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 

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

  • Primary Citation of Related Structures:  1PVP, 1PVQ

  • 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 ...

    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: 
    • 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
    • Directed evolution of the site specificity of Cre recombinase.
      Santoro, S.W.,Schultz, P.G.
      (2002) Proc.Natl.Acad.Sci.USA 99: 4185
    • 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: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Recombinase CRE
A, B
349Enterobacteria phage P1Gene Names: cre
Find proteins for P06956 (Enterobacteria phage P1)
Go to UniProtKB:  P06956
Entity ID: 1
MoleculeChainsLengthOrganism
34-MERC34N/A
Entity ID: 2
MoleculeChainsLengthOrganism
34-MERD34N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.212 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 107.390α = 90.00
b = 121.570β = 90.00
c = 179.950γ = 90.00
Software Package:
Software NamePurpose
TNTrefinement
TNTphasing
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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