Crystal structure of the 5-(Hydroxyethyl)-methylthiazole Kinase ThiM from Klebsiella pneumonia

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.178 

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Structural insight of the 5-(Hydroxyethyl)-methylthiazole kinase ThiM involving vitamin B1 biosynthetic pathway from the Klebsiella pneumoniae.

Chen, Y.Wang, L.Shang, F.Liu, W.Lan, J.Chen, J.Ha, N.C.Quan, C.Nam, K.H.Xu, Y.

(2019) Biochem Biophys Res Commun 518: 513-518

  • DOI: https://doi.org/10.1016/j.bbrc.2019.08.086
  • Primary Citation of Related Structures:  
    6JYY, 6K28

  • PubMed Abstract: 

    Thiamin pyrophosphate (TPP) is an essential co-factor in amino acid and carbohydrate metabolic pathways. The TPP-related vitamin B1 biosynthetic pathway is found in most bacterial, plant and lower eukaryotic processes; however, it is not present in humans. In bacterial thiamin synthesis and salvage pathways, the 5-(hydroxyethyl)-methylthiazole kinase (ThiM) is essential in the pathway forming TPP. Thus, ThiM is considered to be an attractive antibacterial drug target. Here, we determined the crystal structures of ThiM from pathogenic Klebsiella pneumoniae (KpThiM) and KpThiM in complex with its substrate 5-(hydroxyethyl)-4-methylthiazole (TZE). KpThiM, consisting of an α-β-α domain, shows a pseudosymmetric trimeric formation. TZE molecules are located in the interface between the KpThiM subunits in the trimer and interact with Met49 and Cys200. Superimposition of the apo and TZE-complexed structures of KpThiM show that the side chains of the amino acids interacting with TZE and Mg 2+ have a rigid configuration. Comparison of the ThiM structures shows that KpThiM could, in terms of sequence and configuration, be different from other ThiM proteins, which possess different amino acids that recognize TZE and Mg 2+ . The structures will provide new insight into the ThiM subfamily proteins for antibacterial drug development.

  • Organizational Affiliation

    Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian, 116600, Liaoning, China; Key Laboratory of Biotechnology and Bioresources Utilization (Dalian Minzu University), Ministry of Education, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hydroxyethylthiazole kinaseA [auth C],
C [auth A]
257Klebsiella pneumoniaeMutation(s): 0 
Gene Names: thiMBN49_3768
Find proteins for A6TBJ8 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578))
Explore A6TBJ8 
Go to UniProtKB:  A6TBJ8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6TBJ8
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.356α = 90
b = 110.091β = 90
c = 125.448γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXmodel building

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31200556
National Natural Science Foundation of ChinaChina21272031

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2020-05-06
    Changes: Database references
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references