2HOI

Crystal structure of the tetrameric pre-cleavage synaptic complex in the cre-loxp site-specific recombination


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.601 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Synapsis of loxP sites by Cre recombinase.

Ghosh, K.Guo, F.Van Duyne, G.D.

(2007) J.Biol.Chem. 282: 24004-24016

  • DOI: 10.1074/jbc.M703283200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cre recombinase catalyzes site-specific recombination between 34-bp loxP sites in a variety of topological and cellular contexts. An obligatory step in the recombination reaction is the association, or synapsis, of Cre-bound loxP sites to form a tetr ...

    Cre recombinase catalyzes site-specific recombination between 34-bp loxP sites in a variety of topological and cellular contexts. An obligatory step in the recombination reaction is the association, or synapsis, of Cre-bound loxP sites to form a tetrameric protein assembly that is competent for strand exchange. Using analytical ultracentrifugation and electrophoresis approaches, we have studied the energetics of Cre-mediated synapsis of loxP sites. We found that synapsis occurs with a high affinity (Kd = 10 nM) and is pH-dependent but does not require divalent cations. Surprisingly, the catalytically inactive Cre K201A mutant is fully competent for synapsis of loxP sites, yet the inactive Y324F and R173K mutants are defective for synapsis. These findings have allowed us to determine the first crystal structures of a pre-cleavage Cre-loxP synaptic complex in a configuration representing the starting point in the recombination pathway. When combined with a quantitative analysis of synapsis using loxP mutants, the structures explain how the central 8 bp of the loxP site are able to dictate the order of strand exchange in the Cre system.


    Organizational Affiliation

    Department of Biochemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Recombinase Cre
A, B, G, H
343Escherichia phage P1Mutation(s): 1 
Gene Names: cre
Find proteins for P06956 (Escherichia phage P1)
Go to UniProtKB:  P06956
Entity ID: 1
MoleculeChainsLengthOrganism
LoxP DNAC,E35N/A
Entity ID: 2
MoleculeChainsLengthOrganism
LoxP DNAD,F35N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.601 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.184 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 136.784α = 90.00
b = 136.784β = 90.00
c = 218.275γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-06-26
    Type: Initial release
  • Version 1.1: 2007-10-23
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description