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 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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 Biol 2: 120120-120120

  • DOI: 10.1098/rsob.120120
  • Primary Citation of Related Structures:  
    4FZB

  • 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 family, ThyX, are found in a large number of microbial genomes, but are absent in humans ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Probable thymidylate synthase
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
227Paramecium bursaria Chlorella virus 1Mutation(s): 0 
Gene Names: A674RThyX
EC: 2.1.1.148
UniProt
Find proteins for O41156 (Paramecium bursaria Chlorella virus 1)
Explore O41156 
Go to UniProtKB:  O41156
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO41156
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
BB [auth N],
CA [auth E],
EB [auth O],
FA [auth F],
GA [auth F],
BB [auth N],
CA [auth E],
EB [auth O],
FA [auth F],
GA [auth F],
GB [auth P],
MA [auth H],
OA [auth I],
PA [auth I],
Q [auth A],
R [auth A],
SA [auth J],
V [auth B],
VA [auth K],
Y [auth C],
YA [auth M]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
0VJ
Query on 0VJ

Download Ideal Coordinates CCD File 
AA [auth D],
AB [auth M],
CB [auth N],
DA [auth E],
DB [auth O],
AA [auth D],
AB [auth M],
CB [auth N],
DA [auth E],
DB [auth O],
HB [auth P],
IA [auth F],
JA [auth G],
LA [auth H],
RA [auth I],
S [auth A],
TA [auth J],
U [auth A],
UA [auth K],
X [auth B],
XA [auth L]
2-hydroxy-3-(4-methoxybenzyl)naphthalene-1,4-dione
C18 H14 O4
DKOJAMITDVVFPR-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download Ideal Coordinates CCD File 
BA [auth D],
EA [auth E],
FB [auth O],
HA [auth F],
IB [auth P],
BA [auth D],
EA [auth E],
FB [auth O],
HA [auth F],
IB [auth P],
KA [auth G],
NA [auth H],
QA [auth I],
T [auth A],
W [auth B],
WA [auth K],
Z [auth C],
ZA [auth M]
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 
  • R-Value Observed: 0.213 
  • 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
ADSCdata collection
MOLREPphasing
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

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