2DY4 image
Deposition Date 2006-09-06
Release Date 2007-01-09
Last Version Date 2024-10-23
Entry Detail
PDB ID:
2DY4
Keywords:
Title:
Crystal structure of RB69 GP43 in complex with DNA containing Thymine Glycol
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
2.65 Å
R-Value Free:
0.28
R-Value Work:
0.22
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:DNA polymerase
Gene (Uniprot):43
Mutations:D222A, D327A
Chain IDs:I (auth: A), J (auth: B), K (auth: C), L (auth: D)
Chain Length:903
Number of Molecules:4
Biological Source:Enterobacteria phage RB69
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
CTG A DT ?
MSE I MET SELENOMETHIONINE
Primary Citation
A structural rationale for stalling of a replicative DNA polymerase at the most common oxidative thymine lesion, thymine glycol.
Proc.Natl.Acad.Sci.USA 104 814 818 (2007)
PMID: 17210917 DOI: 10.1073/pnas.0606648104

Abstact

Thymine glycol (Tg) is a common product of oxidation and ionizing radiation, including that used for cancer treatment. Although Tg is a poor mutagenic lesion, it has been shown to present a strong block to both repair and replicative DNA polymerases. The 2.65-A crystal structure of a binary complex of the replicative RB69 DNA polymerase with DNA shows that the templating Tg is intrahelical and forms a regular Watson-Crick base pair with the incorporated A. The C5 methyl group protrudes axially from the ring of the damaged pyrimidine and hinders stacking of the adjacent 5' template guanine. The position of the displaced 5' template guanine is such that the next incoming nucleotide cannot be incorporated into the growing primer strand, and it explains why primer extension past the lesion is prohibited even though DNA polymerases can readily incorporate an A across from the Tg lesion.

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Primary Citation of related structures