1AE9 | pdb_00001ae9

STRUCTURE OF THE LAMBDA INTEGRASE CATALYTIC CORE

• PDB DOI: https://doi.org/10.2210/pdb1AE9/pdb

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


• Deposited: 1997-03-06 Released: 1997-11-19 
• Deposition Author(s): Kwon, H.J., Tirumalai, R., Landy, A., Ellenberger, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.232 (Depositor) 
• R-Value Work: 
  0.199 (Depositor) 
• R-Value Observed: 
  0.199 (Depositor) 

Literature

Flexibility in DNA recombination: structure of the lambda integrase catalytic core.

Kwon, H.J., Tirumalai, R., Landy, A., Ellenberger, T.

(1997) Science 276: 126-131

• PubMed: 9082984 
• DOI: https://doi.org/10.1126/science.276.5309.126
• Primary Citation Related Structures: 
  1AE9


• PubMed Abstract: 
  

  Lambda integrase is archetypic of site-specific recombinases that catalyze intermolecular DNA rearrangements without energetic input. DNA cleavage, strand exchange, and religation steps are linked by a covalent phosphotyrosine intermediate in which Tyr342 is attached to the 3'-phosphate of the DNA cut site. The 1.9 angstrom crystal structure of the integrase catalytic domain reveals a protein fold that is conserved in organisms ranging from archaebacteria to yeast and that suggests a model for interaction with target DNA. The attacking Tyr342 nucleophile is located on a flexible loop about 20 angstroms from a basic groove that contains all the other catalytically essential residues. This bipartite active site can account for several apparently paradoxical features of integrase family recombinases, including the capacity for both cis and trans cleavage of DNA.

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Organizational Affiliation: 
• Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston MA 02115, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 40.53 kDa 
• Atom Count: 2,813 
• Modeled Residue Count: 337 
• Deposited Residue Count: 358 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LAMBDA INTEGRASE	A, B	179	Lambdavirus lambda	Mutation(s): 1  EC: 3.1 (UniProt), 2.7.7 (UniProt)
UniProt
Find proteins for P03700 (Escherichia phage lambda) Explore P03700  Go to UniProtKB:  P03700

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.232 (Depositor) 
• R-Value Work:  0.199 (Depositor) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.32	α = 90
b = 107.32	β = 90
c = 108.71	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-11-19 
Deposition Author(s): Kwon, H.J., Tirumalai, R., Landy, A., Ellenberger, T.

Revision History  

• Version 1.0: 1997-11-19
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-11-03
  Changes: Database references, Other
• Version 1.4: 2024-02-07
  Changes: Data collection