1TSW

THYMIDYLATE SYNTHASE R179A MUTANT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Contribution of a salt bridge to binding affinity and dUMP orientation to catalytic rate: mutation of a substrate-binding arginine in thymidylate synthase.

Finer-Moore, J.S.Fauman, E.B.Morse, R.J.Santi, D.V.Stroud, R.M.

(1996) Protein Eng. 9: 69-75

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Invariant arginine 179, one of four arginines that are conserved in all thymidylate synthases (TS) and that bind the phosphate moiety of the substrate 2'-deoxyuridine-5'-monophosphate (dUMP), can be altered even to a negatively charged glutamic acid ...

    Invariant arginine 179, one of four arginines that are conserved in all thymidylate synthases (TS) and that bind the phosphate moiety of the substrate 2'-deoxyuridine-5'-monophosphate (dUMP), can be altered even to a negatively charged glutamic acid with little effect on kcat. In the mutant structures, ordered water or the other phosphate-binding arginines compensate for the hydrogen bonds made by Arg179 in the wild-type enzyme and there is almost no change in the conformation or binding site of dUMP. Correlation of dUMP Kds for TS R179A and TS R179K with the structures of their binary complexes shows, that the positive charge on Arg179 contributes significantly to dUMP binding affinity. kcat/K(m) for dUMP measures the rate of dUMP binding to TS during the ordered bi-substrate reaction, and in the ternary complex dUMP provides a binding surface for the cofactor. kcat/K(m) reflects the ability of the enzyme to accept a properly oriented dUMP for catalysis and is less sensitive than is Kd to the changes in electrostatics at the phosphate binding site.


    Related Citations: 
    • Atomic Structure of Thymidylate Synthase: Target for Rational Drug Design
      Hardy, L.W.,Finer-Moore, J.S.,Montfort, W.R.,Jones, M.O.,Santi, D.V.,Stroud, R.M.
      (1987) Science 235: 448
    • Stereochemistry of a Multistep(Slash)Bipartite Methyl Transfer Reaction: Thymidylate Synthase
      Stroud, R.M.,Finer-Moore, J.S.
      (1993) Faseb J. 7: 671
    • Refined Structures of Substrate-Bound and Phosphate-Bound Thymidylate Synthase from Lactobacillus Casei
      Finer-Moore, J.S.,Fauman, E.B.,Foster, P.G.,Perry, K.M.,Santi, D.V.,Stroud, R.M.
      (1993) J.Mol.Biol. 232: 1101


    Organizational Affiliation

    Department of Biochemistry and Biophysics, University of California at San Francisco 94143-0448, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
THYMIDYLATE SYNTHASE
A
316Lactobacillus caseiMutation(s): 1 
Gene Names: thyA
EC: 2.1.1.45
Find proteins for P00469 (Lactobacillus casei)
Go to UniProtKB:  P00469
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 0.180 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 78.300α = 90.00
b = 78.300β = 90.00
c = 243.200γ = 120.00
Software Package:
Software NamePurpose
XGENdata reduction
X-PLORphasing
X-PLORmodel building
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-03-08
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.3: 2011-11-16
    Type: Atomic model