3UWL

Crystal structure of Enteroccocus faecalis thymidylate synthase (EfTS) in complex with 5-formyl tetrahydrofolate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The structure of Enterococcus faecalis thymidylate synthase provides clues about folate bacterial metabolism.

Pozzi, C.Ferrari, S.Cortesi, D.Luciani, R.Stroud, R.M.Catalano, A.Costi, M.P.Mangani, S.

(2012) Acta Crystallogr.,Sect.D 68: 1232-1241

  • DOI: 10.1107/S0907444912026236

  • PubMed Abstract: 
  • Drug resistance to therapeutic antibiotics poses a challenge to the identification of novel targets and drugs for the treatment of infectious diseases. Infections caused by Enterococcus faecalis are a major health problem. Thymidylate synthase (TS) f ...

    Drug resistance to therapeutic antibiotics poses a challenge to the identification of novel targets and drugs for the treatment of infectious diseases. Infections caused by Enterococcus faecalis are a major health problem. Thymidylate synthase (TS) from E. faecalis is a potential target for antibacterial therapy. The X-ray crystallographic structure of E. faecalis thymidylate synthase (EfTS), which was obtained as a native binary complex composed of EfTS and 5-formyltetrahydrofolate (5-FTHF), has been determined. The structure provides evidence that EfTS is a half-of-the-sites reactive enzyme, as 5-FTHF is bound to two of the four independent subunits present in the crystal asymmetric unit. 5-FTHF is a metabolite of the one-carbon transfer reaction catalysed by 5-formyltetrahydrofolate cyclo-ligase. Kinetic studies show that 5-FTHF is a weak inhibitor of EfTS, suggesting that the EfTS-5-FTHF complex may function as a source of folates and/or may regulate one-carbon metabolism. The structure represents the first example of endogenous 5-FTHF bound to a protein involved in folate metabolism.


    Organizational Affiliation

    Dipartimento di Chimica, University of Siena, Siena, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thymidylate synthase
A, C
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
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Thymidylate synthase
B, 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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

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Download CCD File 
B, C, D
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
FOZ
Query on FOZ

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Download CCD File 
B, D
N-[4-({[(6S)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid
C20 H23 N7 O7
VVIAGPKUTFNRDU-STQMWFEESA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CME
Query on CME
B, D
L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FOZKi: 208000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.160 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 71.940α = 90.00
b = 94.250β = 95.01
c = 96.190γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
MOSFLMdata reduction
REFMACrefinement
SCALAdata scaling
PXSOFTdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-08-29
    Type: Initial release
  • Version 1.1: 2013-01-23
    Type: Database references