9VNS
NADPH and 1-benzyl-4-methylpiperidin-3-one complex structure of glucose dehydrogenase M6 from Bacillus megaterium
This is a non-PDB format compatible entry.
Summary for 9VNS
| Entry DOI | 10.2210/pdb9vns/pdb |
| Descriptor | Glucose 1-dehydrogenase, NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, (4~{R})-4-methyl-1-(phenylmethyl)piperidin-3-one, ... (4 entities in total) |
| Functional Keywords | nadph and 1-benzyl-4-methylpiperidin-3-one complex structure, glucose dehydrogenase m6, oxidoreductase |
| Biological source | Priestia megaterium |
| Total number of polymer chains | 4 |
| Total formula weight | 117078.92 |
| Authors | |
| Primary citation | Yamamoto, K.,Kurisu, G.,Kusunoki, M.,Tabata, S.,Urabe, I.,Osaki, S. Crystal structure of glucose dehydrogenase from Bacillus megaterium IWG3 at 1.7 A resolution. J Biochem, 129:303-312, 2001 Cited by PubMed Abstract: The crystal structure of glucose dehydrogenase (GlcDH) from Bacillus megaterium IWG3 has been determined to an R-factor of 17.9% at 1.7 A resolution. The enzyme consists of four identical subunits, which are similar to those of other short-chain reductases/dehydrogenases (SDRs) in their overall folding and subunit architecture, although cofactor binding sites and subunit interactions differ. Whereas a pair of basic residues is well conserved among NADP(+)-preferring SDRs, only Arg39 was found around the adenine ribose moiety of GlcDH. This suggests that one basic amino acid is enough to determine the coenzyme specificity. The four subunits are interrelated by three mutually perpendicular diad axes (P, Q, and R). While subunit interactions through the P-axis for GlcDH are not so different from those of the other SDRs, those through the Q-axis differ significantly. GlcDH was found to have weaker hydrophobic interactions in the Q-interface. Moreover, GlcDH lacks the salt bridge that stabilizes the subunit interaction in the Q-interface in the other SDRs. Hydrogen bonds between Q-axis related subunits are also less common than in the other SDRs. The GlcDH tetramer dissociates into inactive monomers at pH 9.0, which can be attributed mainly to the weakness of the Q-axis interface. PubMed: 11173533DOI: 10.1093/oxfordjournals.jbchem.a002858 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.09 Å) |
Structure validation
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