3CMV

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.30 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.244 

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Ligand Structure Quality Assessment 


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:  
    3CMT, 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 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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein recA
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H
1,357Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A7G6 (Escherichia coli (strain K12))
Explore P0A7G6 
Go to UniProtKB:  P0A7G6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7G6
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP

Download Ideal Coordinates CCD File 
AB [auth F],
BB [auth F],
CA [auth C],
CB [auth F],
DA [auth C],
AB [auth F],
BB [auth F],
CA [auth C],
CB [auth F],
DA [auth C],
DB [auth F],
EA [auth C],
FA [auth C],
IB [auth G],
JB [auth G],
KA [auth D],
KB [auth G],
LA [auth D],
LB [auth G],
M [auth A],
MA [auth D],
N [auth A],
NA [auth D],
O [auth A],
P [auth A],
QB [auth H],
RB [auth H],
SA [auth E],
SB [auth H],
TA [auth E],
TB [auth H],
U [auth B],
UA [auth E],
V [auth B],
VA [auth E],
W [auth B],
X [auth B]
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth C],
BA [auth C],
EB [auth G],
FB [auth G],
GA [auth D],
AA [auth C],
BA [auth C],
EB [auth G],
FB [auth G],
GA [auth D],
GB [auth G],
HA [auth D],
HB [auth G],
I [auth A],
IA [auth D],
J [auth A],
JA [auth D],
K [auth A],
L [auth A],
MB [auth H],
NB [auth H],
OA [auth E],
OB [auth H],
PA [auth E],
PB [auth H],
Q [auth B],
QA [auth E],
R [auth B],
RA [auth E],
S [auth B],
T [auth B],
WA [auth F],
XA [auth F],
Y [auth C],
YA [auth F],
Z [auth C],
ZA [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.30 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.244 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 176.6α = 90
b = 189.8β = 90
c = 424.3γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

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