6QXS

Crystal structure of Enteroccocus faecalis thymidylate synthase (EfTS) in complex with FdUMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 

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Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Structural Comparison ofEnterococcus faecalisand Human Thymidylate Synthase Complexes with the Substrate dUMP and Its Analogue FdUMP Provides Hints about Enzyme Conformational Variabilities.

Pozzi, C.Ferrari, S.Luciani, R.Tassone, G.Costi, M.P.Mangani, S.

(2019) Molecules 24

  • DOI: 10.3390/molecules24071257
  • Primary Citation of Related Structures:  
    6QXG, 6QXH, 6QXS, 6QYA

  • PubMed Abstract: 
  • Thymidylate synthase (TS) is an enzyme of paramount importance as it provides the only de novo source of deoxy-thymidine monophosphate (dTMP). dTMP, essential for DNA synthesis, is produced by the TS-catalyzed reductive methylation of 2'-deoxyuridine-5'-monophosphate (dUMP) using N⁵,N 10 -methylenetetrahydrofolate (mTHF) as a cofactor ...

    Thymidylate synthase (TS) is an enzyme of paramount importance as it provides the only de novo source of deoxy-thymidine monophosphate (dTMP). dTMP, essential for DNA synthesis, is produced by the TS-catalyzed reductive methylation of 2'-deoxyuridine-5'-monophosphate (dUMP) using N⁵,N 10 -methylenetetrahydrofolate (mTHF) as a cofactor. TS is ubiquitous and a validated drug target. TS enzymes from different organisms differ in sequence and structure, but are all obligate homodimers. The structural and mechanistic differences between the human and bacterial enzymes are exploitable to obtain selective inhibitors of bacterial TSs that can enrich the currently available therapeutic tools against bacterial infections. Enterococcus faecalis is a pathogen fully dependent on TS for dTMP synthesis. In this study, we present four new crystal structures of Enterococcus faecalis and human TSs in complex with either the substrate dUMP or the inhibitor FdUMP. The results provide new clues about the half-site reactivity of Enterococcus faecalis TS and the mechanisms underlying the conformational changes occurring in the two enzymes. We also identify relevant differences in cofactor and inhibitor binding between Enterococcus faecalis and human TS that can guide the design of selective inhibitors against bacterial TSs.


    Organizational Affiliation

    Department of Biotechnology, Chemistry and Pharmacy-Department of Excellence 2018-2020, University of Siena, via Aldo Moro 2, 53100 Siena, Italy. stefano.mangani@unisi.it.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Thymidylate synthaseA315Enterococcus faecalis V583Mutation(s): 0 
Gene Names: thyAEF_1576
EC: 2.1.1.45
UniProt
Find proteins for Q834R3 (Enterococcus faecalis (strain ATCC 700802 / V583))
Explore Q834R3 
Go to UniProtKB:  Q834R3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ834R3
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Thymidylate synthaseB, C, D315Enterococcus faecalisMutation(s): 0 
Gene Names: thyAEF_1576
EC: 2.1.1.45
UniProt
Find proteins for Q834R3 (Enterococcus faecalis (strain ATCC 700802 / V583))
Explore Q834R3 
Go to UniProtKB:  Q834R3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ834R3
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FFO
Query on FFO

Download Ideal Coordinates CCD File 
G [auth B],
J [auth D]
N-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid
C20 H23 N7 O7
VVIAGPKUTFNRDU-STQMWFEESA-N
 Ligand Interaction
UFP
Query on UFP

Download Ideal Coordinates CCD File 
E [auth B],
H [auth D]
5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
C9 H12 F N2 O8 P
HFEKDTCAMMOLQP-RRKCRQDMSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth B],
I [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CME
Query on CME
A L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.04α = 90
b = 94.84β = 94.01
c = 97γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European UnionLSH-2005-2.2.0-8

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-10
    Type: Initial release
  • Version 1.1: 2019-07-10
    Changes: Data collection
  • Version 2.0: 2019-11-20
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary