4FZB

Structure of thymidylate synthase ThyX complexed to a new inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Mechanistic and structural basis for inhibition of thymidylate synthase ThyX.

Basta, T.Boum, Y.Briffotaux, J.Becker, H.F.Lamarre-Jouenne, I.Lambry, J.C.Skouloubris, S.Liebl, U.Graille, M.van Tilbeurgh, H.Myllykallio, H.

(2012) Open Biology 2: 120120-120120

  • DOI: 10.1098/rsob.120120

  • PubMed Abstract: 
  • Nature has established two mechanistically and structurally unrelated families of thymidylate synthases that produce de novo thymidylate or dTMP, an essential DNA precursor. Representatives of the alternative flavin-dependent thymidylate synthase fam ...

    Nature has established two mechanistically and structurally unrelated families of thymidylate synthases that produce de novo thymidylate or dTMP, an essential DNA precursor. Representatives of the alternative flavin-dependent thymidylate synthase family, ThyX, are found in a large number of microbial genomes, but are absent in humans. We have exploited the nucleotide binding pocket of ThyX proteins to identify non-substrate-based tight-binding ThyX inhibitors that inhibited growth of genetically modified Escherichia coli cells dependent on thyX in a manner mimicking a genetic knockout of thymidylate synthase. We also solved the crystal structure of a viral ThyX bound to 2-hydroxy-3-(4-methoxybenzyl)-1,4-naphthoquinone at a resolution of 2.6 Å. This inhibitor was found to bind within the conserved active site of the tetrameric ThyX enzyme, at the interface of two monomers, partially overlapping with the dUMP binding pocket. Our studies provide new chemical tools for investigating the ThyX reaction mechanism and establish a novel mechanistic and structural basis for inhibition of thymidylate synthesis. As essential ThyX proteins are found e.g. in Mycobacterium tuberculosis and Helicobacter pylori, our studies have also potential to pave the way towards the development of new anti-microbial compounds.


    Organizational Affiliation

    Laboratoire d'Optique et Biosciences, INSERM U696, CNRS UMR 7645, Ecole Polytechnique, Palaiseau Cedex, Palaiseau 91228, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Probable thymidylate synthase
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
227Paramecium bursaria Chlorella virus 1Mutation(s): 0 
EC: 2.1.1.148
Find proteins for O41156 (Paramecium bursaria Chlorella virus 1)
Go to UniProtKB:  O41156
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download SDF File 
Download CCD File 
A, B, C, E, F, H, I, J, K, M, N, O, P
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
0VJ
Query on 0VJ

Download SDF File 
Download CCD File 
A, B, D, E, F, G, H, I, J, K, L, M, N, O, P
2-hydroxy-3-(4-methoxybenzyl)naphthalene-1,4-dione
C18 H14 O4
DKOJAMITDVVFPR-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, K, M, O, P
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.211 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 69.975α = 111.65
b = 120.585β = 91.13
c = 128.249γ = 90.18
Software Package:
Software NamePurpose
XDSdata reduction
MOLREPphasing
BUSTERrefinement
XSCALEdata scaling
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-22
    Type: Initial release
  • Version 1.1: 2013-11-06
    Type: Data collection