Asp260Ala Escherichia coli Aminopeptidase P

Experimental Data Snapshot

  • Resolution: 2.90 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Kinetic and Crystallographic Analysis of Mutant Escherichia Coli Aminopeptidase P: Insights Into Substrate Recognition and the Mechanism of Catalysis.

Graham, S.C.Lilley, P.E.Lee, M.Schaeffer, P.M.Kralicek, A.V.Dixon, N.E.Guss, J.M.

(2006) Biochemistry 45: 964

  • DOI: https://doi.org/10.1021/bi0518904
  • Primary Citation of Related Structures:  
    2BWS, 2BWT, 2BWU, 2BWV, 2BWW, 2BWX, 2BWY

  • PubMed Abstract: 

    Aminopeptidase P (APPro) is a manganese-dependent enzyme that cleaves the N-terminal amino acid from polypeptides where the second residue is proline. APPro shares a similar fold, substrate specificity, and catalytic mechanism with methionine aminopeptidase and prolidase. To investigate the roles of conserved residues at the active site, seven mutant forms of APPro were characterized kinetically and structurally. Mutation of individual metal ligands selectively abolished binding of either or both Mn(II) atoms at the active site, and none of these metal-ligand mutants had detectable catalytic activity. Mutation of the conserved active site residues His243 and His361 revealed that both are required for catalysis. We propose that His243 stabilizes substrate binding through an interaction with the carbonyl oxygen of the requisite proline residue of a substrate and that His361 stabilizes substrate binding and the gem-diol catalytic intermediate. Sequence, structural, and kinetic analyses reveal that His350, conserved in APPro and prolidase but not in methionine aminopeptidase, forms part of a hydrophobic binding pocket that gives APPro its proline specificity. Further, peptides in which the required proline residue is replaced by N-methylalanine or alanine are cleaved by APPro, but they are extremely poor substrates due to a loss of interactions between the prolidyl ring of the substrate and the hydrophobic proline-binding pocket.

  • Organizational Affiliation

    School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Australia.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
XAA-PRO AMINOPEPTIDASE P440Escherichia coliMutation(s): 1 
Find proteins for P15034 (Escherichia coli (strain K12))
Explore P15034 
Go to UniProtKB:  P15034
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15034
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.90 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137.588α = 90
b = 137.588β = 90
c = 231.948γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-01-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2019-05-08
    Changes: Data collection, Experimental preparation, Other
  • Version 1.3: 2019-05-15
    Changes: Data collection, Experimental preparation
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description