1CRX

CRE RECOMBINASE/DNA COMPLEX REACTION INTERMEDIATE I

• PDB DOI: https://doi.org/10.2210/pdb1CRX/pdb
• NAKB: 1CRX

• Classification: REPLICATION/DNA
• Organism(s): Punavirus P1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 1997-07-02 Released: 1998-10-14 
• Deposition Author(s): Guo, F., Gopaul, D.N., Van Duyne, G.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.263 
• R-Value Work: 0.201 

Literature

Structure of Cre recombinase complexed with DNA in a site-specific recombination synapse.

Guo, F., Gopaul, D.N., van Duyne, G.D.

(1997) Nature 389: 40-46

• PubMed: 9288963 
• DOI: https://doi.org/10.1038/37925
• Primary Citation of Related Structures:  
  1CRX


• PubMed Abstract: 
  

  During site-specific DNA recombination, which brings about genetic rearrangement in processes such as viral integration and excision and chromosomal segregation, recombinase enzymes recognize specific DNA sequences and catalyse the reciprocal exchange of DNA strands between these sites. The bacteriophage recombinase Cre catalyses site-specific recombination between two 34-base-pair loxP sites. The crystal structure at 2.4 A resolution of Cre bound to a loxP substrate reveals an intermediate in the recombination reaction, in which a Cre molecule has cleaved the substrate to form a covalent 3'-phosphotyrosine linkage with the DNA. Four recombinases and two loxP sites form a synapsed structure in which the DNA resembles models of four-way Holliday-Junction intermediates. The Cre-loxP complex challenges models of site-specific recombination that require large changes in quaternary structure. Subtle allosteric changes at the carboxy termini of the Cre subunits may instead coordinate the cleavage and strand-exchange reactions.

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Organizational Affiliation: 

Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia 19104, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 93.74 kDa 
• Atom Count: 6,977 
• Modelled Residue Count: 712 
• Deposited Residue Count: 712 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
CRE RECOMBINASE	E [auth A], F [auth B]	322	Punavirus P1	Mutation(s): 0  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
DNA (5'-D(*TP*AP*TP*AP*AP*CP*TP*TP*CP*GP*TP*AP*TP*AP*G)-3')	A [auth C]	15	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*TP*AP*TP*GP*CP*TP*AP*TP*AP*CP*GP*AP*AP*GP*TP*TP*AP*T)-3')	B [auth D], D [auth F]	19	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*TP*AP*AP*CP*TP*TP*CP*GP*TP*AP*TP*AP*GP*C)-3')	C [auth E]	15	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	G [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.263 
• R-Value Work: 0.201 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.7	α = 90
b = 121	β = 90
c = 180.4	γ = 90

Software Package:

Software Name	Purpose
MLPHARE	phasing
LOCAL	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
LOCAL	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-10-14 
Deposition Author(s): Guo, F., Gopaul, D.N., Van Duyne, G.D.

Revision History  

• Version 1.0: 1998-10-14
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance