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Catalytic Site Atlas

CSA LITERATURE entry for 1j2u

E.C. namecreatininase
SpeciesPseudomonas putida (Bacteria)
E.C. Number (IntEnz) 3.5.2.10
CSA Homologues of 1j2u
CSA Entries With UniProtID P83772
CSA Entries With EC Number 3.5.2.10
PDBe Entry 1j2u
PDBSum Entry 1j2u
MACiE Entry 1j2u

Literature Report

IntroductionCreatininase (creatinine amidohydrolase) from Pseudomonas putida catalyses the conversion of creatinine to creatine. It is a member of the urease-related amidohydrolase superfamily. The enzyme enables the bacteria to use creatinine as a source of carbon and nitrogen. The biological molecule is trimer of dimers. The active site of each monomer contains a binuclear metal centre located at the bottom of a cleft. In the native form of the enzyme both metal sites are occupied by Zn2+ ions.
MechansimA water molecule bridging the two metal ions is likely to form a hydroxide ion which acts as the nucleophile. The hydroxide attacks the carbonyl carbon of the creatinine substrate. The tetrahedral intermediate is stabilised by coordination to the two metal ions. Ring opening occurs simultaneously with the protonation of the amide nitrogen on the intermediate by a second water molecule which is coordinated to Zn301 and Glu122. After the product is released, a water molecule takes up the position between the two zinc ions and is deprotonated.
Reaction

Catalytic Sites for 1j2u

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
GluA122122macie:sideChainGlu122 forms a hydrogen bond to the water molecule which protonates the amide nitrogen and may help stabilise the hydroxide ion which is formed in the process.
HisA178178macie:sideChainHis178 forms a hydrogen to the nucleophilic hydroxide ion and helps stabilise it.

Annotated By Reference To The Literature - Site 2 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
GluB122122macie:sideChainGlu122 forms a hydrogen bond to the water molecule which protonates the amide nitrogen and may help stabilise the hydroxide ion which is formed in the process.
HisB178178macie:sideChainHis178 forms a hydrogen to the nucleophilic hydroxide ion and helps stabilise it.

Annotated By Reference To The Literature - Site 3 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
GluC122122macie:sideChainGlu122 forms a hydrogen bond to the water molecule which protonates the amide nitrogen and may help stabilise the hydroxide ion which is formed in the process.
HisC178178macie:sideChainHis178 forms a hydrogen to the nucleophilic hydroxide ion and helps stabilise it.

Annotated By Reference To The Literature - Site 4 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
GluD122122macie:sideChainGlu122 forms a hydrogen bond to the water molecule which protonates the amide nitrogen and may help stabilise the hydroxide ion which is formed in the process.
HisD178178macie:sideChainHis178 forms a hydrogen to the nucleophilic hydroxide ion and helps stabilise it.

Annotated By Reference To The Literature - Site 5 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
GluE122122macie:sideChainGlu122 forms a hydrogen bond to the water molecule which protonates the amide nitrogen and may help stabilise the hydroxide ion which is formed in the process.
HisE178178macie:sideChainHis178 forms a hydrogen to the nucleophilic hydroxide ion and helps stabilise it.

Annotated By Reference To The Literature - Site 6 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
GluF122122macie:sideChainGlu122 forms a hydrogen bond to the water molecule which protonates the amide nitrogen and may help stabilise the hydroxide ion which is formed in the process.
HisF178178macie:sideChainHis178 forms a hydrogen to the nucleophilic hydroxide ion and helps stabilise it.

Literature References

Notes:A structure of creatininase with the creatine product bound is availabe in pdb 1v7z. In pdb:1v7z the metal binding site that contains Zn301 in 1j2u, instead contains an Mn2+ ion.
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