4CRX

ASYMMETRIC DNA-BENDING IN THE CRE-LOXP SITE-SPECIFIC RECOMBINATION SYNAPSE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Asymmetric DNA bending in the Cre-loxP site-specific recombination synapse.

Guo, F.Gopaul, D.N.Van Duyne, G.D.

(1999) Proc.Natl.Acad.Sci.USA 96: 7143-7148

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cre recombinase catalyzes site-specific recombination between two 34-bp loxP sites in a variety of DNA substrates. At the start of the recombination pathway, the loxP sites are each bound by two recombinase molecules, and synapsis of the sites is med ...

    Cre recombinase catalyzes site-specific recombination between two 34-bp loxP sites in a variety of DNA substrates. At the start of the recombination pathway, the loxP sites are each bound by two recombinase molecules, and synapsis of the sites is mediated by Cre-Cre interactions. We describe the structures of synaptic complexes formed between a symmetrized loxP site and two Cre mutants that are defective in strand cleavage. The DNA in these complexes is bent sharply at a single base pair step at one end of the crossover region in a manner that is atypical of protein-induced DNA bends. A large negative roll (-49 degrees) and a positive tilt (16 degrees) open the major groove toward the center of the synapse and compress the minor groove toward the protein-DNA interface. The bend direction of the site appears to determine which of the two DNA substrate strands will be cleaved and exchanged in the initial stages of the recombination pathway. These results provide a structural basis for the observation that exchange of DNA strands proceeds in a defined order in some tyrosine recombinase systems. The Cre-loxS synaptic complex structure supports a model in which synapsis of the loxP sites results in formation of a Holliday junction-like DNA architecture that is maintained through the initial cleavage and strand exchange steps in the site-specific recombination pathway.


    Related Citations: 
    • Structure of Cre Recombinase Complexed with DNA in a Site-Specific Recombination Synapse
      Guo, F.,Gopaul, D.N.,Van Duyne, G.D.
      (1997) Nature 389: 40


    Organizational Affiliation

    Department of Biochemistry and Biophysics and Johnson Research Foundation, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (CRE RECOMBINASE)
A, B
322Escherichia phage P1Mutation(s): 1 
Gene Names: cre
Find proteins for P06956 (Escherichia phage P1)
Go to UniProtKB:  P06956
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (35 NUCLEOTIDE CRE RECOGNITION SITE)C,D35N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.213 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 108.800α = 90.00
b = 122.100β = 90.00
c = 181.000γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORmodel building
CCP4data scaling
X-PLORrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-06-14
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance