1KBU

CRE RECOMBINASE BOUND TO A LOXP HOLLIDAY JUNCTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Order of Strand Exchanges in Cre-LoxP Recombination and its Basis Suggested by the Crystal Structure of a Cre-LoxP Holliday Junction Complex

Martin, S.S.Pulido, E.Chu, V.C.Lechner, T.S.Baldwin, E.P.

(2002) J.Mol.Biol. 319: 107-127

  • DOI: 10.1016/S0022-2836(02)00246-2

  • PubMed Abstract: 
  • Cre recombinase uses two pairs of sequential cleavage and religation reactions to exchange homologous DNA strands between 34 base-pair (bp) LoxP recognition sequences. In the oligomeric recombination complex, a switch between "cleaving" and "non-clea ...

    Cre recombinase uses two pairs of sequential cleavage and religation reactions to exchange homologous DNA strands between 34 base-pair (bp) LoxP recognition sequences. In the oligomeric recombination complex, a switch between "cleaving" and "non-cleaving" subunit conformations regulates the number, order, and regio-specificity of the strand exchanges. However, the particular sequence of events has been in question. From analysis of strand composition of the Holliday junction (HJ) intermediate, we determined that Cre initiates recombination of LoxP by cleaving the upper strand on the left arm. Cre preferred to react with the left arm of a LoxP suicide substrate, but at a similar rate to the right arm, indicating that the first strand to be exchanged is selected prior to cleavage. We propose that during complex assembly the cleaving subunit preferentially associates with the LoxP left arm, directing the first strand exchange to that side. In addition, this biased assembly would enforce productive orientation of LoxP sites in the recombination synapses. A novel Cre-HJ complex structure in which LoxP was oriented with the left arm bound by the cleaving Cre subunit suggested a physical basis for the strand exchange order. Lys86 and Lys201 interact with the left arm scissile adenine base differently than in structures that have a scissile guanine. These interactions are associated with positioning the 198-208 loop, a structural component of the conformational switch, in a configuration that is specific to the cleaving conformation. Our results suggest that strand exchange order and site alignment are regulated by an "induced fit" mechanism in which the cleaving conformation is selectively stabilized through protein-DNA interactions with the scissile base on the strand that is cleaved first.


    Related Citations: 
    • Quasi-Equivalence in Site-Specific Recombinase Structure and Function: Crystal Structure and Activity of Trimeric Cre Recombinase Bound to a Three-Way Lox DNA Junction
      Woods, K.C.,Martin, S.S.,Chu, V.C.,Baldwin, E.P.
      (2001) J.Mol.Biol. 313: 49
    • Structure of the Holliday Junction Intermediate in Cre-loxP Site-Specific Recombination
      Gopaul, D.N.,Guo, F.,van Duyne, G.D.
      (1998) Embo J. 17: 4175


    Organizational Affiliation

    Section of Molecular and Cellular Biology, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
CRE RECOMBINASE
A, B
349Enterobacteria phage P1Gene Names: cre
Find proteins for P06956 (Enterobacteria phage P1)
Go to UniProtKB:  P06956
Entity ID: 1
MoleculeChainsLengthOrganism
LOXPC34N/A
Entity ID: 2
MoleculeChainsLengthOrganism
LOXPD34N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.231 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 107.170α = 90.00
b = 121.600β = 90.00
c = 179.310γ = 90.00
Software Package:
Software NamePurpose
TNTphasing
CCP4data scaling
TNTrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-06-07
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance