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 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: 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 ...

    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.


    Related Citations: 
    • Crystal Structure of a Pyrimidine Dimer-Specific Excision Repair Enzyme from Bacteriophage T4: Refinement at 1.45 Angstroms and X-Ray Analysis of the Three Active Site Mutants
      Morikawa, K., Ariyoshi, M., Vassylyev, D.G., Matsumoto, O., Katayanagi, K., Ohtsuka, E.
      (1995) J Mol Biol 249: 360
    • DNA Repair Enzymes
      Morikawa, K.
      (1993) Curr Opin Struct Biol 3: 17
    • Role of the Basic Amino Acid Cluster and Glu-23 in Pyrimidine Dimer Glycosylase Activity of T4 Endonuclease V
      Doi, T., Recktenwald, A., Karaki, Y., Kikuchi, M., Morikawa, K., Ikehara, M., Inaoka, T., Hori, N., Ohtsuka, E.
      (1992) Proc Natl Acad Sci U S A 89: 9420
    • X-Ray Structure of T4 Endonuclease V: An Excision Repair Enzyme Specific for a Pyrimidine Dimer
      Morikawa, K., Matsumoto, O., Tsujimoto, M., Katayanagi, K., Ariyoshi, M., Doi, T., Ikehara, M., Inaoka, T., Ohtsuka, E.
      (1992) Science 256: 523
    • Preliminary Crystallographic Study of Pyrimidine Dimer-Specific Excision Repair Enzyme from Bacteriophage T4
      Morikawa, K., Tsujimoto, M., Ikehara, M., Inaoka, T., Ohtsuka, E.
      (1988) J Mol Biol 202: 683

    Organizational Affiliation

    Protein Engineering Research Institute, Japan.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (T4 ENDONUCLEASE V (E.C.3.1.25.1)) A137Escherichia virus T4Mutation(s): 1 
Gene Names: DENV
EC: 3.2.2.17 (UniProt), 4.2.99.18 (UniProt)
Find proteins for P04418 (Enterobacteria phage T4)
Explore P04418 
Go to UniProtKB:  P04418
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*AP*TP*CP*GP*CP*GP*TP*TP*GP*CP*GP*CP*T)-3')B13N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*TP*AP*GP*CP*GP*CP*AP*AP*CP*GP*CP*GP*A)-3')C13N/A
      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

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • 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