2ZXR

Crystal structure of RecJ in complex with Mg2+ from Thermus thermophilus HB8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.235 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of RecJ exonuclease defines its specificity for single-stranded DNA

Wakamatsu, T.Kitamura, Y.Kotera, Y.Nakagawa, N.Kuramitsu, S.Masui, R.

(2010) J Biol Chem 285: 9762-9769

  • DOI: 10.1074/jbc.M109.096487
  • Primary Citation of Related Structures:  
    2ZXO, 2ZXP, 2ZXR

  • PubMed Abstract: 
  • RecJ is a single-stranded DNA (ssDNA)-specific 5'-3' exonuclease that plays an important role in DNA repair and recombination. To elucidate how RecJ achieves its high specificity for ssDNA, we determined the entire structures of RecJ both in a ligand-free form and in a complex with Mn(2+) or Mg(2+) by x-ray crystallography ...

    RecJ is a single-stranded DNA (ssDNA)-specific 5'-3' exonuclease that plays an important role in DNA repair and recombination. To elucidate how RecJ achieves its high specificity for ssDNA, we determined the entire structures of RecJ both in a ligand-free form and in a complex with Mn(2+) or Mg(2+) by x-ray crystallography. The entire RecJ consists of four domains that form a molecule with an O-like structure. One of two newly identified domains had structural similarities to an oligonucleotide/oligosaccharide-binding (OB) fold. The OB fold domain alone could bind to DNA, indicating that this domain is a novel member of the OB fold superfamily. The truncated RecJ containing only the core domain exhibited much lower affinity for the ssDNA substrate compared with intact RecJ. These results support the hypothesis that these structural features allow specific binding of RecJ to ssDNA. In addition, the structure of the RecJ-Mn(2+) complex suggests that the hydrolysis reaction catalyzed by RecJ proceeds through a two-metal ion mechanism.


    Organizational Affiliation

    Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Single-stranded DNA specific exonuclease RecJA666Thermus thermophilus HB8Mutation(s): 0 
Gene Names: recJTTHA1167
EC: 3.1.11 (PDB Primary Data), 3.1 (UniProt)
Find proteins for Q5SJ47 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore Q5SJ47 
Go to UniProtKB:  Q5SJ47
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.235 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.357α = 90
b = 83.357β = 90
c = 251.056γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MLPHAREphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-01-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance