Crystal structure of myo-inositol dehydrogenase from Bacillus subtilis with bound cofactor NADH and inositol

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.236 

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Structural investigation of myo-inositol dehydrogenase from Bacillus subtilis: implications for catalytic mechanism and inositol dehydrogenase subfamily classification.

van Straaten, K.E.Zheng, H.Palmer, D.R.Sanders, D.A.

(2010) Biochem J 432: 237-247

  • DOI: https://doi.org/10.1042/BJ20101079
  • Primary Citation of Related Structures:  
    3MZ0, 3NT2, 3NT4, 3NT5, 3NTO, 3NTQ, 3NTR

  • PubMed Abstract: 

    Inositol dehydrogenase from Bacillus subtilis (BsIDH) is a NAD+-dependent enzyme that catalyses the oxidation of the axial hydroxy group of myo-inositol to form scyllo-inosose. We have determined the crystal structures of wild-type BsIDH and of the inactive K97V mutant in apo-, holo- and ternary complexes with inositol and inosose. BsIDH is a tetramer, with a novel arrangement consisting of two long continuous β-sheets, formed from all four monomers, in which the two central strands are crossed over to form the core of the tetramer. Each subunit in the tetramer consists of two domains: an N-terminal Rossmann fold domain containing the cofactor-binding site, and a C-terminal domain containing the inositol-binding site. Structural analysis allowed us to determine residues important in cofactor and substrate binding. Lys97, Asp172 and His176 are the catalytic triad involved in the catalytic mechanism of BsIDH, similar to what has been proposed for related enzymes and short-chain dehydrogenases. Furthermore, a conformational change in the nicotinamide ring was observed in some ternary complexes, suggesting hydride transfer to the si-face of NAD+. Finally, comparison of the structure and sequence of BsIDH with other putative inositol dehydrogenases allowed us to differentiate these enzymes into four subfamilies based on six consensus sequence motifs defining the cofactor- and substrate-binding sites.

  • Organizational Affiliation

    Department of Chemistry, University of Saskatchewan, Saskatoon, SK, Canada, S7N 5C9.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase
A, B
344Bacillus subtilisMutation(s): 0 
Gene Names: BSU39700E83GidhiolGNP_391849.2
Find proteins for P26935 (Bacillus subtilis (strain 168))
Explore P26935 
Go to UniProtKB:  P26935
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26935
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.236 
  • Space Group: I 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 184.368α = 90
b = 184.368β = 90
c = 184.368γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
PDB_EXTRACTdata extraction
MxDCdata collection
d*TREKdata 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: 2010-09-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description