4QM6

Structure of bacterial polynucleotide kinase bound to GTP and RNA

4QM6 の概要

• エントリーDOI: 10.2210/pdb4qm6/pdb
• 関連するPDBエントリー: 4JST 4JSY 4JT2 4JT4 4MDE 4MDF 4QM7
• 分子名称: Metallophosphoesterase, RNA, GUANOSINE-5'-TRIPHOSPHATE, ... (7 entities in total)
• 機能のキーワード: rna repair, p-loop phosphotransferase, polynucleotide kinase, hydrolase-rna complex, transferase-rna complex, transferase/rna
• 由来する生物種: Ruminiclostridium thermocellum; 詳細
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 43325.43

構造登録者

Das, U.,Wang, L.K.,Smith, P.,Shuman, S. (登録日: 2014-06-15, 公開日: 2014-10-08, 最終更新日: 2024-02-28)

主引用文献

Das, U.,Wang, L.K.,Smith, P.,Munir, A.,Shuman, S.
Structures of bacterial polynucleotide kinase in a michaelis complex with nucleoside triphosphate (NTP)-Mg2+ and 5'-OH RNA and a mixed substrate-product complex with NTP-Mg2+ and a 5'-phosphorylated oligonucleotide.
J.Bacteriol., 196:4285-4292, 2014

PubMed Abstract: Clostridium thermocellum polynucleotide kinase (CthPnk), the 5'-end-healing module of a bacterial RNA repair system, catalyzes reversible phosphoryl transfer from a nucleoside triphosphate (NTP) donor to a 5'-OH polynucleotide acceptor, either DNA or RNA. Here we report the 1.5-Å crystal structure of CthPnk-D38N in a Michaelis complex with GTP-Mg(2+) and a 5'-OH RNA oligonucleotide. The RNA-binding mode of CthPnk is different from that of the metazoan RNA kinase Clp1. CthPnk makes hydrogen bonds to the ribose 2'-hydroxyls of the 5' terminal nucleoside, via Gln51, and the penultimate nucleoside, via Gln83. The 5'-terminal nucleobase is sandwiched by Gln51 and Val129. Mutating Gln51 or Val129 to alanine reduced kinase specific activity 3-fold. Ser37 and Thr80 donate functionally redundant hydrogen bonds to the terminal phosphodiester; a S37A-T80A double mutation reduced kinase activity 50-fold. Crystallization of catalytically active CthPnk with GTP-Mg(2+) and a 5'-OH DNA yielded a mixed substrate-product complex with GTP-Mg(2+) and 5'-PO4 DNA, wherein the product 5' phosphate group is displaced by the NTP γ phosphate and the local architecture of the acceptor site is perturbed.

PubMed: 25266383
DOI: 10.1128/JB.02197-14

実験手法

X-RAY DIFFRACTION (1.5 Å)