5xak | pdb_00005xak
Crystal structure (form II) of thymidylate kinase from Thermus thermophilus HB8
Structural highlights
FunctionKTHY_THET8 Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis. Publication Abstract from PubMedThymidylate kinase is an important enzyme in DNA synthesis. It catalyzes the conversion of thymidine monophosphate to thymidine diphosphate, with ATP as the preferred phosphoryl donor, in the presence of Mg(2+). In this study, the dynamics of the active site and the communication paths between the substrates, ATP and TMP, are reported for thymidylate kinase from Thermus thermophilus. Conformational changes upon ligand binding and the path for communication between the substrates and the protein are important in understanding the catalytic mechanism of the enzyme. High-resolution X-ray crystal structures of thymidylate kinase in apo and ligand-bound states were solved. This is the first report of structures of binary and ternary complexes of thymidylate kinase with its natural substrates ATP and ATP-TMP, respectively. Distinct conformations of the active-site residues, the P-loop and the LID region observed in the apo and ligand-bound structures revealed that their concerted motion is required for the binding and proper positioning of the substrate TMP. Structural analyses provide an insight into the mode of substrate binding at the active site. The residues involved in communication between the substrates were identified through network analysis using molecular-dynamics simulations. The residues identified showed high sequence conservation across species. Biochemical analyses show that mutations of these residues either resulted in a loss of activity or affected the thermal stability of the protein. Further, molecular-dynamics analyses of mutants suggest that the proper positioning of TMP is important for catalysis. These data also provide an insight into the phosphoryl-transfer mechanism. Structural and functional roles of dynamically correlated residues in thymidylate kinase.,Chaudhary SK, Jeyakanthan J, Sekar K Acta Crystallogr D Struct Biol. 2018 Apr 1;74(Pt 4):341-354. doi:, 10.1107/S2059798318002267. Epub 2018 Apr 6. PMID:29652261[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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