3CMX

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.239 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Protein recAE [auth A], F [auth D]1706Escherichia coliMutation(s): 0 
UniProt
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], C [auth E]15N/A
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*DAP*DAP*DAP*DAP*DAP*DAP*DAP*DAP*DAP*DAP*DAP*DA)-3')B [auth C], D [auth F]12N/A
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Ligands 3 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      ADP
      Query on ADP

      Download Ideal Coordinates CCD File 
      FA [auth D] , GA [auth D] , HA [auth D] , IA [auth D] , JA [auth D] , Q [auth A] , R [auth A] , S [auth A] , 
      FA [auth D],  GA [auth D],  HA [auth D],  IA [auth D],  JA [auth D],  Q [auth A],  R [auth A],  S [auth A],  T [auth A],  U [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 D] , CA [auth D] , EA [auth D] , H [auth A] , J [auth A] , L [auth A] , N [auth A] , P [auth A] , 
      AA [auth D],  CA [auth D],  EA [auth D],  H [auth A],  J [auth A],  L [auth A],  N [auth A],  P [auth A],  W [auth D],  Y [auth D]
      TETRAFLUOROALUMINATE ION
      Al F4
      UYOMQIYKOOHAMK-UHFFFAOYSA-J
       Ligand Interaction
      MG
      Query on MG

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

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 3.40 Å
      • R-Value Free: 0.256 
      • R-Value Work: 0.238 
      • R-Value Observed: 0.239 
      • 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: 2017-07-26
        Changes: Source and taxonomy