5Z9Y

Crystal structure of Mycobacterium tuberculosis thiazole synthase (ThiG) complexed with DXP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 

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Literature

Snapshots of catalysis: Structure of covalently bound substrate trapped in Mycobacterium tuberculosis thiazole synthase (ThiG).

Zhang, J.Zhang, B.Zhao, Y.Yang, X.Huang, M.Cui, P.Zhang, W.Li, J.Zhang, Y.

(2018) Biochem Biophys Res Commun 497: 214-219

  • DOI: https://doi.org/10.1016/j.bbrc.2018.02.056
  • Primary Citation of Related Structures:  
    5Z9Y

  • PubMed Abstract: 

    Increasing drug resistance in Mycobacterium tuberculosis (Mtb) has necessitated the design of new anti-mycobacterial drugs with novel targets. Thiazole synthase (ThiG) is an essential enzyme and a potential drug target in Mtb that catalyzes the formation of the thiazole moiety of thiamin-pyrophosphate from 1-deoxy-d-xylulose-5-phosphate (DXP), dehydroglycine and ThiS-thiocarboxylate. To uncover the catalysis mechanism and design potent and selective anti-mycobacterial compounds targeting ThiG, we determined the crystal structure of MtbThiG at 1.5 Å resolution, for the first time, snapshotting a covalently bound substrate trapped in the catalytic pocket. The structure showed a (β/α) 8 barrel overall fold as well as the dimer form of MtbThiG existing in solution. In the central pocket, Lys98 is the key residue forming a protonated carbinolamine intermediate, a functional Schiff base precursor, with DXP. The carbinolamine is further stabilized by active site residues mainly through hydrogen bonds. This work revealed that a protonated carbinolamine is initially formed and then it is dehydrated to the imine form of Schiff base during the early catalysis steps. Our research will provide useful information for understanding the ThiG function and lay the basis for future drug design by targeting this essential protein.


  • Organizational Affiliation

    Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, 201210, China; National Center for Protein Science Shanghai, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 201210, China. Electronic address: shyaolx@163.com.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thiazole synthase
A, B
252Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: thiGRv0417MTCY22G10.14
EC: 2.8.1.10
UniProt
Find proteins for P9WG73 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WG73 
Go to UniProtKB:  P9WG73
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WG73
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.67α = 90
b = 116.67β = 90
c = 123.32γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data scaling
PDB_EXTRACTdata extraction
PHASERphasing
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-11
    Type: Initial release