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Catalytic Site Atlas Search Results
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Catalytic Site Atlas

CSA LITERATURE entry for 1m21

E.C. namePEPTIDE AMIDASE
SpeciesXanthomonas maltophilia ()
E.C. Number (IntEnz) 3.5.1.-
CSA Homologues of 1m21
CSA Entries With UniProtID
CSA Entries With EC Number 3.5.1.-
PDBe Entry 1m21
PDBSum Entry 1m21
MACiE Entry 1m21

Literature Report

IntroductionPeptide amidase (PAM) from Strenotrophomonas maltophilia (a gram-negative bacterium) catalyses the hydrolysis of the C-terminal amide bond in peptide amides. It is very regio-selective, and those terminal bonds in amino acid side chains are not hydrolysed. PAM belongs to the amidase signature (AS) family, most of which display hydrolase activity. The natural function of periplasmatic PAM is not known.
Mechansim1. Ser 226 acts as the primary nucleophile and attacks the amide carbonyl carbon atom. 2. Simultaneously, Ser 202 protonates the substrate carbonyl oxygen, and deprotonates Ser 226. A tetrahedral intermediate is formed. 3. Lys 123 acts to decrease the nucleophilicity of Ser 202, and increase it's ability to protonate the carbonyl oxygen. 4. Lys 123 protonates Ser 202 which in turn protonates the amido group of the substrate, creating NH3, a good leaving group. 5. Lys 123 deprotonates Ser 202 which in turn deprotonates the O atom of the substrate, causing the reformation of the carbonyl with elimination of NH3. 6. Hydrolysis of the enzyme-acyl intermediate is carried out by nucleophilic attack of a water molecule, which is simultaneously deprotonated by the leaving group Ser 226.

Catalytic Sites for 1m21

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
SerA226226macie:sideChainActs as the primary nucleophile on the substrate carbonyl. Acts as a base by deprotonating a water molecule as it nucleophilically attacks the substrate carbonyl.
LysA123123macie:sideChainActs to decrease the nucleophilicity of Ser 202 by hydrogen bonding to it. Also acts as an acid/base to Ser 202.
SerA202202macie:sideChainActs as an acid/base. Donates a proton to the carbonyl oxygen of the substrate at the same time as abstracting a proton from Ser 226. Accepts a proton from Lys 123 while donating a proton to substrate N atom. Accepts a proton from substrate O atom while donating a proton back to Lys 123.

Annotated By Reference To The Literature - Site 2 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
SerB226226macie:sideChainActs as the primary nucleophile on the substrate carbonyl. Acts as a base by deprotonating a water molecule as it nucleophilically attacks the substrate carbonyl.
LysB123123macie:sideChainActs to decrease the nucleophilicity of Ser 202 by hydrogen bonding to it. Also acts as an acid/base to Ser 202.
SerB202202macie:sideChainActs as an acid/base. Donates a proton to the carbonyl oxygen of the substrate at the same time as abstracting a proton from Ser 226. Accepts a proton from Lys 123 while donating a proton to substrate N atom. Accepts a proton from substrate O atom while donating a proton back to Lys 123.

Literature References

Notes:
Labahn J
An alternative mechanism for amidase signature enzymes.
J Mol Biol 2002 322 1053-1064
PubMed: 12367528
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