3RMA: Crystal Structure of a replicative DNA polymerase bound to DNA containing Thymine Glycol

Thymine glycol (Tg) is the most common oxidation product of thymine and is known to be a strong block to replicative DNA polymerases. A previously solved structure of the bacteriophage RB69 DNA polymerase (RB69 gp43) in complex with Tg in the sequence context 5'-G-Tg-G shed light on how Tg blocks primer elongation: The protruding methyl group of the oxidized thymine displaces the adjacent 5'-G, which can no longer serve as a template for primer elongation [Aller, P., Rould, M. A., Hogg, M, Wallace, S. S. & Doublie S. (2007). 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.]. Several studies showed that in the sequence context 5'-C-Tg-purine, Tg is more likely to be bypassed by Klenow fragment, an A-family DNA polymerase. We set out to investigate the role of sequence context in Tg bypass in a B-family polymerase and to solve the crystal structures of the bacteriophage RB69 DNA polymerase in complex with Tg-containing DNA in the three remaining sequence contexts: 5'-A-Tg-G, 5'-T-Tg-G, and 5'-C-Tg-G. A combination of several factors-including the associated exonuclease activity, the nature of the 3' and 5' bases surrounding Tg, and the cis-trans interconversion of Tg-influences Tg bypass. We also visualized for the first time the structure of a well-ordered exonuclease complex, allowing us to identify and confirm the role of key residues (Phe123, Met256, and Tyr257) in strand separation and in the stabilization of the primer strand in the exonuclease site.
PDB ID: 3RMADownload
MMDB ID: 92561
PDB Deposition Date: 2011/4/20
Updated in MMDB: 2017/11
Experimental Method:
x-ray diffraction
Resolution: 2.84  Å
Source Organism:
Enterobacteria phage RB69
Similar Structures:
Biological Unit for 3RMA: tetrameric; determined by author and by software (PISA)
Molecular Components in 3RMA
Label Count Molecule
Protein (1 molecule)
DNA Polymerase(Gene symbol: 43)
Molecule annotation
Nucleotides(2 molecules)
DNA (5'-d(*cp*gp*ap*(ctg)*gp*ap*ap*tp*gp*ap*cp*ap*gp*cp*cp*gp*cp*g)-3')
Molecule annotation
DNA (5'-d(*gp*cp*gp*gp*cp*tp*gp*tp*cp*ap*tp*tp*cp*a)-3')
Molecule annotation
* Click molecule labels to explore molecular sequence information.

Citing MMDB