5C10

Nuclease domain of the large terminase subunit gp2 of bacterial virus Sf6

5C10 の概要

• エントリーDOI: 10.2210/pdb5c10/pdb
• 関連するPDBエントリー: 4IDH 5C12 5C15 5C2D 5C2F
• 分子名称: Gene 2 protein (2 entities in total)
• 機能のキーワード: nuclease domain, metal binding site, rnase h, metal binding protein
• 由来する生物種: Enterobacteria phage Sf6 (Shigella flexneri bacteriophage VI)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 30779.68

構造登録者

Zhao, H.,Tang, L. (登録日: 2015-06-12, 公開日: 2015-10-21, 最終更新日: 2024-03-06)

主引用文献

Zhao, H.,Lin, Z.,Lynn, A.Y.,Varnado, B.,Beutler, J.A.,Murelli, R.P.,Le Grice, S.F.,Tang, L.
Two distinct modes of metal ion binding in the nuclease active site of a viral DNA-packaging terminase: insight into the two-metal-ion catalytic mechanism.
Nucleic Acids Res., 43:11003-11016, 2015

PubMed Abstract: Many dsDNA viruses encode DNA-packaging terminases, each containing a nuclease domain that resolves concatemeric DNA into genome-length units. Terminase nucleases resemble the RNase H-superfamily nucleotidyltransferases in folds, and share a two-metal-ion catalytic mechanism. Here we show that residue K428 of a bacteriophage terminase gp2 nuclease domain mediates binding of the metal cofactor Mg(2+). A K428A mutation allows visualization, at high resolution, of a metal ion binding mode with a coupled-octahedral configuration at the active site, exhibiting an unusually short metal-metal distance of 2.42 Å. Such proximity of the two metal ions may play an essential role in catalysis by generating a highly positive electrostatic niche to enable formation of the negatively charged pentacovalent phosphate transition state, and provides the structural basis for distinguishing Mg(2+) from Ca(2+). Using a metal ion chelator β-thujaplicinol as a molecular probe, we observed a second mode of metal ion binding at the active site, mimicking the DNA binding state. Arrangement of the active site residues differs drastically from those in RNase H-like nucleases, suggesting a drifting of the active site configuration during evolution. The two distinct metal ion binding modes unveiled mechanistic details of the two-metal-ion catalysis at atomic resolution.

PubMed: 26450964
DOI: 10.1093/nar/gkv1018

実験手法

X-RAY DIFFRACTION (1.55 Å)