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CSA entry for 1ybq
Original Entry
Title:
Hydrolase
Compound:
Isoaspartyl dipeptidase
Mutant:
Yes
UniProt/Swiss-Prot:
P39377-IADA_ECOLI
EC Class:
3.4.19.-
Other CSA Entries:
Overview of all sites for 1ybq
Homologues of 1ybq
Entries for UniProt/Swiss-Prot: P39377
Entries for EC: 3.4.19.-
Other Databases:
PDB entry: 1ybq
PDBsum entry: 1ybq
UniProt/Swiss-Prot: P39377
IntEnz entry: 3.4.19.-
Literature Report:
Introduction:
Isoaspartyl dipeptidase (IAD) from Escherichia coli is a member of the amidohydrolase superfamily. It catalyses the hydrolysis of dipeptides containing a peptide bond to the beta-carboxylate group of aspartic acid. The apparent physiological role of IAD is to prevent the accumulation of beta-aspartyl dipeptides after proteolysis of these proteins. IAD shows little activity towards the hydrolysis of tripeptides or gamma-glutamyl dipeptides.
Mechanism:
1. The presence of the two Zn2+ ions lowers the pKa of a water molecule to such an extent that it exists as a hydroxide ion.
2. The interaction between the carbonyl oxygen and Zn 2 increases the electrophilic character of the carbonyl carbon atom.
3. Asp 285 acts as a general base by abstracting the proton from the hydroxide ion, causing the oxygen atom to nucleophilically attack the substrate carbonyl carbon atom.
4. This forms a negatively charged, tetrahedral intermediate.
5. As the carbonyl is reformed, the scissile C-N bond is broken, facilitated by
Asp 285 acting as a general acid by donating a proton to the leaving group N atom.
Sites:

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Found by:
Literature reference 

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
1 1
ElectrostaticWater
Error
Evidence from paper Evidence concerns Evidence type
PubMed ID 15882050 Current protein pH dependence of reaction
PubMed ID 15882050 Current protein Residue is positioned appropriately (ligand position known)

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
2 2
ElectrostaticSubstrate
ElectrostaticWater
Error
Evidence from paper Evidence concerns Evidence type
PubMed ID 15882050 Current protein Residue is positioned appropriately (ligand position known)
PubMed ID 15882050 Current protein pH dependence of reaction

ResidueChainNumberUniProt numberFunctional part FunctionTargetDescription
ASNA 285 285
Acid/baseSubstrate
Acid/baseWater
Error
Evidence from paper Evidence concerns Evidence type
PubMed ID 15882050 Current protein Conservation of residue
PubMed ID 15882050 Current protein Structural similarity to homologue of known mechanism
PubMed ID 15882050 Current protein Mutagenesis of residue
Notes:

References:
1
Mechanism of the reaction catalyzed by isoaspartyl dipeptidase from Escherichia coli.
R. Martí-Arbona and V. Fresquet and J. B. Thoden and M. L. Davis and H. M. Holden and F. M. Raushel
Biochemistry 44, (19) 7115-24, (2005).
15882050
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