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CSA entry for 1r6w
Original Entry
Title:
Lyase
Compound:
O-succinylbenzoate synthase
Mutant:
Yes
UniProt/Swiss-Prot:
P29208-MENC_ECOLI
EC Class:
4.2.1.-
Other CSA Entries:
Overview of all sites for 1r6w
Homologues of 1r6w
Entries for UniProt/Swiss-Prot: P29208
Entries for EC: 4.2.1.-
Other Databases:
PDB entry: 1r6w
PDBsum entry: 1r6w
UniProt/Swiss-Prot: P29208
IntEnz entry: 4.2.1.-
Literature Report:
Introduction:
o-Succinylbenzoate synthase (OSBS) is a member of the muconate lactonising enzyme subgroup of the enolase superfamily. It catalyses the exergonic dehydration reaction in the menaquinone biosynthesis pathway in which 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate(SHCHC) is converted to o-succinylbenzoate.
Mechanism:
The dehydration is initiated by the abstraction of a proton from the C1, the carbon adjacent to the carboxylate group by Lys133, forming an enediolate anion intermediate. The negatively charged intermediate is stabilised by Lys235 through a cation-pi interaction to the cyclohexadienyl moiety and by Mg2+ ion through a bidentate coordination to the carboxylate group. Lys133 is also responsible for protonation of the departing water molecule.
Sites:

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Found by:
Literature reference 

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
736 0
ElectrostaticTransition state
It forms a bidentate coordination to the C1 carboxylate group, stabilising the negative charges developed on the intermediate and thus stabilises the transition state.
Evidence from paper Evidence concerns Evidence type
PubMed ID 14661953 Current protein Ligand is essential for catalysis
PubMed ID 14661953 Current protein Structural similarity to homologue of known mechanism

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
ARGA 133 133Sidechain
Acid/baseWater
Acid/baseSubstrate
It removes a proton from C1 to initiate the dehydration. It then donates a proton to the departing water molecule.
Evidence from paper Evidence concerns Evidence type
PubMed ID 14661953 Current protein Structural similarity to homologue of known mechanism
PubMed ID 14661953 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 14661953 Current protein Mutagenesis of residue

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
LYSA 235 235Sidechain
ElectrostaticTransition state
It stabilises the transition state by the a cation-pi interaction with the enediolate intermediate.
Evidence from paper Evidence concerns Evidence type
PubMed ID 14661953 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 14661953 Current protein Structural similarity to homologue of known mechanism
PubMed ID 14661953 Current protein Mutagenesis of residue
References:
1
Evolution of enzymatic activity in the enolase superfamily: structural and mutagenic studies of the mechanism of the reaction catalyzed by o-succinylbenzoate synthase from Escherichia coli.
V. A. Klenchin and E. A. Taylor Ringia and J. A. Gerlt and I. Rayment
Biochemistry 42, (49) 14427-33, (2003).
14661953
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