1JAW

AMINOPEPTIDASE P FROM E. COLI LOW PH FORM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.2 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.USA 95: 3472-3477

  • Primary Citation of Related Structures:  

  • 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 inac ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AMINOPEPTIDASE P
A
440Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: pepP
EC: 3.4.11.9
Find proteins for P15034 (Escherichia coli (strain K12))
Go to UniProtKB:  P15034
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.182 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 139.710α = 90.00
b = 139.710β = 90.00
c = 230.870γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
X-PLORmodel building
X-PLORphasing
SCALEPACKdata scaling
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-04-06
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance