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 

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


  • 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, containin ...

    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: 
    • 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
    • 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.USA 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
    • 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


    Organizational Affiliation

    Protein Engineering Research Institute, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (T4 ENDONUCLEASE V (E.C.3.1.25.1))
A
137Enterobacteria phage T4Mutation(s): 1 
EC: 3.2.2.17
Find proteins for P04418 (Enterobacteria phage T4)
Go to UniProtKB:  P04418
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*AP*TP*CP*GP*CP*GP*TP*TP*GP*CP*GP*CP*T)-3')B13N/A
Entity ID: 2
MoleculeChainsLengthOrganism
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 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 118.820α = 90.00
b = 118.820β = 90.00
c = 36.280γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement
ELMSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-01-31
    Type: Initial release
  • Version 1.1: 2008-05-22
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2013-05-01
    Type: Derived calculations, Other