6F6Z

Mouse Thymidylate Synthase Cocrystallized with N(4)OHdCMP and Soaked in Methylenetetrahydrofolate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Molecular Mechanism of Thymidylate Synthase Inhibition by N4-Hydroxy-dCMP in View of Spectrophotometric and Crystallographic Studies

Maj, P.Jarmula, A.Wilk, P.Prokopowicz, M.Rypniewski, W.Zielinski, Z.Dowiercial, A.Bzowska, A.Rode, W.

(2021) Int J Mol Sci 22

  • DOI: https://doi.org/10.3390/ijms22094758
  • Primary Citation of Related Structures:  
    5M4Z, 6F6Z

  • PubMed Abstract: 

    Novel evidence is presented allowing further clarification of the mechanism of the slow-binding thymidylate synthase (TS) inhibition by N 4 -hydroxy-dCMP (N 4 -OH-dCMP). Spectrophotometric monitoring documented time- and temperature-, and N 4 -OH-dCMP-dependent TS-catalyzed dihydrofolate production, accompanying the mouse enzyme incubation with N 4 -OH-dCMP and N 5,10 -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 Trichinella spiralis , both co-crystallized with N 4 -OH-dCMP and N 5,10 -methylenetetrahdrofolate. The crystal structure of the mouse TS-N 4 -OH-dCMP complex soaked with N 5,10 -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.


  • Organizational Affiliation

    Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur St., PL-02-093 Warszawa, Poland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thymidylate synthase
A, B
307Mus musculusMutation(s): 0 
Gene Names: Tyms
EC: 2.1.1.45
UniProt
Find proteins for P07607 (Mus musculus)
Explore P07607 
Go to UniProtKB:  P07607
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07607
Sequence Annotations
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
NOH BindingDB:  6F6Z Kd: 1000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.212 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 160.36α = 90
b = 89.16β = 97.47
c = 66.56γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-30
    Type: Initial release
  • Version 1.1: 2022-01-12
    Changes: Database references
  • Version 1.2: 2022-01-26
    Changes: Database references
  • Version 1.3: 2024-01-17
    Changes: Data collection, Refinement description