3GIL: Dpo4 extension ternary complex with oxoG(anti)-T(anti) pair

Citation:
Abstract
7,8-Dihydro-8-oxoguanine (oxoG), the predominant oxidative DNA damage lesion, is processed differently by high-fidelity and Y-family lesion bypass polymerases. Although high-fidelity polymerases extend predominantly from an A base opposite an oxoG, the Y-family polymerases Dpo4 and human Pol eta preferentially extend from the oxoG*C base pair. We have determined crystal structures of extension Dpo4 ternary complexes with oxoG opposite C, A, G, or T and the next nascent base pair. We demonstrate that neither template backbone nor the architecture of the active site is perturbed by the oxoG(anti)*C and oxoG*A pairs. However, the latter manifest conformational heterogeneity, adopting both oxoG(syn)*A(anti) and oxoG(anti)*A(syn) alignment. Hence, the observed reduced primer extension from the dynamically flexible 3'-terminal primer base A is explained. Because of homology between Dpo4 and Pol eta, such a dynamic screening mechanism might be utilized by Dpo4 and Pol eta to regulate error-free versus error-prone bypass of oxoG and other lesions.
PDB ID: 3GILDownload
MMDB ID: 72795
PDB Deposition Date: 2009/3/5
Updated in MMDB: 2011/12
Experimental Method:
x-ray diffraction
Resolution: 2.71  Å
Source Organism:
Sulfolobus solfataricus P2
Similar Structures:
Biological Unit for 3GIL: trimeric; determined by author and by software (PISA)
Molecular Components in 3GIL
Label Count Molecule
Protein (1 molecule)
1
DNA Polymerase IV(Gene symbol: SSO_RS11880)
Molecule annotation
Nucleotides(2 molecules)
1
5'-d(*gp*tp*tp*gp*gp*ap*tp*gp*gp*tp*ap*gp*(2dt))-3'
Molecule annotation
1
5'-d(*cp*tp*ap*ap*cp*(8og)p*cp*tp*ap*cp*cp*ap*tp*cp*cp*ap*ap*c)-3'
Molecule annotation
Chemicals (4 molecules)
1
1
2
3
* Click molecule labels to explore molecular sequence information.

Citing MMDB
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