Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 99.43 kDa 
• Atom Count: 6738 
• Modelled Residue Count: 708 
• Deposited Residue Count: 766 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

1PVP

BASIS FOR A SWITCH IN SUBSTRATE SPECIFICITY: CRYSTAL STRUCTURE OF SELECTED VARIANT OF CRE SITE-SPECIFIC RECOMBINASE, ALSHG BOUND TO THE ENGINEERED RECOGNITION SITE LOXM7

• PDB DOI: 10.2210/pdb1PVP/pdb
• NDB: PD0457

• Classification: RECOMBINATION/DNA
• Organism(s): Escherichia virus P1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2003-06-28 Released: 2004-02-17 
• Deposition Author(s): Baldwin, E.P., Martin, S.S., Abel, J., Gelato, K.A., Kim, H., Schultz, P.G., Santoro, S.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.294 
• R-Value Work: 0.232 
• R-Value Observed: 0.232 

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

• PubMed: 14652076 
• DOI: 10.1016/j.chembiol.2003.10.015
• Primary Citation of Related Structures:  
  1PVP, 1PVQ, 1PVR


• 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. 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.

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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

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Organizational Affiliation: 

Section of Molecular and Cellular Biology, University of California, Davis, 1 Shields Avenue, Davis, CA 95616, USA. [e-mail]

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Recombinase cre	C [auth A], D [auth B]	349	Escherichia virus P1	Mutation(s): 5  Gene Names: cre
UniProt
Find proteins for P06956 (Escherichia phage P1) Explore P06956  Go to UniProtKB:  P06956

Entity ID: 1
Molecule	Chains	Length	Organism	Image
34-MER	A [auth C]	34	Escherichia virus P1

Entity ID: 2
Molecule	Chains	Length	Organism	Image
34-MER	B [auth D]	34	Escherichia virus P1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.294 
• R-Value Work: 0.232 
• R-Value Observed: 0.232 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.78	α = 90
b = 121.47	β = 90
c = 180.69	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
TNT	refinement
TNT	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-06-28 
• Released Date: 2004-02-17 
Deposition Author(s): Baldwin, E.P., Martin, S.S., Abel, J., Gelato, K.A., Kim, H., Schultz, P.G., Santoro, S.W.

Revision History  

• 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
• Version 1.3: 2012-02-01
  Changes: Other
• Version 2.0: 2021-04-07
  Changes: Advisory, Database references, Non-polymer description, Source and taxonomy, Structure summary