1MA7

Crystal structure of Cre site-specific recombinase complexed with a mutant DNA substrate, LoxP-A8/T27


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.239 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Modulation of the active complex assembly and turnover rate by protein-DNA interactions in Cre-LoxP recombination

Martin, S.S.Chu, V.C.Baldwin, E.P.

(2003) Biochemistry 42: 6814-6826

  • DOI: 10.1021/bi0272306
  • Primary Citation of Related Structures:  
    1MA7

  • PubMed Abstract: 
  • Cre promotes recombination at the 34 bp LoxP sequence. Substitution of a critical C-G base pair in LoxP with an A-T base pair, to give LoxAT, reduced Cre binding in vitro and abolished recombination in vivo [Hartung, M., and Kisters-Woike, B. (1998) J. Biol ...

    Cre promotes recombination at the 34 bp LoxP sequence. Substitution of a critical C-G base pair in LoxP with an A-T base pair, to give LoxAT, reduced Cre binding in vitro and abolished recombination in vivo [Hartung, M., and Kisters-Woike, B. (1998) J. Biol. Chem. 273, 22884-22891].We demonstrated that LoxAT can be recombined in vitro. However, Cre discriminates against this substrate both before and after DNA binding. The preference for LoxP over LoxAT is the result of reduced binding and a slower turnover rate, amplified by changes in cooperativity of complex assembly. With LoxAT, similar levels of substrate turnover required 2-2.5-fold higher protein-DNA concentrations compared to LoxP, but the sigmoidal behavior of the concentration dependence was more pronounced. Further, the Cre-LoxAT complexes reacted 4-5-fold more slowly. In the 2.3 A resolution Cre-LoxAT complex structure, the major groove Arg259-guanine interaction was disrupted, explaining the reduced binding. Overall structural shifts and mobility changes indicate more favorable interactions between subunits, providing a hypothesis for the reduced turnover rate. Concomitant with the displacement of Arg259 from the DNA, adjacent charged residues Glu262 and Glu266 shifted to form salt bridges with the Arg259 guanidinium moiety. Substitution of Glu262 and Glu266 with glutamine increased Cre complex assembly efficiency and reaction rates with both LoxAT and LoxP, but diminished Cre's ability to distinguish them. The increased rate of this variant suggests that DNA substrate binding and turnover are coupled. The improved efficiency, made at some expense of sequence discrimination, may be useful for enhancing recombination in vivo.


    Related Citations: 
    • 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
    • Structure of Cre recombinase complexed with DNA in a site-specific recombination synapse
      Guo, F., Gopaul, D., van Duyne, G.D.
      (1997) Nature 389: 40
    • A structural view of cre-loxp site-specific recombination
      van Duyne, G.D.
      (2001) Annu Rev Biophys Biomol Struct 30: 87

    Organizational Affiliation

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



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
CRE RECOMBINASEC [auth A], D [auth B]349Escherichia virus P1Mutation(s): 0 
Gene Names: cre
UniProt
Find proteins for P06956 (Escherichia phage P1)
Explore P06956 
Go to UniProtKB:  P06956
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
LOXPA [auth C]34N/A
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
LOXPB [auth D]34N/A
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.239 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.54α = 90
b = 122.24β = 90
c = 180.03γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
TNTrefinement
TNTphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-07-08
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance