1GYT

E. coli Aminopeptidase A (PepA)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history. 

Literature

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: 10.1093/emboj/18.16.4513

  • 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 recombinatio ...

    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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYTOSOL AMINOPEPTIDASE
A, B, C, D, E, F, G, H, I, J, K, L
503Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: pepA (carP, xerB)
EC: 3.4.11.1
Find proteins for P68767 (Escherichia coli (strain K12))
Go to UniProtKB:  P68767
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL
Download SDF File 
Download CCD File 
B, F, G, K
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CO3
Query on CO3
Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.165 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 178.000α = 90.00
b = 178.000β = 90.00
c = 244.400γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2002-04-29 
  • Released Date: 2002-06-06 
  • Deposition Author(s): Straeter, N.

Revision History 

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