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Catalytic Site Atlas

CSA LITERATURE entry for 1azw

E.C. nameprolyl aminopeptidase
SpeciesXanthomonas smithii subsp. citri ()
E.C. Number (IntEnz)
CSA Homologues of 1azwThere are 58 Homologs
CSA Entries With UniProtID P52279
CSA Entries With EC Number
PDBe Entry 1azw
PDBSum Entry 1azw
MACiE Entry 1azw

Literature Report

IntroductionThe proline iminopeptidase from X. campestris pv. citri is a serine peptidase that catalyses the removal of N-terminal proline residues from peptides with high specificity. The mechanism of the serine proteases is commonly believed to be among the best understood of all enzymes. As their name suggests, they are involved in hydrolysis of proteins using a serine nucleophile.
MechansimThe key feature of the mechanism is the presence of the catalytic triad of serine, histidine and aspartate. Serine, having been deprotonated by histidine, attacks the carbonyl of the substrate. The negatively charged tetrahedral intermediate is stabilised by the oxyanion hole, while the positive charge on histidine is stabilised by the aspartate residue. When the tetrahedral intermediate collapses, the amide bond of the substrate is broken. The acylenzyme intermediate is hydrolysed by a water molecule, activated by histidine, to release the product and restore the enzyme to its active state.

Catalytic Sites for 1azw

Annotated By Reference To The Literature - Site 1 (Perform Site Search)
ResidueChainNumberUniProtKB NumberFunctional PartFunctionTargetDescription
SerA110110macie:sideChainWhen activated by histidine, serine is the nucleophile which attacks the substrate carbonyl, forming a covalent intermediate.
HisA294294macie:sideChainForms part of the catalytic triad. Deprotonates serine to activate it as a nucleophile, and is stabilised by hydrogen bonding interactions with aspartate. In the deacylation step, deprotonates a water molecule to activate it as a nucleophile.
AspA266266macie:sideChainForms part of the catalytic triad. Stabilises the positive charge on histidine.
TrpA111111macie:mainChainAmideForms part of the oxyanion hole which stabilises the negatively charged oxygen in the transition state.
GlyA4343macie:mainChainAmideForms part of the oxyanion hole which stabilises the negatively charged oxygen in the transition state.

Literature References

Medrano FJ
Structure of proline iminopeptidase from Xanthomonas campestris pv. citri: a prototype for the prolyl oligopeptidase family.
EMBO J 1998 17 1-9
PubMed: 9427736
Topf M
Molecular dynamics simulations of the acyl-enzyme and the tetrahedral intermediate in the deacylation step of serine proteases.
Proteins 2002 47 357-369
PubMed: 11948789
Yoshimoto T
Crystal structure of prolyl aminopeptidase from Serratia marcescens.
J Biochem 1999 126 559-565
PubMed: 10467172