3vdq | pdb_00003vdq

Crystal structure of alcaligenes faecalis D-3-hydroxybutyrate dehydrogenase in complex with NAD(+) and acetate

spinqualitylabelsall models 3vdq, resolution 2.20Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 3vdq is a 4 chain structure with sequence from Alcaligenes faecalis. This structure supersedes the now removed PDB entry 2zea. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: ACT, CA, CL, NAD Related: 2yz7, 3vdr Activity: 3-hydroxybutyrate dehydrogenase, with EC number 1.1.1.30 Resources: FirstGlance, OCA, RCSB, PDBsum Publication Abstract from PubMed D-3-Hydroxybutyrate dehydrogenase, which catalyzes the reversible reaction between D-3-hydroxybutyrate and acetoacetate, has been classified into the short-chain dehydrogenase/reductase family and is a useful marker in the assay of diabetes mellitus and/or ketoacidosis. The enzyme from Alcaligenes faecalis was crystallized in the apo form and in the holo form with acetate as a substrate analogue. The crystal structures of both forms were determined at 2.2 angstroms resolution. The enzyme is a tetramer composed of four subunits assembled with noncrystallographic 222 point symmetry. Each subunit has two domains. The principal domain adopts the Rossmann fold essential for nucleotide binding, which is a common feature of the SDR family. NAD+ is bound in a large cleft in the domain. The pyrophosphate group of NAD+ is covered by the small additional domain, which is supported by two extended arms allowing domain movement. In the catalytic site, a water molecule is trapped by the catalytic Tyr155 and Ser142 residues in the vicinity of the bound NAD+ and acetate. The substrate analogue acetate is bound above the nicotinamide plane. A substrate (D-3-hydroxybutylate) bound model can reasonably be constructed by adding two C atoms into the void space between the water O atom and the methyl group of the acetate, suggesting a substrate-bound state before enzymatic reaction occurs. Based on these structural features, a reaction mechanism has been proposed. The structures of Alcaligenes faecalis D-3-hydroxybutyrate dehydrogenase before and after NAD+ and acetate binding suggest a dynamical reaction mechanism as a member of the SDR family.,Hoque MM, Shimizu S, Hossain MT, Yamamoto T, Imamura S, Suzuki K, Tsunoda M, Amano H, Sekiguchi T, Takenaka A Acta Crystallogr D Biol Crystallogr. 2008 May;64(Pt 5):496-505. Epub 2008, Apr 19. PMID:18453685 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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