1ESQ

CRYSTAL STRUCTURE OF THIAZOLE KINASE MUTANT (C198S) WITH ATP AND THIAZOLE PHOSPHATE.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of 4-methyl-5-beta-hydroxyethylthiazole kinase from Bacillus subtilis at 1.5 A resolution.

Campobasso, N.Mathews, I.I.Begley, T.P.Ealick, S.E.

(2000) Biochemistry 39: 7868-7877

  • Primary Citation of Related Structures:  1C3Q, 1EKK, 1EKQ, 1ESJ

  • PubMed Abstract: 
  • 4-Methyl-5-beta-hydroxyethylthiazole kinase (ThiK) catalyzes the phosphorylation of the hydroxyl group of 4-methyl-5-beta-hydroxyethylthiazole (Thz). This enzyme is a salvage enzyme in the thiamin biosynthetic pathway and enables the cell to use recy ...

    4-Methyl-5-beta-hydroxyethylthiazole kinase (ThiK) catalyzes the phosphorylation of the hydroxyl group of 4-methyl-5-beta-hydroxyethylthiazole (Thz). This enzyme is a salvage enzyme in the thiamin biosynthetic pathway and enables the cell to use recycled Thz as an alternative to its synthesis from 1-deoxy-D-xylulose-5-phosphate, cysteine, and tyrosine. The structure of ThiK in the rhombohedral crystal form has been determined to 1.5 A resolution and refined to a final R-factor of 21. 6% (R-free 25.1%). The structures of the enzyme/Thz complex and the enzyme/Thz-phosphate/ATP complex have also been determined. ThiK is a trimer of identical subunits. Each subunit contains a large nine-stranded central beta-sheet flanked by helices. The overall fold is similar to that of ribokinase and adenosine kinase, although sequence similarity is not immediately apparent. The area of greatest similarity occurs in the ATP-binding site where several key residues are highly conserved. Unlike adenosine kinase and ribokinase, in which the active site is located between two domains within a single subunit, the ThiK active site it formed at the interface between two subunits within the trimer. The structure of the enzyme/ATP/Thz-phosphate complex suggests that phosphate transfer occurs by an inline mechanism. Although this mechanism is similar to that proposed for both ribokinase and adenosine kinase, ThiK lacks an absolutely conserved Asp thought to be important for catalysis in the other two enzymes. Instead, ThiK has a conserved cysteine (Cys198) in this position. When this Cys is mutated to Asp, the enzymatic activity increases 10-fold. Further sequence analysis suggests that another thiamin biosynthetic enzyme (ThiD), which catalyzes the formation of 2-methyl-4-amino-5-hydroxymethylpyrimidine pyrophosphate by two sequential phosphorylation reactions, belongs to the same family of small molecule kinases.


    Related Citations: 
    • Thiamin Biosynthesis in Prokaryotes.
      Begley, T.P.,Downs, D.,Ealick, S.,McLafferty, F.,Van Loon, D.,Taylor, S.,Campobasso, N.,Chiu, H.J.,Kinsland, C.,Reddick, J.J.,Xi, J.
      (1999) Arch.Microbiol. 171: 293


    Organizational Affiliation

    Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HYDROXYETHYLTHIAZOLE KINASE
A, B, C
284Bacillus subtilis (strain 168)Gene Names: thiM (thiK, ywbJ)
EC: 2.7.1.50
Find proteins for P39593 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P39593
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A, B, C
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

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

Download SDF File 
Download CCD File 
A, B, C
4-METHYL-5-HYDROXYETHYLTHIAZOLE PHOSPHATE
C6 H10 N O4 P S
OCYMERZCMYJQQO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.209 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 54.080α = 90.00
b = 100.840β = 95.10
c = 72.510γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
CNSphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-08-09
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-31
    Type: Experimental preparation