5XB2

ADP-Mg-F-dTMP bound Crystal structure of thymidylate kinase (aq_969) from Aquifex Aeolicus VF5

Summary for 5XB2

• Entry DOI: 10.2210/pdb5xb2/pdb
• Related: 5XAI 5XB3 5XB5 5XBH
• Descriptor: Thymidylate kinase, ADENOSINE-5'-DIPHOSPHATE, THYMIDINE-5'-PHOSPHATE, ... (6 entities in total)
• Functional Keywords: kinase, tranferase, complex, nucleotide binding, transferase
• Biological source: Aquifex aeolicus (strain VF5)
• Total number of polymer chains: 2
• Total formula weight: 46386.04

Authors

Biswas, A.,Jeyakanthan, J.,Sekar, K. (deposition date: 2017-03-15, release date: 2017-06-28, Last modification date: 2023-11-22)

Primary citation

Biswas, A.,Shukla, A.,Chaudhary, S.K.,Santhosh, R.,Jeyakanthan, J.,Sekar, K.
Structural studies of a hyperthermophilic thymidylate kinase enzyme reveal conformational substates along the reaction coordinate
FEBS J., 284:2527-2544, 2017

PubMed Abstract: Thymidylate kinase (TMK) is a key enzyme which plays an important role in DNA synthesis. It belongs to the family of nucleoside monophosphate kinases, several of which undergo structure-encoded conformational changes to perform their function. However, the absence of three-dimensional structures for all the different reaction intermediates of a single TMK homolog hinders a clear understanding of its functional mechanism. We herein report the different conformational states along the reaction coordinate of a hyperthermophilic TMK from Aquifex aeolicus, determined via X-ray diffraction and further validated through normal-mode studies. The analyses implicate an arginine residue in the Lid region in catalysis, which was confirmed through site-directed mutagenesis and subsequent enzyme assays on the wild-type protein and mutants. Furthermore, the enzyme was found to exhibit broad specificity toward phosphate group acceptor nucleotides. Our comprehensive analyses of the conformational landscape of TMK, together with associated biochemical experiments, provide insights into the mechanistic details of TMK-driven catalysis, for example, the order of substrate binding and the reaction mechanism for phosphate transfer. Such a study has utility in the design of potent inhibitors for these enzymes.

PubMed: 28627020
DOI: 10.1111/febs.14140

Experimental method

X-RAY DIFFRACTION (2.161 Å)