4KPW

Crystal structure of His-tagged human thymidylate synthase R175A mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.2 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:  

  • 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 aim ...

    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

    ∥Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy.,⊥Ecole Polytechnique, CNRS UMR7645, INSERM U696, 91128 Palaiseau, France.,‡Department of Biochemistry and Biophysics, University of California-San Francisco, San Francisco, California 94158, United States.,§Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy.,#Center for Molecular Biology, DKFZ-ZMBH Alliance, and Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, 69120 Heidelberg, Germany.,†Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thymidylate synthase
A
325Homo sapiensMutation(s): 1 
Gene Names: TYMS (TS)
EC: 2.1.1.45
Find proteins for P04818 (Homo sapiens)
Go to Gene View: TYMS
Go to UniProtKB:  P04818
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SCH
Query on SCH
A
L-PEPTIDE LINKINGC4 H9 N O2 S2CYS
CME
Query on CME
A
L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.161 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 96.320α = 90.00
b = 96.320β = 90.00
c = 82.690γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
MOLREPphasing
SCALAdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-05-14 
  • Released Date: 2014-05-14 
  • Deposition Author(s): Pozzi, C., Mangani, S.

Revision History 

  • Version 1.0: 2014-05-14
    Type: Initial release
  • Version 1.1: 2015-05-06
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description