1FFL

CRYSTAL STRUCTURE OF THE APO-THYMIDYLATE SYNTHASE R166Q MUTANT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.94 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structures of thymidylate synthase mutant R166Q: Structural basis for the nearly complete loss of catalytic activity.

Sotelo-Mundo, R.R.Changchien, L.Maley, F.Montfort, W.R.

(2006) J.Biochem.Mol.Toxicol. 20: 88-92

  • DOI: 10.1002/jbt.20122
  • Primary Citation of Related Structures:  1FWM

  • PubMed Abstract: 
  • Thymidylate synthase (TS) catalyzes the folate-dependent methylation of deoxyuridine monophosphate (dUMP) to form thymidine monophosphate (dTMP). We have investigated the role of invariant arginine 166, one of four arginines that contact the dUMP pho ...

    Thymidylate synthase (TS) catalyzes the folate-dependent methylation of deoxyuridine monophosphate (dUMP) to form thymidine monophosphate (dTMP). We have investigated the role of invariant arginine 166, one of four arginines that contact the dUMP phosphate, using site-directed mutagenesis, X-ray crystallography, and TS from Escherichia coli. The R166Q mutant was crystallized in the presence of dUMP and a structure determined to 2.9 A resolution, but neither the ligand nor the sulfate from the crystallization buffer was found in the active site. A second structure determined with crystals prepared in the presence of dUMP and the antifolate 10-propargyl-5,8-dideazafolate revealed that the inhibitor was bound in an extended, nonproductive conformation, partially occupying the nucleotide-binding site. A sulfate ion, rather than dUMP, was found in the nucleotide phosphate-binding site. Previous studies have shown that the substitution at three of the four arginines of the dUMP phosphate-binding site is permissive; however; for Arg166, all the mutations lead to a near-inactive mutant. The present structures of TS R166Q reveal that the phosphate-binding site is largely intact, but with a substantially reduced affinity for phosphate, despite the presence of the three remaining arginines. The position of Cys146, which initiates catalysis, is shifted in the mutant and resides in a position that interferes with the binding of the dUMP pyrimidine moiety.


    Related Citations: 
    • Crystallographic Studies of Thymidylate Synthase : Structure of a Mammalian Enzyme and Analyses of Invariant Non-Catalytic Residues in a Bacterial Enzyme.
      Sotelo-Mundo, R.R.
      (1999) Thesis --: --


    Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721, USA. rrs@cascabel.ciad.mx




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
THYMIDYLATE SYNTHASE
A
264Escherichia coli (strain K12)Gene Names: thyA
EC: 2.1.1.45
Find proteins for P0A884 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A884
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CXM
Query on CXM
A
L-PEPTIDE LINKINGC6 H11 N O4 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.94 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.171 
  • Space Group: I 21 3
Unit Cell:
Length (Å)Angle (°)
a = 132.500α = 90.00
b = 132.500β = 90.00
c = 132.500γ = 90.00
Software Package:
Software NamePurpose
ROTAVATAdata scaling
CNSphasing
CCP4data scaling
CNSrefinement
MADNESSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-07-28
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description