5CGA

Structure of Hydroxyethylthiazole kinase ThiM from Staphylococcus aureus in complex with substrate analog 2-(1,3,5-trimethyl-1H-pyrazole-4-yl)ethanol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of ThiM from Vitamin B1 biosynthetic pathway of Staphylococcus aureus - Insights into a novel pro-drug approach addressing MRSA infections.

Drebes, J.Kunz, M.Windshugel, B.Kikhney, A.G.Muller, I.B.Eberle, R.J.Oberthur, D.Cang, H.Svergun, D.I.Perbandt, M.Betzel, C.Wrenger, C.

(2016) Sci Rep 6: 22871-22871

  • DOI: 10.1038/srep22871
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Infections caused by the methicillin-resistant Staphylococcus aureus (MRSA) are today known to be a substantial threat for global health. Emerging multi-drug resistant bacteria have created a substantial need to identify and discover new drug targets ...

    Infections caused by the methicillin-resistant Staphylococcus aureus (MRSA) are today known to be a substantial threat for global health. Emerging multi-drug resistant bacteria have created a substantial need to identify and discover new drug targets and to develop novel strategies to treat bacterial infections. A promising and so far untapped antibiotic target is the biosynthesis of vitamin B1 (thiamin). Thiamin in its activated form, thiamin pyrophosphate, is an essential co-factor for all organisms. Therefore, thiamin analogous compounds, when introduced into the vitamin B1 biosynthetic pathway and further converted into non-functional co-factors by the bacterium can function as pro-drugs which thus block various co-factor dependent pathways. We characterized one of the key enzymes within the S. aureus vitamin B1 biosynthetic pathway, 5-(hydroxyethyl)-4-methylthiazole kinase (SaThiM; EC 2.7.1.50), a potential target for pro-drug compounds and analyzed the native structure of SaThiM and complexes with the natural substrate 5-(hydroxyethyl)-4-methylthiazole (THZ) and two selected substrate analogues.


    Organizational Affiliation

    University Hamburg, c/o DESY, Laboratory for Structural Biology of Infection and Inflammation, Hamburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hydroxyethylthiazole kinase
A, B, C, E, F, H
277Staphylococcus aureus (strain MRSA252)Mutation(s): 0 
Gene Names: thiM
EC: 2.7.1.50
Find proteins for Q6GEY3 (Staphylococcus aureus (strain MRSA252))
Go to UniProtKB:  Q6GEY3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, E
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
KP6
Query on KP6

Download SDF File 
Download CCD File 
A, B, C, E, F, H
2-(1,3,5-trimethyl-1H-pyrazol-4-yl)ethanol
C8 H14 N2 O
QESMYIFDOLAREQ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.169 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 62.026α = 92.59
b = 62.362β = 91.39
c = 108.320γ = 101.28
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
LEXI-SDIGermany--

Revision History 

  • Version 1.0: 2016-03-23
    Type: Initial release
  • Version 1.1: 2018-03-07
    Type: Advisory, Data collection