Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 

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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

  • DOI: https://doi.org/10.1093/protein/9.1.69
  • Primary Citation of Related Structures:  
    1TSV, 1TSW, 1TSX, 1TSY, 1TSZ

  • 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 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
THYMIDYLATE SYNTHASE316Lacticaseibacillus caseiMutation(s): 1 
Find proteins for P00469 (Lacticaseibacillus casei)
Explore P00469 
Go to UniProtKB:  P00469
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00469
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on UMP

Download Ideal Coordinates CCD File 
C9 H13 N2 O8 P
Binding Affinity Annotations 
IDSourceBinding Affinity
UMP PDBBind:  1TSY Kd: 1.10e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Work: 0.206 
  • R-Value Observed: 0.206 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.8α = 90
b = 78.8β = 90
c = 242γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
R-AXISdata reduction

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-03-08
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2021-11-03
    Changes: Database references, Derived calculations, Other
  • Version 1.4: 2024-02-14
    Changes: Data collection