6NL0

Ternary complex crystal structure of K289M variant of DNA polymerase Beta with "hot-spot sequence" with beta-gamma CF2 analogue of dGTP

6NL0 の概要

• エントリーDOI: 10.2210/pdb6nl0/pdb
• 分子名称: DNA (5'-D(*CP*CP*GP*AP*AP*CP*AP*AP*GP*CP*AP*TP*CP*AP*GP*C)-3'), DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*TP*(2DT))-3'), DNA (5'-D(P*TP*TP*CP*GP*G)-3'), ... (9 entities in total)
• 機能のキーワード: dna polymerase beta, conformational change, enzyme mechanism, lfer, transcription-dna complex, transcription/dna
• 由来する生物種: Homo sapiens (Human); 詳細
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 48320.81

構造登録者

Batra, V.K.,Wilson, S.H. (登録日: 2019-01-07, 公開日: 2020-01-08, 最終更新日: 2024-03-13)

主引用文献

Batra, V.K.,Alnajjar, K.S.,Sweasy, J.B.,McKenna, C.E.,Goodman, M.F.,Wilson, S.H.
Revealing an Internal Stabilization Deficiency in the DNA Polymerase beta K289M Cancer Variant through the Combined Use of Chemical Biology and X-ray Crystallography.
Biochemistry, 59:955-963, 2020

PubMed Abstract: The human DNA polymerase (pol) β cancer variant K289M has altered polymerase activity , and the structure of wild-type pol β reveals that the K289 side chain contributes to a network of stabilizing interactions in a C-terminal region of the enzyme distal to the active site. Here, we probed the capacity of the K289M variant to tolerate strain introduced within the C-terminal region and active site. Strain was imposed by making use of a dGTP analogue containing a CF group substitution for the β-γ bridging oxygen atom. The ternary complex structure of the K289M variant displays an alteration in the C-terminal region, whereas the structure of wild-type pol β is not altered in the presence of the dGTP CF analogue. The alteration in the K289M variant impacts the active site, because the enzyme in the ternary complex fails to adopt the normal open to closed conformational change and assembly of the catalytically competent active site. These results reveal the importance of the K289-mediated stabilizing network in the C-terminal region of pol β and suggest an explanation for why the K289M cancer variant is deficient in polymerase activity even though the position 289 side chain is distal to the active site.

PubMed: 31999437
DOI: 10.1021/acs.biochem.9b01072

実験手法

X-RAY DIFFRACTION (1.97 Å)