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Search The CSA
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Catalytic Site Atlas

CSA LITERATURE entry for 1ybq

E.C. nameisoaspartyl dipeptidase
SpeciesEschericia coli ()
E.C. Number (IntEnz) 3.4.19.-
CSA Homologues of 1ybq
CSA Entries With UniProtID P39377
CSA Entries With EC Number 3.4.19.-
PDBe Entry 1ybq
PDBSum Entry 1ybq
MACiE Entry M0172

Literature Report

IntroductionIsoaspartyl 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.
Mechansim1. 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.

Catalytic Sites for 1ybq

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
AsnA285285macie:sideChainError

Annotated By Reference To The Literature - Site 2 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
AsnB285285macie:sideChainActs as a general base by abstracting a proton from the hydroxide ion, activating it further for nucleophilic attack. Acts as a general acid by donating that proton to the leaving group N atom.

Literature References

Notes:
Martí-Arbona R
Mechanism of the reaction catalyzed by isoaspartyl dipeptidase from Escherichia coli.
Biochemistry 2005 44 7115-7124
PubMed: 15882050
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