4TWZ

Crystal Structure Analysis of E Coli. RecA Protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Loop L1 governs the DNA-binding specificity and order for RecA-catalyzed reactions in homologous recombination and DNA repair

Shinohara, T.Ikawa, S.Iwasaki, W.Hiraki, T.Hikima, T.Mikawa, T.Arai, N.Kamiya, N.Shibata, T.

(2015) Nucleic Acids Res. 43: 973-986

  • DOI: 10.1093/nar/gku1364

  • PubMed Abstract: 
  • In all organisms, RecA-family recombinases catalyze homologous joint formation in homologous genetic recombination, which is essential for genome stability and diversification. In homologous joint formation, ATP-bound RecA/Rad51-recombinases first bi ...

    In all organisms, RecA-family recombinases catalyze homologous joint formation in homologous genetic recombination, which is essential for genome stability and diversification. In homologous joint formation, ATP-bound RecA/Rad51-recombinases first bind single-stranded DNA at its primary site and then interact with double-stranded DNA at another site. The underlying reason and the regulatory mechanism for this conserved binding order remain unknown. A comparison of the loop L1 structures in a DNA-free RecA crystal that we originally determined and in the reported DNA-bound active RecA crystals suggested that the aspartate at position 161 in loop L1 in DNA-free RecA prevented double-stranded, but not single-stranded, DNA-binding to the primary site. This was confirmed by the effects of the Ala-replacement of Asp-161 (D161A), analyzed directly by gel-mobility shift assays and indirectly by DNA-dependent ATPase activity and SOS repressor cleavage. When RecA/Rad51-recombinases interact with double-stranded DNA before single-stranded DNA, homologous joint-formation is suppressed, likely by forming a dead-end product. We found that the D161A-replacement reduced this suppression, probably by allowing double-stranded DNA to bind preferentially and reversibly to the primary site. Thus, Asp-161 in the flexible loop L1 of wild-type RecA determines the preference for single-stranded DNA-binding to the primary site and regulates the DNA-binding order in RecA-catalyzed recombinase reactions.


    Organizational Affiliation

    Cellular & Molecular Biology Unit, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan Advanced Catalysis Research Group, RIKEN Center for Sustainable Resource Science, Wako-shi, Saitama 351-0198, Japan.,Cellular & Molecular Biology Unit, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan Advanced Catalysis Research Group, RIKEN Center for Sustainable Resource Science, Wako-shi, Saitama 351-0198, Japan Department of Supramolecular Biology, Graduate School of Nanobiosciences, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.,Advanced Photon Technology Division, Research Infrastructure Group, RIKEN SPring-8 Center, RIKEN Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan.,Cellular & Molecular Biology Unit, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan.,Cellular & Molecular Biology Unit, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan Advanced Catalysis Research Group, RIKEN Center for Sustainable Resource Science, Wako-shi, Saitama 351-0198, Japan Department of Supramolecular Biology, Graduate School of Nanobiosciences, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan tshibata@riken.jp.,Department of Applied Biological Science, Nihon University College of Bioresource Sciences, 1866 Kameino, Fujisawa-shi, Kanagawa 252-8510, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein RecA
A
352Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: recA (lexB, recH, rnmB, tif, umuB, zab)
Find proteins for P0A7G6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7G6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.168 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 103.719α = 90.00
b = 103.719β = 90.00
c = 72.061γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
MOLREPphasing
HKL-2000data scaling
MOLREPmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-07-08
    Type: Initial release