1Z19

Crystal structure of a lambda integrase(75-356) dimer bound to a COC' core site

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 

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This is version 1.3 of the entry. See complete history. 


Literature

A structural basis for allosteric control of DNA recombination by lambda integrase.

Biswas, T., Aihara, H., Radman-Livaja, M., Filman, D., Landy, A., Ellenberger, T.

(2005) Nature 435: 1059-1066

  • DOI: 10.1038/nature03657
  • Primary Citation of Related Structures:  
    1Z19, 1Z1B, 1Z1G

  • PubMed Abstract: 

    • Site-specific DNA recombination is important for basic cellular functions including viral integration, control of gene expression, production of genetic diversity and segregation of newly replicated chromosomes, and is used by bacteriophage lambda to integrate or excise its genome into and out of the host chromosome ...

    Site-specific DNA recombination is important for basic cellular functions including viral integration, control of gene expression, production of genetic diversity and segregation of newly replicated chromosomes, and is used by bacteriophage lambda to integrate or excise its genome into and out of the host chromosome. lambda recombination is carried out by the bacteriophage-encoded integrase protein (lambda-int) together with accessory DNA sites and associated bending proteins that allow regulation in response to cell physiology. Here we report the crystal structures of lambda-int in higher-order complexes with substrates and regulatory DNAs representing different intermediates along the reaction pathway. The structures show how the simultaneous binding of two separate domains of lambda-int to DNA facilitates synapsis and can specify the order of DNA strand cleavage and exchange. An intertwined layer of amino-terminal domains bound to accessory (arm) DNAs shapes the recombination complex in a way that suggests how arm binding shifts the reaction equilibrium in favour of recombinant products.

    Organizational Affiliation: 

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
IntegraseD [auth A],
E [auth B]		283Escherichia virus LambdaMutation(s): 9 
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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03700
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-D(*CP*TP*CP*GP*TP*TP*CP*AP*GP*CP*TP*TP*TP*TP*TP*T)-3'A [auth C]16N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-D(P*TP*TP*TP*AP*TP*AP*CP*TP*AP*AP*GP*TP*TP*GP*GP*CP*AP*TP*TP*A)-3'B [auth D]20N/A
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsLengthOrganismImage
33-MERC [auth E]33N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE		D [auth A],
E [auth B]		L-PEPTIDE LINKINGC5 H11 N O2 SeMET
PTR
Query on PTR		D [auth A],
E [auth B]		L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.297α = 90
b = 121.481β = 90
c = 65.387γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
TRUNCATEdata reduction
MLPHAREphasing
CNSrefinement
HKL-2000data reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-06-28
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations