1A16

AMINOPEPTIDASE P FROM E. COLI WITH THE INHIBITOR PRO-LEU


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure and mechanism of a proline-specific aminopeptidase from Escherichia coli.

Wilce, M.C.Bond, C.S.Dixon, N.E.Freeman, H.C.Guss, J.M.Lilley, P.E.Wilce, J.A.

(1998) Proc Natl Acad Sci U S A 95: 3472-3477

  • DOI: https://doi.org/10.1073/pnas.95.7.3472
  • Primary Citation of Related Structures:  
    1A16, 1JAW

  • PubMed Abstract: 

    The structure of the proline-specific aminopeptidase (EC 3.4.11.9) from Escherichia coli has been solved and refined for crystals of the native enzyme at a 2.0-A resolution, for a dipeptide-inhibited complex at 2.3-A resolution, and for a low-pH inactive form at 2.7-A resolution. The protein crystallizes as a tetramer, more correctly a dimer of dimers, at both high and low pH, consistent with observations from analytical ultracentrifuge studies that show that the protein is a tetramer under physiological conditions. The monomer folds into two domains. The active site, in the larger C-terminal domain, contains a dinuclear manganese center in which a bridging water molecule or hydroxide ion appears poised to act as the nucleophile in the attack on the scissile peptide bond of Xaa-Pro. The metal-binding residues are located in a single subunit, but the residues surrounding the active site are contributed by three subunits. The fold of the protein resembles that of creatine amidinohydrolase (creatinase, not a metalloenzyme). The C-terminal catalytic domain is also similar to the single-domain enzyme methionine aminopeptidase that has a dinuclear cobalt center.


  • Organizational Affiliation

    Department of Biochemistry, University of Sydney, New South Wales 2006, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AMINOPEPTIDASE P440Escherichia coliMutation(s): 0 
EC: 3.4.11.9
UniProt
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
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LEU
Query on LEU

Download Ideal Coordinates CCD File 
C [auth A]LEUCINE
C6 H13 N O2
ROHFNLRQFUQHCH-YFKPBYRVSA-N
PRO
Query on PRO

Download Ideal Coordinates CCD File 
B [auth A]PROLINE
C5 H9 N O2
ONIBWKKTOPOVIA-BYPYZUCNSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.184 
  • Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 177.3α = 90
b = 177.3β = 90
c = 96.5γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-04-06
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2024-02-07
    Changes: Data collection, Database references, Derived calculations