3NT2: Crystal structure of myo-inositol dehydrogenase from Bacillus subtilis with bound cofactor

Citation:
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 beta-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.
PDB ID: 3NT2Download
MMDB ID: 84862
PDB Deposition Date: 2010/7/2
Updated in MMDB: 2010/12
Experimental Method:
x-ray diffraction
Resolution: 2.3003  Å
Source Organism:
Similar Structures:
Biological Unit for 3NT2: tetrameric; determined by author and by software (PISA)
Molecular Components in 3NT2
Label Count Molecule
Proteins (4 molecules)
4
Inositol 2-dehydrogenase/d-chiro-inositol 3-dehydrogenase(Gene symbol: iolG)
Molecule annotation
Chemicals (4 molecules)
1
2
2
2
* Click molecule labels to explore molecular sequence information.

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