5YTC

Large fragment of DNA Polymerase I from Thermus aquaticus in a closed ternary complex with the unnatural base M-fC pair with dATP in the active site

5YTC の概要

• エントリーDOI: 10.2210/pdb5ytc/pdb
• 分子名称: DNA polymerase I, thermostable, DNA (5'-D(*GP*AP*CP*CP*AP*CP*GP*GP*CP*GP*CP*(DOC)P*(DOC))-3'), DNA (5'-D(*AP*AP*AP*(92F)P*GP*GP*CP*GP*CP*CP*GP*TP*GP*GP*TP*C)-3'), ... (6 entities in total)
• 機能のキーワード: dna, replication, transferase-dna complex, transferase/dna
• 由来する生物種: Thermus aquaticus; 詳細
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 70296.48

構造登録者

Zeng, H.,Mondal, M.,Song, R.Y.,Zhang, J.,Xia, B.,Yi, C.Q. (登録日: 2017-11-17, 公開日: 2018-11-21, 最終更新日: 2023-11-22)

主引用文献

Zeng, H.,Mondal, M.,Song, R.,Zhang, J.,Xia, B.,Liu, M.,Zhu, C.,He, B.,Gao, Y.Q.,Yi, C.
Unnatural Cytosine Bases Recognized as Thymines by DNA Polymerases by the Formation of the Watson-Crick Geometry.
Angew. Chem. Int. Ed. Engl., 58:130-133, 2019

PubMed Abstract: The emergence of unnatural DNA bases provides opportunities to demystify the mechanisms by which DNA polymerases faithfully decode chemical information on the template. It was previously shown that two unnatural cytosine bases (termed "M-fC" and "I-fC"), which are chemical labeling adducts of the epigenetic base 5-formylcytosine, can induce C-to-T transition during DNA amplification. However, how DNA polymerases recognize such unnatural cytosine bases remains enigmatic. Herein, crystal structures of unnatural cytosine bases pairing to dA/dG in the KlenTaq polymerase-host-guest complex system and pairing to dATP in the KlenTaq polymerase active site were determined. Both M-fC and I-fC base pair with dA/dATP, but not with dG, in a Watson-Crick geometry. This study reveals that the formation of the Watson-Crick geometry, which may be enabled by the A-rule, is important for the recognition of unnatural cytosines.

PubMed: 30407705
DOI: 10.1002/anie.201807845

実験手法

X-RAY DIFFRACTION (2.28 Å)