4jsy

Structure of Clostridium thermocellum polynucleotide kinase bound to GTP

spinqualitylabelsall models 4jsy, resolution 2.14Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 4jsy is a 2 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. Method: X-ray diffraction, Resolution 2.14Å Ligands: GTP, MG, MSE Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function A3DJ38_ACET2 Publication Abstract from PubMed Clostridium thermocellum Pnkp is the end-healing and end-sealing subunit of a bacterial RNA repair system. CthPnkp is composed of three catalytic modules: an N-terminal 5'-OH polynucleotide kinase, a central 2',3' phosphatase, and a C-terminal ligase. The crystal structure of the kinase domain bound to ATP*Mg2+ revealed a rich network of ionic and hydrogen-bonding contacts to the alpha, beta, and gamma phosphates. By contrast, there are no enzymic contacts to the ribose and none with the adenine base other than a pi-cation interaction with Arg116. Here we report that the enzyme uses ATP, GTP, CTP, UTP, or dATP as a phosphate donor for the 5'-OH kinase reaction. The enzyme also catalyzes the reverse reaction, in which a polynucleotide 5'-PO4 group is transferred to ADP, GDP, CDP, UDP, or dADP to form the corresponding NTP. We report new crystal structures of the kinase in complexes with GTP, CTP, UTP, and dATP in which the respective nucleobases are stacked on Arg116 but make no other enzymic contacts. Mutating Arg116 to alanine elicits a 10-fold increase in Km for ATP but has little effect on kcat. These findings illuminate the basis for nonspecific donor nucleotide utilization by a P-loop phosphotransferase. Structural and Biochemical Analysis of the Phosphate Donor Specificity of the Polynucleotide Kinase Component of the Bacterial Pnkp*Hen1 RNA Repair System.,Das U, Wang LK, Smith P, Shuman S Biochemistry. 2013 Jun 26. PMID:23721485 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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