4YFU

Crystal structure of open Bacillus fragment DNA polymerase bound to DNA and dTTP

4YFU の概要

• エントリーDOI: 10.2210/pdb4yfu/pdb
• 関連するBIRD辞書のPRD_ID: PRD_900003
• 分子名称: DNA polymerase, Primer DNA, Template DNA, ... (7 entities in total)
• 機能のキーワード: protein-dna complex, transferase-dna complex, transferase/dna
• 由来する生物種: Geobacillus stearothermophilus; 詳細
• タンパク質・核酸の鎖数: 6
• 化学式量合計: 147910.23

構造登録者

Wu, E.Y. (登録日: 2015-02-25, 公開日: 2015-07-22, 最終更新日: 2024-11-06)

主引用文献

Miller, B.R.,Beese, L.S.,Parish, C.A.,Wu, E.Y.
The Closing Mechanism of DNA Polymerase I at Atomic Resolution.
Structure, 23:1609-1620, 2015

PubMed Abstract: DNA polymerases must quickly and accurately distinguish between similar nucleic acids to form Watson-Crick base pairs and avoid DNA replication errors. Deoxynucleoside triphosphate (dNTP) binding to the DNA polymerase active site induces a large conformational change that is difficult to characterize experimentally on an atomic level. Here, we report an X-ray crystal structure of DNA polymerase I bound to DNA in the open conformation with a dNTP present in the active site. We use this structure to computationally simulate the open to closed transition of DNA polymerase in the presence of a Watson-Crick base pair. Our microsecond simulations allowed us to characterize the key steps involved in active site assembly, and propose the sequence of events involved in the prechemistry steps of DNA polymerase catalysis. They also reveal new features of the polymerase mechanism, such as a conserved histidine as a potential proton acceptor from the primer 3'-hydroxyl.

PubMed: 26211612
DOI: 10.1016/j.str.2015.06.016

実験手法

X-RAY DIFFRACTION (1.5 Å)