1PVR

BASIS FOR A SWITCH IN SUBSTRATE SPECIFICITY: CRYSTAL STRUCTURE OF SELECTED VARIANT OF CRE SITE-SPECIFIC RECOMBINASE, LNSGG BOUND TO THE LOXP (WILDTYPE) RECOGNITION SITE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.212 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A specificity switch in selected cre recombinase variants is mediated by macromolecular plasticity and water.

Baldwin, E.P.Martin, S.S.Abel, J.Gelato, K.A.Kim, H.Schultz, P.G.Santoro, S.W.

(2003) Chem Biol 10: 1085-1094

  • DOI: 10.1016/j.chembiol.2003.10.015
  • Primary Citation of Related Structures:  
    1PVR, 1PVQ, 1PVP

  • PubMed Abstract: 
  • The basis for the altered DNA specificities of two Cre recombinase variants, obtained by mutation and selection, was revealed by their cocrystal structures. The proteins share similar substitutions but differ in their preferences for the natural LoxP substrate and an engineered substrate that is inactive with wild-type Cre, LoxM7 ...

    The basis for the altered DNA specificities of two Cre recombinase variants, obtained by mutation and selection, was revealed by their cocrystal structures. The proteins share similar substitutions but differ in their preferences for the natural LoxP substrate and an engineered substrate that is inactive with wild-type Cre, LoxM7. One variant preferentially recombines LoxM7 and contacts the substituted bases through a hydrated network of novel interlocking protein-DNA contacts. The other variant recognizes both LoxP and LoxM7 utilizing the same DNA backbone contact but different base contacts, facilitated by an unexpected DNA shift. Assisted by water, novel interaction networks can arise from few protein substitutions, suggesting how new DNA binding specificities might evolve. The contributions of macromolecular plasticity and water networks in specific DNA recognition observed here present a challenge for predictive schemes.


    Related Citations: 
    • Directed evolution of the site specificity of Cre recombinase.
      Santoro, S.W., Schultz, P.G.
      (2002) Proc Natl Acad Sci U S A 99: 4185
    • 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.
      (2003) Biochemistry 42: 6814
    • 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

    Organizational Affiliation

    Section of Molecular and Cellular Biology, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA. epbaldwin@ucdavis.edu



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Recombinase CREC [auth A], D [auth B]349Escherichia virus P1Mutation(s): 5 
Gene Names: cre
UniProt
Find proteins for P06956 (Escherichia phage P1)
Explore P06956 
Go to UniProtKB:  P06956
Protein Feature View
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
34-MERA [auth C]34N/A
Protein Feature View
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsLengthOrganismImage
34-MERB [auth D]34N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.212 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.39α = 90
b = 121.57β = 90
c = 179.95γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
TNTrefinement
TNTphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-02-17
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance