3GIM

Dpo4 extension ternary complex with oxoG(anti)-G(syn) pair

Summary for 3GIM

• Entry DOI: 10.2210/pdb3gim/pdb
• Related: 2ASD 2ASJ 2ASL 3GII 3GIJ 3GIK 3GIL
• Descriptor: DNA polymerase IV, 5'-D(*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(DDG))-3', 5'-D(*CP*TP*AP*AP*CP*(8OG)P*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*C)-3', ... (6 entities in total)
• Functional Keywords: dna polymerase, 8-oxoguanine, y-family, lesion bypass, dna damage, dna repair, dna replication, dna-binding, dna-directed dna polymerase, magnesium, metal-binding, mutator protein, nucleotidyltransferase, transferase, transferase-dna complex, transferase/dna
• Biological source: Sulfolobus solfataricus P2; More
• Cellular location: Cytoplasm : Q97W02
• Total number of polymer chains: 3
• Total formula weight: 49064.98

Authors

Rechkoblit, O.,Malinina, L.,Patel, D.J. (deposition date: 2009-03-05, release date: 2009-05-19, Last modification date: 2023-09-06)

Primary citation

Rechkoblit, O.,Malinina, L.,Cheng, Y.,Geacintov, N.E.,Broyde, S.,Patel, D.J.
Impact of conformational heterogeneity of OxoG lesions and their pairing partners on bypass fidelity by Y family polymerases.
Structure, 17:725-736, 2009

PubMed 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.

PubMed: 19446528
DOI: 10.1016/j.str.2009.03.011

Experimental method

X-RAY DIFFRACTION (2.7 Å)