1TYS

WATER-MEDIATED SUBSTRATE(SLASH)PRODUCT DISCRIMINATION: THE PRODUCT COMPLEX OF THYMIDYLATE SYNTHASE AT 1.83 ANGSTROMS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Water-mediated substrate/product discrimination: the product complex of thymidylate synthase at 1.83 A.

Fauman, E.B.Rutenber, E.E.Maley, G.F.Maley, F.Stroud, R.M.

(1994) Biochemistry 33: 1502-1511


  • PubMed Abstract: 
  • In an irreversible enzyme-catalyzed reaction, strong binding of the products would lead to substantial product inhibition. The X-ray crystal structure of the product complex of thymidylate synthase (1.83-A resolution, R factor = 0.183 for all data be ...

    In an irreversible enzyme-catalyzed reaction, strong binding of the products would lead to substantial product inhibition. The X-ray crystal structure of the product complex of thymidylate synthase (1.83-A resolution, R factor = 0.183 for all data between 7.0 and 1.83 A) identifies a bound water molecule that serves to disfavor binding of the product nucleotide, dTMP. This water molecule is hydrogen bonded to absolutely conserved Tyr 146 (using the Lactobacillus casei numbering system) and is displaced by the C7 methyl group of the reaction product thymidylate. The relation between this observation and kinetic and thermodynamic values is discussed. The structure reveals a carbamate modified N-terminus that binds in a highly conserved site, replaced by side chains that can exploit the same site in other TS sequences. The enzyme-products complex is compared to the previously determined structure of enzyme-substrate-cofactor analog. This comparison reveals changes that occur between the first covalent complex formed between enzyme and substrate with an inhibitory cofactor analog and the completed reaction. The almost identical arrangement of ligands in these two structures contributes to our model for the TS reaction and verifies the physiological relevance of the mode in which potent inhibitors bind to this target for rational drug design.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
THYMIDYLATE SYNTHASE
A
264Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: thyA
EC: 2.1.1.45
Find proteins for P0A884 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A884
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TMP
Query on TMP

Download SDF File 
Download CCD File 
A
THYMIDINE-5'-PHOSPHATE
C10 H15 N2 O8 P
GYOZYWVXFNDGLU-XLPZGREQSA-N
 Ligand Interaction
DHF
Query on DHF

Download SDF File 
Download CCD File 
A
DIHYDROFOLIC ACID
C19 H21 N7 O6
OZRNSSUDZOLUSN-LBPRGKRZSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CXM
Query on CXM
A
L-PEPTIDE LINKINGC6 H11 N O4 SMET
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DHFKd: 3270 nM BINDINGMOAD
TMPKd: 3270 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Work: 0.183 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 71.970α = 90.00
b = 71.970β = 90.00
c = 115.040γ = 120.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORrefinement
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-06-22
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance