1GYT

E. coli Aminopeptidase A (PepA)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • 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 1.5 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
  • Primary Citation of Related Structures:  
    1GYT

  • 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 ...

    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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CYTOSOL AMINOPEPTIDASE
A, B, C, D, E, F, G, H, I, J, K, L
A, B, C, D, E, F, G, H, I, J, K, L
503Escherichia coli K-12Mutation(s): 0 
Gene Names: pepA, carP, xerB, b4260, JW4217
EC: 3.4.11.1 (PDB Primary Data), 3.4.11.10 (UniProt)
UniProt
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
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]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
CO3
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]
CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
FA [auth F],
JA [auth G],
S [auth B],
WA [auth K]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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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  (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