Glu383Ala Escherichia coli aminopeptidase P in complex with substrate

Experimental Data Snapshot

  • Resolution: 1.56 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.140 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


Complexes of Mutants of Escherichia Coli Aminopeptidase P and the Tripeptide Substrate Valproleu.

Graham, S.C.Guss, J.M.

(2008) Arch Biochem Biophys 469: 200

  • DOI: https://doi.org/10.1016/j.abb.2007.10.009
  • Primary Citation of Related Structures:  
    2V3X, 2V3Y, 2V3Z

  • PubMed Abstract: 

    Aminopeptidase P (APPro) is a manganese-containing enzyme that catalyses the hydrolysis of the N-terminal residue of a polypeptide if the second residue is proline. Structures of APPro mutants with reduced or negligible activity have been determined in complex with the tripeptide substrate ValProLeu. In the complex of Glu383Ala APPro with ValProLeu one of the two metal sites is only partly occupied, indicating an essential role for Glu383 in metal binding in the presence of substrate. His361Ala APPro clearly possesses residual activity as the ValProLeu substrate has been cleaved in the crystals; difference electron density consistent with bound ProLeu dipeptide and a disordered Val amino acid is present at the active site. Contrary to previous suggestions, the His243Ala mutant is capable of binding substrate. The structure of the His243Ala APPro complex with ValProLeu shows that the peptide interacts with one of the active-site metal atoms via its terminal amino group. The implications of these complexes for the roles of the respective residues in APPro catalysis are discussed.

  • Organizational Affiliation

    Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
XAA-PRO AMINOPEPTIDASE440Escherichia 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

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
TRIPEPTIDE (VALINE-PROLINE-LEUCINE)3Escherichia coliMutation(s): 0 
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on CSO
Experimental Data & Validation

Experimental Data

  • Resolution: 1.56 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.140 
  • Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 177.695α = 90
b = 177.695β = 90
c = 96.433γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-11-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2019-03-06
    Changes: Data collection, Derived calculations, Experimental preparation, Other
  • Version 1.3: 2019-09-25
    Changes: Data collection, Experimental preparation
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Refinement description