3vdr

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[[Image:3vdr.jpg|left|200px]]
 
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==Crystal structure of D-3-hydroxybutyrate dehydrogenase, prepared in the presence of the substrate D-3-hydroxybutyrate and NAD(+)==
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The line below this paragraph, containing "STRUCTURE_3vdr", creates the "Structure Box" on the page.
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<StructureSection load='3vdr' size='340' side='right'caption='[[3vdr]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[3vdr]] 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=3eew 3eew]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VDR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VDR FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3HR:(3R)-3-HYDROXYBUTANOIC+ACID'>3HR</scene>, <scene name='pdbligand=AAE:ACETOACETIC+ACID'>AAE</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=NAI:1,4-DIHYDRONICOTINAMIDE+ADENINE+DINUCLEOTIDE'>NAI</scene></td></tr>
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{{STRUCTURE_3vdr| PDB=3vdr | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3vdr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vdr OCA], [https://pdbe.org/3vdr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vdr RCSB], [https://www.ebi.ac.uk/pdbsum/3vdr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vdr ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/D0VWQ0_ALCFA D0VWQ0_ALCFA]
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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===Crystal structure of D-3-hydroxybutyrate dehydrogenase, prepared in the presence of the substrate D-3-hydroxybutyrate and NAD(+)===
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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<ref>PMID:19342772</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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The line below this paragraph, {{ABSTRACT_PUBMED_19342772}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 3vdr" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 19342772 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_19342772}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[3vdr]] is a 4 chain structure with sequence from [http://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=3eew 3eew]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VDR OCA].
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==Reference==
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<ref group="xtra">PMID:019342772</ref><references group="xtra"/>
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[[Category: 3-hydroxybutyrate dehydrogenase]]
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[[Category: Alcaligenes faecalis]]
[[Category: Alcaligenes faecalis]]
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[[Category: Amano, H.]]
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[[Category: Large Structures]]
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[[Category: Hoque, M M.]]
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[[Category: Amano H]]
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[[Category: Hossain, M T.]]
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[[Category: Hoque MM]]
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[[Category: Imamura, S.]]
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[[Category: Hossain MT]]
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[[Category: Juan, E C.M.]]
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[[Category: Imamura S]]
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[[Category: Sato, Y.]]
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[[Category: Juan ECM]]
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[[Category: Sekiguchi, T.]]
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[[Category: Sato Y]]
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[[Category: Shimizu, S.]]
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[[Category: Sekiguchi T]]
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[[Category: Suzuki, K.]]
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[[Category: Shimizu S]]
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[[Category: Takenaka, A.]]
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[[Category: Suzuki K]]
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[[Category: Tsunoda, M.]]
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[[Category: Takenaka A]]
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[[Category: Yamamoto, T.]]
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[[Category: Tsunoda M]]
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[[Category: Ketone body]]
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[[Category: Yamamoto T]]
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[[Category: Nad dependent enzyme]]
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[[Category: Oxidoreductase]]
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Current revision

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

PDB ID 3vdr

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