3H9K

Structures of Thymidylate Synthase R163K with Substrates and Inhibitors Show Subunit Asymmetry


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.214 

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Literature

Structures of human thymidylate synthase R163K with dUMP, FdUMP and glutathione show asymmetric ligand binding.

Gibson, L.M.Celeste, L.R.Lovelace, L.L.Lebioda, L.

(2011) Acta Crystallogr D Biol Crystallogr 67: 60-66

  • DOI: 10.1107/S0907444910044732
  • Primary Citation of Related Structures:  
    3H9K, 3HB8, 3OB7

  • PubMed Abstract: 
  • Thymidylate synthase (TS) is a well validated target in cancer chemotherapy. Here, a new crystal form of the R163K variant of human TS (hTS) with five subunits per asymmetric part of the unit cell, all with loop 181-197 in the active conformation, is reported ...

    Thymidylate synthase (TS) is a well validated target in cancer chemotherapy. Here, a new crystal form of the R163K variant of human TS (hTS) with five subunits per asymmetric part of the unit cell, all with loop 181-197 in the active conformation, is reported. This form allows binding studies by soaking crystals in artificial mother liquors containing ligands that bind in the active site. Using this approach, crystal structures of hTS complexes with FdUMP and dUMP were obtained, indicating that this form should facilitate high-throughput analysis of hTS complexes with drug candidates. Crystal soaking experiments using oxidized glutathione revealed that hTS binds this ligand. Interestingly, the two types of binding observed are both asymmetric. In one subunit of the physiological dimer covalent modification of the catalytic nucleophile Cys195 takes place, while in another dimer a noncovalent adduct with reduced glutathione is formed in one of the active sites.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of South Carolina, Columbia, 29208, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Thymidylate synthaseA, B, C, D, E313Homo sapiensMutation(s): 1 
Gene Names: TYMSTSOK/SW-cl.29
EC: 2.1.1.45
UniProt & NIH Common Fund Data Resources
Find proteins for P04818 (Homo sapiens)
Explore P04818 
Go to UniProtKB:  P04818
PHAROS:  P04818
Protein Feature View
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
UFP BindingDB:  3H9K Ki: min: 10, max: 30 (nM) from 4 assay(s)
IC50: min: 8, max: 1.00e+4 (nM) from 4 assay(s)
PDBBind:  3H9K Ki: 14 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.214 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 200.284α = 90
b = 122.19β = 115.18
c = 99.828γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-05-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-03-27
    Changes: Database references
  • Version 1.3: 2017-11-01
    Changes: Refinement description
  • Version 1.4: 2021-10-13
    Changes: Database references, Derived calculations