1VAS

ATOMIC MODEL OF A PYRIMIDINE DIMER SPECIFIC EXCISION REPAIR ENZYME COMPLEXED WITH A DNA SUBSTRATE: STRUCTURAL BASIS FOR DAMAGED DNA RECOGNITION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.152 

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This is version 1.5 of the entry. See complete history


Literature

Atomic model of a pyrimidine dimer excision repair enzyme complexed with a DNA substrate: structural basis for damaged DNA recognition.

Vassylyev, D.G.Kashiwagi, T.Mikami, Y.Ariyoshi, M.Iwai, S.Ohtsuka, E.Morikawa, K.

(1995) Cell 83: 773-782

  • DOI: https://doi.org/10.1016/0092-8674(95)90190-6
  • Primary Citation of Related Structures:  
    1VAS

  • PubMed Abstract: 

    T4 endonuclease V is a DNA repair enzyme from bacteriophage T4 that catalyzes the first reaction step of the pyrimidine dimer-specific base excision repair pathway. The crystal structure of this enzyme complexed with a duplex DNA substrate, containing a thymine dimer, has been determined at 2.75 A resolution. The atomic structure of the complex reveals the unique conformation of the DNA duplex, which exhibits a sharp kink with a 60 degree inclination at the central thymine dimer. The adenine base complementary to the 5' side of the thymine dimer is completely flipped out of the DNA duplex and trapped in a cavity on the protein surface. These structural features allow an understanding of the catalytic mechanism and implicate a general mechanism of how other repair enzymes recognize damaged DNA duplexes.


  • Organizational Affiliation

    Protein Engineering Research Institute, Japan.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (T4 ENDONUCLEASE V (E.C.3.1.25.1))C [auth A]137Tequatrovirus T4Mutation(s): 1 
Gene Names: DENV
UniProt
Find proteins for P04418 (Enterobacteria phage T4)
Explore P04418 
Go to UniProtKB:  P04418
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04418
Sequence Annotations
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  • Reference Sequence

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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*TP*CP*GP*CP*GP*TP*TP*GP*CP*GP*CP*T)-3')A [auth B]13N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*AP*GP*CP*GP*CP*AP*AP*CP*GP*CP*GP*A)-3')B [auth C]13N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.152 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.82α = 90
b = 118.82β = 90
c = 36.28γ = 120
Software Package:
Software NamePurpose
X-PLORrefinement
ELMSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-01-31
    Type: Initial release
  • Version 1.1: 2008-05-22
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2013-05-01
    Changes: Derived calculations, Other
  • Version 1.4: 2021-11-03
    Changes: Database references, Derived calculations
  • Version 1.5: 2024-02-14
    Changes: Data collection