4QM6

Structure of bacterial polynucleotide kinase bound to GTP and RNA

Summary for 4QM6

• Entry DOI: 10.2210/pdb4qm6/pdb
• Related: 4JST 4JSY 4JT2 4JT4 4MDE 4MDF 4QM7
• Descriptor: Metallophosphoesterase, RNA, GUANOSINE-5'-TRIPHOSPHATE, ... (7 entities in total)
• Functional Keywords: rna repair, p-loop phosphotransferase, polynucleotide kinase, hydrolase-rna complex, transferase-rna complex, transferase/rna
• Biological source: Ruminiclostridium thermocellum; More
• Total number of polymer chains: 4
• Total formula weight: 43325.43

Authors

Das, U.,Wang, L.K.,Smith, P.,Shuman, S. (deposition date: 2014-06-15, release date: 2014-10-08, Last modification date: 2024-02-28)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (1.5 Å)