2AU0
Unmodified preinsertion binary complex
Summary for 2AU0
Entry DOI | 10.2210/pdb2au0/pdb |
Related | 2ASD 2ASJ 2ASL 2ATL |
Descriptor | 5'-D(*GP*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*(DDG))-3', 5'-D(*CP*TP*AP*AP*CP*G*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3', Dpo4 polymerase IV, ... (5 entities in total) |
Functional Keywords | dna polymerase, y-family, lesion bypass, binary complex, transferase-dna complex, transferase/dna |
Biological source | Sulfolobus solfataricus |
Cellular location | Cytoplasm (Probable): Q97W02 |
Total number of polymer chains | 6 |
Total formula weight | 101301.80 |
Authors | Rechkoblit, O.,Malinina, L.,Cheng, Y.,Kuryavyi, V.,Broyde, S.,Geacintov, N.E.,Patel, D.J. (deposition date: 2005-08-26, 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 Cited by 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: 16379496DOI: 10.1371/journal.pbio.0040011 PDB entries with the same primary citation |
Experimental method | X-RAY DIFFRACTION (2.7 Å) |
Structure validation
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