E. coli Aminopeptidase A (PepA)

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.165 

wwPDB Validation   3D Report Full Report

This is version 1.6 of the entry. See complete history


X-Ray Structure of Aminopeptidase a from Escherichia Coli and a Model for the Nucleoprotein Complex in Xer Site-Specific Recombination

Straeter, N.Sherratt, D.J.Colloms, S.D.

(1999) EMBO J 18: 4513

  • DOI: https://doi.org/10.1093/emboj/18.16.4513
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The structure of aminopeptidase A (PepA), which functions as a DNA-binding protein in Xer site-specific recombination and in transcriptional control of the carAB operon in Escherichia coli, has been determined at 2.5 A resolution. In Xer recombination at cer, PepA and the arginine repressor (ArgR) serve as accessory proteins, ensuring that recombination is exclusively intramolecular. In contrast, PepA homologues from other species have no known DNA-binding activity and are not implicated in transcriptional regulation or control of site-specific recombination. PepA comprises two domains, which have similar folds to the two domains of bovine lens leucine aminopeptidase (LAP). However, the N-terminal domain of PepA, which probably plays a significant role in DNA binding, is rotated by 19 degrees compared with its position in LAP. PepA is a homohexamer of 32 symmetry. A groove that runs from one trimer face across the 2-fold molecular axis to the other trimer face is proposed to be the DNA-binding site. Molecular modelling supports a structure of the Xer complex in which PepA, ArgR and a second PepA molecule are sandwiched along their 3-fold molecular axes, and the accessory sequences of the two recombination sites wrap around the accessory proteins as a right-handed superhelix such that three negative supercoils are trapped.

  • Organizational Affiliation

    Institut für Kristallographie, Freie Universität Berlin, Takustrasse 6, 14195 Berlin, Germany. strater@chemie.fu-berlin.de

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
503Escherichia coli K-12Mutation(s): 0 
Find proteins for P68767 (Escherichia coli (strain K12))
Explore P68767 
Go to UniProtKB:  P68767
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68767
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth E]
CA [auth F]
DA [auth F]
GA [auth G]
HA [auth G]
AA [auth E],
CA [auth F],
DA [auth F],
GA [auth G],
HA [auth G],
KA [auth H],
LA [auth H],
M [auth A],
N [auth A],
NA [auth I],
OA [auth I],
P [auth B],
Q [auth B],
QA [auth J],
RA [auth J],
T [auth C],
TA [auth K],
U [auth C],
UA [auth K],
W [auth D],
X [auth D],
XA [auth L],
YA [auth L],
Z [auth E]
Query on CO3

Download Ideal Coordinates CCD File 
BA [auth E]
EA [auth F]
IA [auth G]
MA [auth H]
O [auth A]
BA [auth E],
EA [auth F],
IA [auth G],
MA [auth H],
O [auth A],
PA [auth I],
R [auth B],
SA [auth J],
V [auth C],
VA [auth K],
Y [auth D],
ZA [auth L]
C O3
Query on CL

Download Ideal Coordinates CCD File 
FA [auth F],
JA [auth G],
S [auth B],
WA [auth K]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.165 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 178α = 90
b = 178β = 90
c = 244.4γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2002-06-06 
  • Deposition Author(s): Straeter, N.

Revision History  (Full details and data files)

  • Version 1.0: 2002-06-06
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-07-12
    Changes: Derived calculations
  • Version 1.4: 2018-02-07
    Changes: Source and taxonomy
  • Version 1.5: 2019-07-24
    Changes: Data collection
  • Version 1.6: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other