4qm7

Structure of bacterial polynucleotide kinase bound to GTP and pDNA

spinqualitylabelsall models 4qm7, resolution 1.80Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 4qm7 is a 3 chain structure with sequence from Acetivibrio thermocellus ATCC 27405. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: GTP, MG, MSE Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function A3DJ38_ACET2 Publication Abstract from PubMed 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 A crystal structure of CthPnk-D38N in a Michaelis complex with GTP*Mg2+ 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*Mg2+ and a 5'-OH DNA yielded a mixed substrate/product complex with GTP*Mg2+ and 5'-PO4 DNA, wherein the product 5'-phosphate group is displaced by the NTP gamma phosphate and the local architecture of the acceptor site is perturbed. Structures of bacterial polynucleotide kinase in a Michaelis complex with NTP*Mg2+ and 5'-OH RNA and a mixed substrate-product complex with NTP*Mg2+ and a 5'-phosphorylated oligonucleotide.,Das U, Wang LK, Smith P, Munir A, Shuman S J Bacteriol. 2014 Sep 29. pii: JB.02197-14. PMID:25266383 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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