5X8C

AMPPCP and TMP bound crystal structure of thymidylate kinase from thermus thermophilus HB8

Summary for 5X8C

• Entry DOI: 10.2210/pdb5x8c/pdb
• Related: 5X86 5X8A 5X8B 5X8D 5X8J 5X8K 5X8V 5X98 5X99
• Descriptor: Thymidylate kinase, THYMIDINE-5'-PHOSPHATE, MAGNESIUM ION, ... (6 entities in total)
• Functional Keywords: nucleotide monophosphate kinase, transferase
• Biological source: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
• Total number of polymer chains: 2
• Total formula weight: 45613.33

Authors

Chaudhary, S.K.,Jeyakanthan, J.,Sekar, K. (deposition date: 2017-03-02, release date: 2018-03-14, Last modification date: 2023-11-22)

Primary citation

Chaudhary, S.K.,Jeyakanthan, J.,Sekar, K.
Structural and functional roles of dynamically correlated residues in thymidylate kinase.
Acta Crystallogr D Struct Biol, 74:341-354, 2018

PubMed Abstract: Thymidylate 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. 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.

PubMed: 29652261
DOI: 10.1107/S2059798318002267

Experimental method

X-RAY DIFFRACTION (2.07 Å)