5FUY

catalytic domain of Thymidine kinase from Trypanosoma brucei with dTMP

Summary for 5FUY

• Entry DOI: 10.2210/pdb5fuy/pdb
• Related: 5FUV 5FUW 5FUX
• Descriptor: THYMDINE KINASE, PHOSPHATE ION, [(2R,3S,5R)-3-HYDROXY-5-[(5S)-5-METHYL-2,4-DIOXO-1,3-DIAZINAN-1-YL]OXOLAN-2-YL]METHYL DIHYDROGEN PHOSPHATE, ... (5 entities in total)
• Functional Keywords: transferase, thymidine kinase, t.brucei, tbtk, tkii, dtmp
• Biological source: TRYPANOSOMA BRUCEI
• Total number of polymer chains: 6
• Total formula weight: 126354.35

Authors

Timm, J.,Valente, M.,Castillo-Acosta, V.,Balzarini, T.,Nettleship, J.E.,Rada, H.,Wilson, K.S.,Gonzalez-Pacanowska, D. (deposition date: 2016-01-31, release date: 2016-07-27, Last modification date: 2024-01-10)

Primary citation

Valente, M.,Timm, J.,Castillo-Acosta, V.M.,Ruiz-Perez, L.M.,Balzarini, T.,Nettleship, J.E.,Bird, L.E.,Rada, H.,Wilson, K.S.,Gonzalez-Pacanowska, D.
Cell Cycle Regulation and Novel Structural Features of Thymidine Kinase, an Essential Enzyme in Trypanosoma Brucei.
Mol.Microbiol., 102:365-, 2016

PubMed Abstract: Thymidine kinase (TK) is a key enzyme in the pyrimidine salvage pathway which catalyzes the transfer of the γ-phosphate of ATP to 2'-deoxythymidine (dThd) forming thymidine monophosphate (dTMP). Unlike other type II TKs, the Trypanosoma brucei enzyme (TbTK) is a tandem protein with two TK homolog domains of which only the C-terminal one is active. In this study, we establish that TbTK is essential for parasite viability and cell cycle progression, independently of extracellular pyrimidine concentrations. We show that expression of TbTK is cell cycle regulated and that depletion of TbTK leads to strongly diminished dTTP pools and DNA damage indicating intracellular dThd to be an essential intermediate metabolite for the synthesis of thymine-derived nucleotides. In addition, we report the X-ray structure of the catalytically active domain of TbTK in complex with dThd and dTMP at resolutions up to 2.2 Å. In spite of the high conservation of the active site residues, the structures reveal a widened active site cavity near the nucleobase moiety compared to the human enzyme. Our findings strongly support TbTK as a crucial enzyme in dTTP homeostasis and identify structural differences within the active site that could be exploited in the process of rational drug design.

PubMed: 27426054
DOI: 10.1111/MMI.13467

Experimental method

X-RAY DIFFRACTION (2.8 Å)