2IEF

Structure of the cooperative Excisionase (Xis)-DNA complex reveals a micronucleoprotein filament

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

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


Literature

Structure of the cooperative Xis-DNA complex reveals a micronucleoprotein filament that regulates phage lambda intasome assembly.

Abbani, M.A., Papagiannis, C.V., Sam, M.D., Cascio, D., Johnson, R.C., Clubb, R.T.

(2007) Proc Natl Acad Sci U S A 104: 2109-2114

  • DOI: 10.1073/pnas.0607820104
  • Primary Citation of Related Structures:  
    2IEF

  • PubMed Abstract: 

    • The DNA architectural protein Xis regulates the construction of higher-order nucleoprotein intasomes that integrate and excise the genome of phage lambda from the Escherichia coli chromosome. Xis modulates the directionality of site-specific recombination by stimulating phage excision 10(6)-fold, while simultaneously inhibiting phage reintegration ...

    The DNA architectural protein Xis regulates the construction of higher-order nucleoprotein intasomes that integrate and excise the genome of phage lambda from the Escherichia coli chromosome. Xis modulates the directionality of site-specific recombination by stimulating phage excision 10(6)-fold, while simultaneously inhibiting phage reintegration. Control is exerted by cooperatively assembling onto a approximately 35-bp DNA regulatory element, which it distorts to preferentially stabilize an excisive intasome. Here, we report the 2.6-A crystal structure of the complex between three cooperatively bound Xis proteins and a 33-bp DNA containing the regulatory element. Xis binds DNA in a head-to-tail orientation to generate a micronucleoprotein filament. Although each protomer is anchored to the duplex by a similar set of nonbase specific contacts, malleable protein-DNA interactions enable binding to sites that differ in nucleotide sequence. Proteins at the ends of the duplex sequence specifically recognize similar binding sites and participate in cooperative binding via protein-protein interactions with a bridging Xis protomer that is bound in a less specific manner. Formation of this polymer introduces approximately 72 degrees of curvature into the DNA with slight positive writhe, which functions to connect disparate segments of DNA bridged by integrase within the excisive intasome.

    Organizational Affiliation: 

    Department of Chemistry, University of California, 611 Charles Young Drive East, Los Angeles, CA 90095-1570, USA.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
ExcisionaseD [auth A],
E [auth B],
F [auth C]		55Escherichia virus LambdaMutation(s): 1 
Gene Names: xis
UniProt
Find proteins for P03699 (Escherichia phage lambda)
Explore P03699 
Go to UniProtKB:  P03699
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03699
Protein Feature View
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Entity ID: 1
MoleculeChainsLengthOrganismImage
15-mer DNAA [auth D]15N/A
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Entity ID: 2
MoleculeChainsLengthOrganismImage
19-mer DNAB [auth E]19N/A
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Entity ID: 3
MoleculeChainsLengthOrganismImage
34-mer DNAC [auth F]34N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.655α = 90
b = 111.655β = 90
c = 76.268γ = 120
Software Package:
Software NamePurpose
BOSdata collection
SHELXmodel building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-02-06
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2021-10-20
    Changes: Database references