3CMT

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.217 

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

  • 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 ...

    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: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Protein recA
A, D
1706Escherichia coli (strain K12)Gene Names: recA (lexB, recH, rnmB, tif, umuB, zab)
Find proteins for P0A7G6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7G6
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*DTP*DTP*DTP*DTP*DTP*DCP*DCP*DCP*DAP*DCP*DCP*DTP*DTP*DTP*DT)-3')B,E15N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(P*DGP*DGP*DTP*DGP*DGP*DG)-3')C,F6N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
A, D
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
ALF
Query on ALF

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Download CCD File 
A, D
TETRAFLUOROALUMINATE ION
Al F4
UYOMQIYKOOHAMK-UHFFFAOYSA-J
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.217 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 159.000α = 90.00
b = 300.500β = 90.00
c = 80.100γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-05-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-07-26
    Type: Advisory, Source and taxonomy