Summary information and primary citation
- PDB-id
- 4qm6; SNAP-derived features in text and JSON formats;
DNAproDB
- Class
- transferase-RNA
- Method
- X-ray (1.5 Å)
- Summary
- Structure of bacterial polynucleotide kinase bound to gtp and RNA
- Reference
- Das U, Wang LK, Smith P, Munir A, Shuman S (2014): "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. doi: 10.1128/JB.02197-14.
- Abstract
- Clostridium thermocellum polynucleotide kinase (CthPnk), the 5' end-healing module of a bacterial RNA repair system, catalyzes reversible phosphoryl transfer from an 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 by 3-fold. Ser37 and Thr80 donate functionally redundant hydrogen bonds to the terminal phosphodiester; a S37A-T80A double mutation reduced kinase activity by 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.
