4JEF

Crystal structure of human thymidylate synthase Y202A in inactive conformation.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Hotspots in an obligate homodimeric anticancer target. Structural and functional effects of interfacial mutations in human thymidylate synthase.

Salo-Ahen, O.M., Tochowicz, A., Pozzi, C., Cardinale, D., Ferrari, S., Boum, Y., Mangani, S., Stroud, R.M., Saxena, P., Myllykallio, H., Costi, M.P., Ponterini, G., Wade, R.C.

(2015) J Med Chem 58: 3572-3581

  • DOI: 10.1021/acs.jmedchem.5b00137
  • Primary Citation of Related Structures:  
    4KPW, 4JEF

  • PubMed Abstract: 

    • Human thymidylate synthase (hTS), a target for antiproliferative drugs, is an obligate homodimer. Single-point mutations to alanine at the monomer-monomer interface may enable the identification of specific residues that delineate sites for drugs aimed a ...

    Human thymidylate synthase (hTS), a target for antiproliferative drugs, is an obligate homodimer. Single-point mutations to alanine at the monomer-monomer interface may enable the identification of specific residues that delineate sites for drugs aimed at perturbing the protein-protein interactions critical for activity. We computationally identified putative hotspot residues at the interface and designed mutants to perturb the intersubunit interaction. Dimer dissociation constants measured by a FRET-based assay range from 60 nM for wild-type hTS up to about 1 mM for single-point mutants and agree with computational predictions of the effects of these mutations. Mutations that are remote from the active site retain full or partial activity, although the substrate KM values were generally higher and the dimer was less stable. The lower dimer stability of the mutants can facilitate access to the dimer interface by small molecules and thereby aid the design of inhibitors that bind at the dimer interface.

    Organizational Affiliation: 

    #Center for Molecular Biology, DKFZ-ZMBH Alliance, and Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, 69120 Heidelberg, Germany.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Thymidylate synthase A286Homo sapiensMutation(s): 1 
Gene Names: TYMS, TS, OK/SW-cl.29
EC: 2.1.1.45
Find proteins for P04818 (Homo sapiens)
Explore P04818 
Go to UniProtKB:  P04818
NIH Common Fund Data Resources
PHAROS:  P04818
GTEx:  ENSG00000176890
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download Ideal Coordinates CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CME
Query on CME		AL-PEPTIDE LINKINGC5 H11 N O3 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.955α = 90
b = 95.955β = 90
c = 82.649γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-08-20
    Type: Initial release
  • Version 1.1: 2015-05-06
    Changes: Database references