1VAS

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

• PDB DOI: https://doi.org/10.2210/pdb1VAS/pdb
• NAKB: 1VAS

• Classification: HYDROLASE/DNA
• Organism(s): Tequatrovirus T4
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1995-09-08 Released: 1996-01-31 
• Deposition Author(s): Vassylyev, D.G., Kashiwagi, T., Mikami, Y., Ariyoshi, M., Iwai, S., Ohtsuka, E., Morikawa, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.240 (Depositor) 
• R-Value Work: 
  0.152 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.152 (Depositor) 

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: 8521494 
• 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.

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Organizational Affiliation: 

Protein Engineering Research Institute, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 23.92 kDa 
• Atom Count: 1,799 
• Modelled Residue Count: 163 
• Deposited Residue Count: 163 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (T4 ENDONUCLEASE V (E.C.3.1.25.1))	C [auth A]	137	Tequatrovirus T4	Mutation(s): 1  Gene Names: DENV EC: 3.2.2.17 (UniProt), 4.2.99.18 (UniProt)
UniProt
Find proteins for P04418 (Enterobacteria phage T4) Explore P04418  Go to UniProtKB:  P04418

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*TP*CP*GP*CP*GP*TP*TP*GP*CP*GP*CP*T)-3')	A [auth B]	13	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*AP*GP*CP*GP*CP*AP*AP*CP*GP*CP*GP*A)-3')	B [auth C]	13	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.240 (Depositor) 
• R-Value Work:  0.152 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.152 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.82	α = 90
b = 118.82	β = 90
c = 36.28	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	refinement
ELMS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 1996-01-31 
Deposition Author(s): Vassylyev, D.G., Kashiwagi, T., Mikami, Y., Ariyoshi, M., Iwai, S., Ohtsuka, E., Morikawa, K.

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
• Version 1.4: 2021-11-03
  Changes: Database references, Derived calculations
• Version 1.5: 2024-02-14
  Changes: Data collection