1wmb

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[[Image:1wmb.gif|left|200px]]
 
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==Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase==
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The line below this paragraph, containing "STRUCTURE_1wmb", creates the "Structure Box" on the page.
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<StructureSection load='1wmb' size='340' side='right'caption='[[1wmb]], [[Resolution|resolution]] 2.00&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'>[[1wmb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_fragi Pseudomonas fragi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WMB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WMB FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 2&#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=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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{{STRUCTURE_1wmb| PDB=1wmb | 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=1wmb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wmb OCA], [https://pdbe.org/1wmb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wmb RCSB], [https://www.ebi.ac.uk/pdbsum/1wmb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wmb ProSAT]</span></td></tr>
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</table>
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'''Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase'''
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== Function ==
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[https://www.uniprot.org/uniprot/Q5KST5_PSEFR Q5KST5_PSEFR]
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== Evolutionary Conservation ==
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==Overview==
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[[Image:Consurf_key_small.gif|200px|right]]
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The gene coding for d-3-hydroxybutyrate dehydrogenase (HBDH) was cloned from Pseudomonas fragi. The nucleotide sequence contained a 780 bp open reading frame encoding a 260 amino acid residue protein. The recombinant enzyme was efficiently expressed in Escherichia coli cells harboring pHBDH11 and was purified to homogeneity as judged by SDS-PAGE. The enzyme showed a strict stereospecificity to the D-enantiomer (3R-configuration) of 3-hydroxybutyrate as a substrate. Crystals of the ligand-free HBDH and of the enzyme-NAD+ complex were obtained using the hanging-drop, vapor-diffusion method. The crystal structure of the HBDH was solved by the multiwavelength anomalous diffraction method using the SeMet-substituted enzyme and was refined to 2.0 A resolution. The overall structure of P.fragi HBDH, including the catalytic tetrad of Asn114, Ser142, Tyr155, and Lys159, shows obvious relationships with other members of the short-chain dehydrogenase/reductase (SDR) family. A cacodylate anion was observed in both the ligand-free enzyme and the enzyme-NAD+ complex, and was located near the catalytic tetrad. It was shown that the cacodylate inhibited the NAD+-dependent D-3-hydroxybutyrate dehydrogenation competitively, with a Ki value of 5.6 mM. From the interactions between cacodylate and the enzyme, it is predicted that substrate specificity is achieved through the recognition of the 3-methyl and carboxyl groups of the substrate.
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Check<jmol>
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<jmolCheckbox>
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==About this Structure==
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wm/1wmb_consurf.spt"</scriptWhenChecked>
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1WMB is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_fragi Pseudomonas fragi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WMB OCA].
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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==Reference==
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</jmolCheckbox>
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D-3-hydroxybutyrate dehydrogenase from Pseudomonas fragi: molecular cloning of the enzyme gene and crystal structure of the enzyme., Ito K, Nakajima Y, Ichihara E, Ogawa K, Katayama N, Nakashima K, Yoshimoto T, J Mol Biol. 2006 Jan 27;355(4):722-33. Epub 2005 Nov 14. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16325199 16325199]
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1wmb ConSurf].
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[[Category: 3-hydroxybutyrate dehydrogenase]]
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<div style="clear:both"></div>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Pseudomonas fragi]]
[[Category: Pseudomonas fragi]]
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[[Category: Single protein]]
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[[Category: Ichihara E]]
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[[Category: Ichihara, E.]]
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[[Category: Ito K]]
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[[Category: Ito, K.]]
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[[Category: Nakajima Y]]
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[[Category: Nakajima, Y.]]
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[[Category: Ogawa K]]
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[[Category: Ogawa, K.]]
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[[Category: Yoshimoto T]]
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[[Category: Yoshimoto, T.]]
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[[Category: Nad]]
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[[Category: Nadh]]
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[[Category: Oxidoreductase]]
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[[Category: Short chain dehydrogenase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 13:52:18 2008''
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Current revision

Crystal structure of NAD dependent D-3-hydroxybutylate dehydrogenase

PDB ID 1wmb

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