5WO0

DNA polymerase beta substrate complex with incoming 5-FodUTP

5WO0 の概要

• エントリーDOI: 10.2210/pdb5wo0/pdb
• 分子名称: DNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3'), DNA (5'-D(P*GP*TP*CP*GP*G)-3'), ... (9 entities in total)
• 機能のキーワード: dna ligase/dna, transferase, dna ligase-dna, transferase complex
• 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: 48420.52

構造登録者

Schaich, M.A.,Smith, M.R.,Cloud, A.S.,Holloran, S.M.,Freudenthal, B.D. (登録日: 2017-08-01, 公開日: 2017-09-13, 最終更新日: 2023-10-04)

主引用文献

Schaich, M.A.,Smith, M.R.,Cloud, A.S.,Holloran, S.M.,Freudenthal, B.D.
Structures of a DNA Polymerase Inserting Therapeutic Nucleotide Analogues.
Chem. Res. Toxicol., 30:1993-2001, 2017

PubMed Abstract: Members of the nucleoside analogue class of cancer therapeutics compete with canonical nucleotides to disrupt numerous cellular processes, including nucleotide homeostasis, DNA and RNA synthesis, and nucleotide metabolism. Nucleoside analogues are triphosphorylated and subsequently inserted into genomic DNA, contributing to the efficacy of therapeutic nucleosides in multiple ways. In some cases, the altered base acts as a mutagen, altering the DNA sequence to promote cellular death; in others, insertion of the altered nucleotide triggers DNA repair pathways, which produce lethal levels of cytotoxic intermediates such as single and double stranded DNA breaks. As a prerequisite to many of these biological outcomes, the modified nucleotide must be accommodated in the DNA polymerase active site during nucleotide insertion. Currently, the molecular contacts that mediate DNA polymerase insertion of modified nucleotides remain unknown for multiple therapeutic compounds, despite decades of clinical use. To determine how modified bases are inserted into duplex DNA, we used mammalian DNA polymerase β (pol β) to visualize the structural conformations of four therapeutically relevant modified nucleotides, 6-thio-2'-deoxyguanosine-5'-triphosphate (6-TdGTP), 5-fluoro-2'-deoxyuridine-5'-triphosphate (5-FdUTP), 5-formyl-deoxycytosine-5'-triphosphate (5-FodCTP), and 5-formyl-deoxyuridine-5'-triphosphate (5-FodUTP). Together, the structures reveal a pattern in which the modified nucleotides utilize Watson-Crick base pairing interactions similar to that of unmodified nucleotides. The nucleotide modifications were consistently positioned in the major groove of duplex DNA, accommodated by an open cavity in pol β. These results provide novel information for the rational design of new therapeutic nucleoside analogues and a greater understanding of how modified nucleotides are tolerated by polymerases.

PubMed: 28862449
DOI: 10.1021/acs.chemrestox.7b00173

実験手法

X-RAY DIFFRACTION (1.6 Å)