3vdq: Difference between revisions

<table><tr><td colspan='2'>[[3vdq]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Alcaligenes_faecalis Alcaligenes faecalis]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2zea 2zea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VDQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VDQ FirstGlance]. <br>

<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3vdq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vdq OCA], [https://pdbe.org/3vdq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vdq RCSB], [https://www.ebi.ac.uk/pdbsum/3vdq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vdq ProSAT]</span></td></tr>

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<ref>PMID:18453685</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>

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