Fkb8) and C327Hyg5 (A331Fkb8) are the same. The optimized active site structure of Hyg5 complex is superpositioned with that of Fkbo, overview. Two nonconserved active site residues are responsible for the different reaction mechanism of CH-Fkbo and CH-Hyg5. In CH-Hyg5, the lack of methyl in G240Hyg5 leads to the different conformation of the side chain of E334 (or E338) in Hyg5 and Fkbo. This small change eventually decreases the ESP charge of C3 atom of the substrate, which facilitates the cleavage of C3-O8 bond in Hyg5. Furthermore, C327Hyg5 is involved in the selective product formation in Hyg5 enzyme
Streptomyces hygroscopicus
Other publictions for EC 3.3.2.13
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Synonyms
Temperature Optimum [°C]
Temperature Range [°C]
Temperature Stability [°C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [°C] (protein specific)
Temperature Range [°C] (protein specific)
Temperature Stability [°C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
753274
Zhang
How chorismatases regulate di ...
Streptomyces hygroscopicus
Chemistry
25
1326-1336
2019
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755348
Dong
Comparative studies of the ca ...
Streptomyces hygroscopicus
Proteins
85
1146-1158
2017
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748026
Hubrich
Chorismatase mechanisms revea ...
Streptomyces hygroscopicus subsp. ascomyceticus
J. Am. Chem. Soc.
137
11032-11037
2015
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725723
Juneja
Mechanistic implications for t ...
Streptomyces hygroscopicus subsp. ascomyceticus
J. Mol. Biol.
426
105-115
2014
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732211
Hubrich
In vitro production and purifi ...
Streptomyces hygroscopicus
J. Biotechnol.
191
93-98
2014
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724541
Hubrich
Cinnamic acid derivatives as i ...
Streptomyces hygroscopicus subsp. ascomyceticus
Bioorg. Med. Chem. Lett.
23
1477-1481
2013
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726377
Andexer
Biosynthesis of the immunosupp ...
Streptomyces hygroscopicus subsp. ascomyceticus
Proc. Natl. Acad. Sci. USA
108
4776-4781
2011
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