1BP6

THYMIDYLATE SYNTHASE R23I, R179T DOUBLE MUTANT


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Energetic contributions of four arginines to phosphate-binding in thymidylate synthase are more than additive and depend on optimization of "effective charge balance".

Morse, R.J.Kawase, S.Santi, D.V.Finer-Moore, J.Stroud, R.M.

(2000) Biochemistry 39: 1011-1020

  • Primary Citation of Related Structures:  1BO7, 1BO8, 1BP0, 1BPJ

  • PubMed Abstract: 
  • In thymidylate synthase, four conserved arginines provide two hydrogen bonds each to the oxygens of the phosphate group of the substrate, 2'-deoxyuridine-5'-monophosphate. Of these, R23, R178, and R179 are far removed from the site of methyl transfer ...

    In thymidylate synthase, four conserved arginines provide two hydrogen bonds each to the oxygens of the phosphate group of the substrate, 2'-deoxyuridine-5'-monophosphate. Of these, R23, R178, and R179 are far removed from the site of methyl transfer and contribute to catalysis solely through binding and orientation of ligands. These arginines can be substituted by other residues, while still retaining more than 1% activity of the wild-type enzyme. We compared the kinetics and determined the crystal structures of dUMP complexes of three of the most active, uncharged single mutants of these arginines, R23I, R178T, and R179T, and of double mutants (R23I, R179T) and (R178T, R179T). The dramatically higher K(m) for R178T compared to the other two single mutants arises from the effects of R178 substitution on the orientation of dUMP; 10-15-fold increases in for R23I and R178T reflect the role of these residues in stabilizing the closed conformation of TS in ternary complexes. The free energy for productive dUMP binding, DeltaG(S), increases by at least 1 kcal/mol for each mutant, even when dUMP orientation and mobility in the crystal structure is the same as in wild-type enzyme. Thus, the four arginines do not contribute excess positive charge to the PO(4)(-2) binding site; rather, they ideally complement the charge and geometry of the phosphate moiety. More-than-additive increases in DeltaG(S) seen in the double mutants are consistent with quadratic increases in DeltaG(S) predicted for deviations from ideal electrostatic interactions and may also reflect cooperative binding of the arginines to the phosphate oxygens.


    Related Citations: 
    • 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
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (THYMIDYLATE SYNTHASE)
A
316Lactobacillus caseiGene Names: thyA
EC: 2.1.1.45
Find proteins for P00469 (Lactobacillus casei)
Go to UniProtKB:  P00469
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
UMP
Query on UMP

Download SDF File 
Download CCD File 
A
2'-DEOXYURIDINE 5'-MONOPHOSPHATE
DUMP
C9 H13 N2 O8 P
JSRLJPSBLDHEIO-SHYZEUOFSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DUKi: 2260 nM (99) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.197 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 78.500α = 90.00
b = 78.500β = 90.00
c = 243.400γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
X-PLORphasing
DENZOdata reduction
X-PLORmodel building
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-08-19
    Type: Initial release
  • Version 1.1: 2007-10-16
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance