4O5C

Structure of human DNA polymerase complexed with N7-MG as the template base in a 1-nucleotide gapped DNA

4O5C の概要

• エントリーDOI: 10.2210/pdb4o5c/pdb
• 関連するPDBエントリー: 1BPX 3ISB 4O5E 4O5K
• 分子名称: DNA polymerase beta, DNA (5'-D(*CP*CP*GP*AP*CP*(FMG)P*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*A)-3'), ... (6 entities in total)
• 機能のキーワード: dna binding, polymerase fold, nucleotidyl transfer, dna, nucleus, transferase, lyase-dna complex, lyase/dna
• 由来する生物種: Homo sapiens (human); 詳細
• 細胞内の位置: Nucleus: P06746
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 47080.98

構造登録者

Koag, M.C.,Lee, S. (登録日: 2013-12-19, 公開日: 2014-07-02, 最終更新日: 2024-02-28)

主引用文献

Koag, M.C.,Kou, Y.,Ouzon-Shubeita, H.,Lee, S.
Transition-state destabilization reveals how human DNA polymerase beta proceeds across the chemically unstable lesion N7-methylguanine.
Nucleic Acids Res., 42:8755-8766, 2014

PubMed Abstract: N7-Methyl-2'-deoxyguanosine (m7dG) is the predominant lesion formed by methylating agents. A systematic investigation on the effect of m7dG on DNA replication has been difficult due to the chemical instability of m7dG. To gain insights into the m7dG effect, we employed a 2'-fluorine-mediated transition-state destabilzation strategy. Specifically, we determined kinetic parameters for dCTP insertion opposite a chemically stable m7dG analogue, 2'-fluoro-m7dG (Fm7dG), by human DNA polymerase β (polβ) and solved three X-ray structures of polβ in complex with the templating Fm7dG paired with incoming dCTP or dTTP analogues. The kinetic studies reveal that the templating Fm7dG slows polβ catalysis ∼ 300-fold, suggesting that m7dG in genomic DNA may impede replication by some DNA polymerases. The structural analysis reveals that Fm7dG forms a canonical Watson-Crick base pair with dCTP, but metal ion coordination is suboptimal for catalysis in the polβ-Fm7dG:dCTP complex, which partially explains the slow insertion of dCTP opposite Fm7dG by polβ. In addition, the polβ-Fm7dG:dTTP structure shows open protein conformations and staggered base pair conformations, indicating that N7-methylation of dG does not promote a promutagenic replication. Overall, the first systematic studies on the effect of m7dG on DNA replication reveal that polβ catalysis across m7dG is slow, yet highly accurate.

PubMed: 24966350
DOI: 10.1093/nar/gku554

実験手法

X-RAY DIFFRACTION (2.363 Å)