8ILD

The crystal structure of native dGTP:DNApre-I:Pol X substrate ternary complex

8ILD の概要

• エントリーDOI: 10.2210/pdb8ild/pdb
• 分子名称: Repair DNA polymerase X, DNA (5'-D(*CP*AP*GP*GP*AP*TP*CP*CP*T)-3'), GUANOSINE-5'-TRIPHOSPHATE, ... (6 entities in total)
• 機能のキーワード: dna polymerase, substrate complex, replication-dna complex, replication/dna
• 由来する生物種: African swine fever virus (strain Badajoz 1971 Vero-adapted) (Ba71V, ASFV); 詳細
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 47999.41

構造登録者

Qin, T.,Chen, Y.Q.,Gan, J.H.,Huang, Z. (登録日: 2023-03-03, 公開日: 2024-01-10)

主引用文献

Qin, T.,Hu, B.,Zhao, Q.,Wang, Y.,Wang, S.,Luo, D.,Lyu, J.,Chen, Y.,Gan, J.,Huang, Z.
Structural Insight into Polymerase Mechanism via a Chiral Center Generated with a Single Selenium Atom.
Int J Mol Sci, 24:-, 2023

PubMed Abstract: DNA synthesis catalyzed by DNA polymerase is essential for all life forms, and phosphodiester bond formation with phosphorus center inversion is a key step in this process. Herein, by using a single-selenium-atom-modified dNTP probe, we report a novel strategy to visualize the reaction stereochemistry and catalysis. We capture the before- and after-reaction states and provide explicit evidence of the center inversion and in-line attacking S2 mechanism of DNA polymerization, while solving the diastereomer absolute configurations. Further, our kinetic and thermodynamic studies demonstrate that in the presence of Mg ions (or Mn), the binding affinity () and reaction selectivity (/) of dGTPαSe-Rp were 51.1-fold (or 19.5-fold) stronger and 21.8-fold (or 11.3-fold) higher than those of dGTPαSe-Sp, respectively, indicating that the diastereomeric Se-Sp atom was quite disruptive of the binding and catalysis. Our findings reveal that the third metal ion is much more critical than the other two metal ions in both substrate recognition and bond formation, providing insights into how to better design the polymerase inhibitors and discover the therapeutics.

PubMed: 37958741
DOI: 10.3390/ijms242115758

実験手法

X-RAY DIFFRACTION (2.25 Å)