5J7W

Enterococcus faecalis thymidylate synthase complex with methotrexate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

X-ray crystal structures of Enterococcus faecalis thymidylate synthase with folate binding site inhibitors.

Catalano, A.Luciani, R.Carocci, A.Cortesi, D.Pozzi, C.Borsari, C.Ferrari, S.Mangani, S.

(2016) Eur.J.Med.Chem. 123: 649-664

  • DOI: 10.1016/j.ejmech.2016.07.066
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Infections caused by Enterococcus faecalis (Ef) represent nowadays a relevant health problem. We selected Thymidylate synthase (TS) from this organism as a potential specific target for antibacterial therapy. We have previously demonstrated that spec ...

    Infections caused by Enterococcus faecalis (Ef) represent nowadays a relevant health problem. We selected Thymidylate synthase (TS) from this organism as a potential specific target for antibacterial therapy. We have previously demonstrated that species-specific inhibition of the protein can be achieved despite the relatively high structural similarity among bacterial TSs and human TS. We had previously obtained the EfTS crystal structure of the protein in complex with the metabolite 5-formyl-tetrahydrofolate (5-FTHF) suggesting the protein role as metabolite reservoir; however, protein-inhibitors complexes were still missing. In the present work we identified some inhibitors bearing the phthalimidic core from our in-house library and we performed crystallographic screening towards EfTS. We obtained two X-ray crystallographic structures: the first with a weak phthalimidic inhibitor bound in one subunit and 5-hydroxymethylene-6-hydrofolic acid (5-HMHF) in the other subunit; a second X-ray structure complex with methotrexate. The structural information achieved confirm the role of EfTS as an enzyme involved in the folate pool system and provide a structural basis for structure-based drug design.


    Organizational Affiliation

    Dipartimento di Farmacia-Scienze del Farmaco, Università degli Studi di Bari "Aldo Moro", Via Orabona 4, 70125 Bari, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thymidylate synthase
A, B, C, D
315Enterococcus faecalis (strain ATCC 700802 / V583)Mutation(s): 0 
Gene Names: thyA
EC: 2.1.1.45
Find proteins for Q834R3 (Enterococcus faecalis (strain ATCC 700802 / V583))
Go to UniProtKB:  Q834R3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MTX
Query on MTX

Download SDF File 
Download CCD File 
C, D
METHOTREXATE
C20 H22 N8 O5
FBOZXECLQNJBKD-ZDUSSCGKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.200 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 72.227α = 90.00
b = 94.144β = 94.14
c = 96.293γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
PDB_EXTRACTdata extraction
MOSFLMdata reduction
PHENIXrefinement
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-04-07 
  • Released Date: 2016-09-28 
  • Deposition Author(s): Mangani, S., Pozzi, C.

Funding OrganizationLocationGrant Number
MIUR-PRIN2009Italy200925BPZ5_004

Revision History 

  • Version 1.0: 2016-09-28
    Type: Initial release