3NT4

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

Summary for 3NT4

• Entry DOI: 10.2210/pdb3nt4/pdb
• Related: 3MZ0 3NT2 3NT5 3NTQ 3NTR
• Descriptor: Inositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase, 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE, 1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE, ... (4 entities in total)
• Functional Keywords: bsidh, oxidoreductase, n-terminal rossmann fold domain, glyceraldehyde-3-phosphate like c-terminal domain, cofactor nad(h), substrate inositol
• Biological source: Bacillus subtilis
• Total number of polymer chains: 2
• Total formula weight: 78480.26

Authors

Van Straaten, K.E.,Palmer, D.R.J.,Sanders, D.A.R. (deposition date: 2010-07-02, release date: 2010-09-15, Last modification date: 2023-09-06)

Primary citation

van Straaten, K.E.,Zheng, H.,Palmer, D.R.,Sanders, D.A.
Structural investigation of myo-inositol dehydrogenase from Bacillus subtilis: implications for catalytic mechanism and inositol dehydrogenase subfamily classification.
Biochem.J., 432:237-247, 2010

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.

PubMed: 20809899
DOI: 10.1042/BJ20101079

Experimental method

X-RAY DIFFRACTION (2.5001 Å)