3CMW

Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.214 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Mechanism of homologous recombination from the RecA-ssDNA/dsDNA structures.

Chen, Z.Yang, H.Pavletich, N.P.

(2008) Nature 453: 489-494

  • DOI: 10.1038/nature06971
  • Primary Citation of Related Structures:  
    3CMU, 3CMV, 3CMW, 3CMX, 3CMT

  • PubMed Abstract: 
  • The RecA family of ATPases mediates homologous recombination, a reaction essential for maintaining genomic integrity and for generating genetic diversity. RecA, ATP and single-stranded DNA (ssDNA) form a helical filament that binds to double-stranded DNA (dsDNA), searches for homology, and then catalyses the exchange of the complementary strand, producing a new heteroduplex ...

    The RecA family of ATPases mediates homologous recombination, a reaction essential for maintaining genomic integrity and for generating genetic diversity. RecA, ATP and single-stranded DNA (ssDNA) form a helical filament that binds to double-stranded DNA (dsDNA), searches for homology, and then catalyses the exchange of the complementary strand, producing a new heteroduplex. Here we have solved the crystal structures of the Escherichia coli RecA-ssDNA and RecA-heteroduplex filaments. They show that ssDNA and ATP bind to RecA-RecA interfaces cooperatively, explaining the ATP dependency of DNA binding. The ATP gamma-phosphate is sensed across the RecA-RecA interface by two lysine residues that also stimulate ATP hydrolysis, providing a mechanism for DNA release. The DNA is underwound and stretched globally, but locally it adopts a B-DNA-like conformation that restricts the homology search to Watson-Crick-type base pairing. The complementary strand interacts primarily through base pairing, making heteroduplex formation strictly dependent on complementarity. The underwound, stretched filament conformation probably evolved to destabilize the donor duplex, freeing the complementary strand for homology sampling.


    Organizational Affiliation

    Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York 10021, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Protein recAC [auth A], D [auth C]1706Escherichia coliMutation(s): 0 
Find proteins for P0A7G6 (Escherichia coli (strain K12))
Explore P0A7G6 
Go to UniProtKB:  P0A7G6
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DTP*DT)-3')A [auth B], B [auth D]15N/A
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    ADP
    Query on ADP

    Download Ideal Coordinates CCD File 
    DA [auth C] , EA [auth C] , FA [auth C] , GA [auth C] , HA [auth C] , O [auth A] , P [auth A] , Q [auth A] , 
    DA [auth C],  EA [auth C],  FA [auth C],  GA [auth C],  HA [auth C],  O [auth A],  P [auth A],  Q [auth A],  R [auth A],  S [auth A]
    ADENOSINE-5'-DIPHOSPHATE
    C10 H15 N5 O10 P2
    XTWYTFMLZFPYCI-KQYNXXCUSA-N
     Ligand Interaction
    ALF
    Query on ALF

    Download Ideal Coordinates CCD File 
    AA [auth C] , CA [auth C] , F [auth A] , H [auth A] , J [auth A] , L [auth A] , N [auth A] , U [auth C] , 
    AA [auth C],  CA [auth C],  F [auth A],  H [auth A],  J [auth A],  L [auth A],  N [auth A],  U [auth C],  W [auth C],  Y [auth C]
    TETRAFLUOROALUMINATE ION
    Al F4
    UYOMQIYKOOHAMK-UHFFFAOYSA-J
     Ligand Interaction
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    BA [auth C] , E [auth A] , G [auth A] , I [auth A] , K [auth A] , M [auth A] , T [auth C] , V [auth C] , 
    BA [auth C],  E [auth A],  G [auth A],  I [auth A],  K [auth A],  M [auth A],  T [auth C],  V [auth C],  X [auth C],  Z [auth C]
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.80 Å
    • R-Value Free: 0.236 
    • R-Value Work: 0.214 
    • R-Value Observed: 0.214 
    • Space Group: P 21 21 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 159α = 90
    b = 300.5β = 90
    c = 80.1γ = 90
    Software Package:
    Software NamePurpose
    REFMACrefinement

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    • Deposited Date: 2008-03-24 
    • Released Date: 2008-05-20 
    • Deposition Author(s): Pavletich, N.P.

    Revision History  (Full details and data files)

    • Version 1.0: 2008-05-20
      Type: Initial release
    • Version 1.1: 2011-07-13
      Changes: Version format compliance
    • Version 1.2: 2015-01-21
      Changes: Database references
    • Version 1.3: 2017-07-26
      Changes: Source and taxonomy