2ASD

oxoG-modified Insertion Ternary Complex

Summary for 2ASD

• Entry DOI: 10.2210/pdb2asd/pdb
• Related: 2ASJ 2ASL 2ATL 2AU0
• Descriptor: 5'-D(*GP*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*(DDG))-3', 5'-D(*CP*T*AP*AP*CP*(8OG)P*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3', DNA polymerase IV, ... (6 entities in total)
• Functional Keywords: dna polymerase, 8-oxoguanine, y-family, lesion bypass, transferase-dna complex, transferase/dna
• Biological source: Sulfolobus solfataricus
• Cellular location: Cytoplasm (Probable): Q97W02
• Total number of polymer chains: 6
• Total formula weight: 102428.42

Authors

Rechkoblit, O.,Malinina, L.,Cheng, Y.,Kuryavyi, V.,Broyde, S.,Geacintov, N.E.,Patel, D.J. (deposition date: 2005-08-23, release date: 2006-01-10, Last modification date: 2023-08-23)

Primary citation

Rechkoblit, O.,Malinina, L.,Cheng, Y.,Kuryavyi, V.,Broyde, S.,Geacintov, N.E.,Patel, D.J.
Stepwise Translocation of Dpo4 Polymerase during Error-Free Bypass of an oxoG Lesion
Plos Biol., 4:1-18, 2006

PubMed Abstract: 7,8-dihydro-8-oxoguanine (oxoG), the predominant lesion formed following oxidative damage of DNA by reactive oxygen species, is processed differently by replicative and bypass polymerases. Our kinetic primer extension studies demonstrate that the bypass polymerase Dpo4 preferentially inserts C opposite oxoG, and also preferentially extends from the oxoG*C base pair, thus achieving error-free bypass of this lesion. We have determined the crystal structures of preinsertion binary, insertion ternary, and postinsertion binary complexes of oxoG-modified template-primer DNA and Dpo4. These structures provide insights into the translocation mechanics of the bypass polymerase during a complete cycle of nucleotide incorporation. Specifically, during noncovalent dCTP insertion opposite oxoG (or G), the little-finger domain-DNA phosphate contacts translocate by one nucleotide step, while the thumb domain-DNA phosphate contacts remain fixed. By contrast, during the nucleotidyl transfer reaction that covalently incorporates C opposite oxoG, the thumb-domain-phosphate contacts are translocated by one nucleotide step, while the little-finger contacts with phosphate groups remain fixed. These stepwise conformational transitions accompanying nucleoside triphosphate binding and covalent nucleobase incorporation during a full replication cycle of Dpo4-catalyzed bypass of the oxoG lesion are distinct from the translocation events in replicative polymerases.

PubMed: 16379496
DOI: 10.1371/journal.pbio.0040011

Experimental method

X-RAY DIFFRACTION (1.95 Å)