5M4Z

Crystal structure of the complex of T.spiralis thymidylate synthase with N(4)-hydroxy-2'-deoxycytidine-5'-monophosphate, crystallized in the presence of N(5,10)-methylenetetrahydrofolate

Summary for 5M4Z

• Entry DOI: 10.2210/pdb5m4z/pdb
• Descriptor: Thymidylate synthase, [(2~{R},3~{S},5~{R})-5-[(4~{E})-4-hydroxyimino-2-oxidanylidene-1,3-diazinan-1-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate, GLYCEROL, ... (4 entities in total)
• Functional Keywords: enzyme-inhibitor complex, high-resolution structure, anticancer target, transferase
• Biological source: Trichinella spiralis (Trichina worm)
• Total number of polymer chains: 2
• Total formula weight: 75591.64

Authors

Wilk, P.,Maj, P.,Jarmula, A.,Dowiercial, A.,Rode, W. (deposition date: 2016-10-19, release date: 2017-12-20, Last modification date: 2024-11-06)

Primary citation

Maj, P.,Jarmula, A.,Wilk, P.,Prokopowicz, M.,Rypniewski, W.,Zielinski, Z.,Dowiercial, A.,Bzowska, A.,Rode, W.
Molecular Mechanism of Thymidylate Synthase Inhibition by N 4 -Hydroxy-dCMP in View of Spectrophotometric and Crystallographic Studies.
Int J Mol Sci, 22:-, 2021

PubMed Abstract: Novel evidence is presented allowing further clarification of the mechanism of the slow-binding thymidylate synthase (TS) inhibition by N-hydroxy-dCMP (N-OH-dCMP). Spectrophotometric monitoring documented time- and temperature-, and N-OH-dCMP-dependent TS-catalyzed dihydrofolate production, accompanying the mouse enzyme incubation with N-OH-dCMP and N-methylenetetrahydrofolate, known to inactivate the enzyme by the covalent binding of the inhibitor, suggesting the demonstrated reaction to be uncoupled from the pyrimidine C(5) methylation. The latter was in accord with the hypothesis based on the previously presented structure of mouse TS (cf. PDB ID: 4EZ8), and with conclusions based on the present structure of the parasitic nematode , both co-crystallized with N-OH-dCMP and N-methylenetetrahdrofolate. The crystal structure of the mouse TS-N-OH-dCMP complex soaked with N-methylenetetrahydrofolate revealed the reaction to run via a unique imidazolidine ring opening, leaving the one-carbon group bound to the N(10) atom, thus too distant from the pyrimidine C(5) atom to enable the electrophilic attack and methylene group transfer.

PubMed: 33946210
DOI: 10.3390/ijms22094758

Experimental method

X-RAY DIFFRACTION (1.179 Å)