3vdr | pdb_00003vdr

Crystal structure of D-3-hydroxybutyrate dehydrogenase, prepared in the presence of the substrate D-3-hydroxybutyrate and NAD(+)

spinqualitylabelsall models 3vdr, resolution 3.00Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 3vdr is a 4 chain structure with sequence from Alcaligenes faecalis. This structure supersedes the now removed PDB entry 3eew. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 3Å Ligands: 3HR, AAE, CA, CL, NAD, NAI Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function D0VWQ0_ALCFA Publication Abstract from PubMed D-3-hydroxybutyrate dehydrogenase from Alcaligenes faecalis catalyzes the reversible conversion between D-3-hydroxybutyrate and acetoacetate. The enzyme was crystallized in the presence of the substrate D-3-hydroxybutyrate and the cofactor NAD(+) at the optimum pH for the catalytic reaction. The structure, which was solved by X-ray crystallography, is isomorphous to that of the complex with the substrate analogue acetate. The product as well as the substrate molecule are accommodated well in the catalytic site. Their binding geometries suggest that the reversible reactions occur by shuttle movements of a hydrogen negative ion from the C3 atom of the substrate to the C4 atom of NAD(+) and from the C4 atom of NADH to the C3 atom of the product. The reaction might be further coupled to the withdrawal of a proton from the hydroxyl group of the substrate by the ionized Tyr155 residue. These structural features strongly support the previously proposed reaction mechanism of D-3-hydroxybutyrate dehydrogenase, which was based on the acetate-bound complex structure. Structure of D-3-hydroxybutyrate dehydrogenase prepared in the presence of the substrate D-3-hydroxybutyrate and NAD+.,Hoque MM, Shimizu S, Juan EC, Sato Y, Hossain MT, Yamamoto T, Imamura S, Suzuki K, Amano H, Sekiguchi T, Tsunoda M, Takenaka A Acta Crystallogr Sect F Struct Biol Cryst Commun. 2009 Apr 1;65(Pt, 4):331-5. Epub 2009 Mar 26. PMID:19342772 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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