ISDA: 1VAS

Deposition Date 1995-09-08

Release Date 1996-01-31

Last Version Date 2024-02-14

Entry Detail

PDB ID:

1VAS

Keywords:

HYDROLASE/DNA

Title:

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

Biological Source:

Source Organism:

Enterobacteria phage T4 (Taxon ID: 10665)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.75 Å

R-Value Free:

0.24

R-Value Work:

0.15

R-Value Observed:

0.15

Space Group:

P 65

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Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:PROTEIN (T4 ENDONUCLEASE V (E.C.3.1.25.1))
Chain IDs:C (auth: A)
Chain Length:137
Number of Molecules:1
Biological Source:Enterobacteria phage T4

UniProt ID:P04418 Pfam ID:PF03013 EC:3.1.25.1

Primary Citation

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, Morikawa, K, Ariyoshi, M, Vassylyev, D.G, Matsumoto, O, Katayanagi, K, Ohtsuka, E, Morikawa, K, Doi, T, Recktenwald, A, Karaki, Y, Kikuchi, M, Morikawa, K, Ikehara, M, Inaoka, T, Hori, N, Ohtsuka, E, Morikawa, K, Matsumoto, O, Tsujimoto, M, Katayanagi, K, Ariyoshi, M, Doi, T, Ikehara, M, Inaoka, T, Ohtsuka, E, Morikawa, K, Tsujimoto, M, Ikehara, M, Inaoka, T, Ohtsuka, E.Show

Cell(Cambridge,Mass.) 83 773 782 (1995)

PMID: 8521494 DOI: 10.1016/0092-8674(95)90190-6

Abstact

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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Primary Citation of related structures

Abstact

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