9NKC

Dpo4 DNA polymerase (Wild Type) in complex with DNA containing an 8oxoG template lesion

9NKC の概要

• エントリーDOI: 10.2210/pdb9nkc/pdb
• 分子名称: DNA polymerase IV, Extended Primer Strand, Template DNA, ... (6 entities in total)
• 機能のキーワード: dna polymerase translesion synthesis 8oxog damage, transferase, transferase-dna complex, transferase/dna
• 由来する生物種: Saccharolobus solfataricus P2; 詳細
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 50378.47

構造登録者

Pata, J.D.,Liang, B. (登録日: 2025-02-28, 公開日: 2025-09-24, 最終更新日: 2025-10-08)

主引用文献

Disha, S.S.,Punchipatabendi, T.I.,Kaszubowski, J.D.,Liang, B.,Pata, J.D.,Trakselis, M.A.
Residues in the little finger domain of the Y-family Dpo4 DNA polymerase communicate to restrict synthesis past 8-oxoguanine lesions.
Nucleic Acids Res., 53:-, 2025

PubMed Abstract: Endogenous reactive oxygen species are responsible for abundant 8-oxo-7,8-dihydroguanine (8-oxoG) lesion formation in all three domains of life. In the archaeal Saccharolobus solfataricus(Sso), a specialized translesion synthesis (TLS) polymerase, SsoDpo4, is recruited to bypass lesions when the high-fidelity polymerase stalls. Previous studies have found that SsoDpo4 can accurately bypass 8-oxoG lesions with deoxycytosine and then efficiently extend three nucleotides beyond the lesion to the +3 position. Here, we have mutated several arginines within the little finger (LF) domain that track along the phosphate backbone near the active site and tested their extension ability and DNA binding properties. Mutation of two key residues, R332 or R336, to alanine relieves +3 intermediate accumulation, resulting in more efficient full-length extension. Interestingly, the wild-type enzyme binds progressively weaker downstream of a bypassed 8-oxoG lesion, indicating decreased binding stability after lesion bypass. X-ray crystallography has captured these mutants on the +3 extended primer/8-oxoG template to structurally characterize how these LF residues communicate to restrict downstream synthesis past 8-oxoG. Our results offer mechanistic and structural insights into how TLS polymerases restrict downstream synthesis past a lesion by sensing backbone distortions and altering domain conformations to limit catalysis and destabilize binding.

PubMed: 41002026
DOI: 10.1093/nar/gkaf950

実験手法

X-RAY DIFFRACTION (2.5 Å)