Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 87.8 kDa 
• Atom Count: 5,884 
• Modelled Residue Count: 638 
• Deposited Residue Count: 644 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

 1P7D

Crystal structure of the Lambda Integrase (residues 75-356) bound to DNA

• PDB DOI: 10.2210/pdb1P7D/pdb
• NDB: PD0428

• Classification: DNA Binding Protein/DNA
• Organism(s): Lambdavirus lambda
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-05-01 Released: 2003-08-12 
• Deposition Author(s): Aihara, H., Kwon, H.J., Nunes-Duby, S.E., Landy, A., Ellenberger, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 0.259 
• R-Value Work: 0.231 

Literature

A Conformational Switch Controls the DNA Cleavage Activity of Lambda Integrase

Aihara, H., Kwon, H.J., Nunes-Duby, S.E., Landy, A., Ellenberger, T.

(2003) Mol Cell 12: 187-198

• PubMed: 12887904 
• DOI: 10.1016/s1097-2765(03)00268-5
• Primary Citation of Related Structures:  
  1P7D


• PubMed Abstract: 
  

The bacteriophage lambda integrase protein (lambda Int) belongs to a family of tyrosine recombinases that catalyze DNA rearrangements. We have determined a crystal structure of lambda Int complexed with a cleaved DNA substrate through a covalent phosphotyrosine bond. In comparison to an earlier unliganded structure, we observe a drastic conformational change in DNA-bound lambda Int that brings Tyr342 into the active site for cleavage of the DNA in cis. A flexible linker connects the central and the catalytic domains, allowing the protein to encircle the DNA. Binding specificity is achieved through direct interactions with the DNA and indirect readout of the flexibility of the att site. The conformational switch that activates lambda Int for DNA cleavage exposes the C-terminal 8 residues for interactions with a neighboring Int molecule. The protein interactions mediated by lambda Int's C-terminal tail offer a mechanism for the allosteric control of cleavage activity in higher order lambda Int complexes.

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Organizational Affiliation: 

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrase	E [auth A], F [auth B]	283	Lambdavirus lambda	Mutation(s): 1  Gene Names: int EC: 2.7.7 (UniProt), 3.1 (UniProt)
UniProt
Find proteins for P03700 (Escherichia phage lambda) Explore P03700  Go to UniProtKB:  P03700

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*CP*AP*AP*TP*GP*CP*CP*AP*AP*CP*TP*TP*T)-3'	A [auth C], C [auth E]	13	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
26-MER	B [auth D], D [auth F]	26	N/A

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	E [auth A], F [auth B]	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 0.259 
• R-Value Work: 0.231 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.021	α = 90
b = 106.161	β = 92.1
c = 73.165	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
TRUNCATE	data reduction
MLPHARE	phasing
CNS	refinement
HKL-2000	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-08-12 
Deposition Author(s): Aihara, H., Kwon, H.J., Nunes-Duby, S.E., Landy, A., Ellenberger, T.

Revision History  

• Version 1.0: 2003-08-12
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance