Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 39234.46 
• Atom Count: 2723 
• Residue Count: 344 
• Unique protein chains: 1

3MZ0

Crystal structure of apo myo-inositol dehydrogenase from Bacillus subtilis

• DOI: 10.2210/pdb3MZ0/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bacillus subtilis (strain 168)
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2010-05-11 Released: 2010-09-29 
• Deposition Author(s): Van Straaten, K.E., Palmer, D.R.J., Sanders, D.A.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.539 Å
• R-Value Free: 0.194 
• R-Value Work: 0.175 

Literature

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

• PubMed: 20809899 
• DOI: 10.1042/BJ20101079
• Primary Citation of Related Structures:  
  3NTR, 3NTQ, 3NTO, 3NT5, 3NT4, 3NT2


• 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.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase	A	344	Bacillus subtilis (strain 168)	Mutation(s): 0  Gene Names: iolG (idh) EC: 1.1.1.18, 1.1.1.369
Find proteins for P26935 (Bacillus subtilis (strain 168)) Go to UniProtKB:  P26935

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
PGE	A	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.539 Å
• R-Value Free: 0.194 
• R-Value Work: 0.175 
• Space Group: I 2 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 52.207	α = 90.00
b = 120.054	β = 90.00
c = 129.254	γ = 90.00

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data collection
HKL-2000	data scaling
HKL-2000	data reduction
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-05-11 
• Released Date: 2010-09-29 
• Deposition Author(s): Van Straaten, K.E., Palmer, D.R.J., Sanders, D.A.R.

Revision History 

• Version 1.0: 2010-09-29
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance