2ASD

oxoG-modified Insertion Ternary Complex

2ASD の概要

• エントリーDOI: 10.2210/pdb2asd/pdb
• 関連するPDBエントリー: 2ASJ 2ASL 2ATL 2AU0
• 分子名称: 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)
• 機能のキーワード: dna polymerase, 8-oxoguanine, y-family, lesion bypass, transferase-dna complex, transferase/dna
• 由来する生物種: Sulfolobus solfataricus
• 細胞内の位置: Cytoplasm (Probable): Q97W02
• タンパク質・核酸の鎖数: 6
• 化学式量合計: 102428.42

構造登録者

Rechkoblit, O.,Malinina, L.,Cheng, Y.,Kuryavyi, V.,Broyde, S.,Geacintov, N.E.,Patel, D.J. (登録日: 2005-08-23, 公開日: 2006-01-10, 最終更新日: 2023-08-23)

主引用文献

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

実験手法

X-RAY DIFFRACTION (1.95 Å)