Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.230 

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This is version 1.5 of the entry. See complete history


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

  • DOI: https://doi.org/10.1021/bi0000061
  • Primary Citation of Related Structures:  
    1C3Q, 1EKK, 1EKQ, 1ESJ, 1ESQ

  • 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 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C
284Bacillus subtilisMutation(s): 1 
Find proteins for P39593 (Bacillus subtilis (strain 168))
Explore P39593 
Go to UniProtKB:  P39593
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39593
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.230 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.06α = 90
b = 100.89β = 96.02
c = 73.07γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-08-09
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-01-31
    Changes: Advisory, Experimental preparation
  • Version 1.4: 2021-11-03
    Changes: Advisory, Database references, Derived calculations
  • Version 1.5: 2024-02-07
    Changes: Data collection