3hrd

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{{Seed}}
 
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[[Image:3hrd.png|left|200px]]
 
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==Crystal structure of nicotinate dehydrogenase==
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The line below this paragraph, containing "STRUCTURE_3hrd", creates the "Structure Box" on the page.
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<StructureSection load='3hrd' size='340' side='right'caption='[[3hrd]], [[Resolution|resolution]] 2.20&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'>[[3hrd]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Eubacterium_barkeri Eubacterium barkeri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HRD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HRD 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]] 2.2&#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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=MCN:PTERIN+CYTOSINE+DINUCLEOTIDE'>MCN</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MOS:DIOXOTHIOMOLYBDENUM(VI)+ION'>MOS</scene>, <scene name='pdbligand=NIO:NICOTINIC+ACID'>NIO</scene>, <scene name='pdbligand=NO3:NITRATE+ION'>NO3</scene>, <scene name='pdbligand=SE:SELENIUM+ATOM'>SE</scene></td></tr>
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{{STRUCTURE_3hrd| PDB=3hrd | 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=3hrd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hrd OCA], [https://pdbe.org/3hrd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hrd RCSB], [https://www.ebi.ac.uk/pdbsum/3hrd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hrd ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/NDLMS_EUBBA NDLMS_EUBBA] Catalyzes the hydroxylation of nicotinate to 6-hydroxynicotinate. Also active against 2-pyrazinecarboxylic acid, but inactive against other nicotinate analogs.<ref>PMID:8555176</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hr/3hrd_consurf.spt"</scriptWhenChecked>
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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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</jmolCheckbox>
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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=3hrd ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Nicotinate dehydrogenase (NDH) from Eubacterium barkeri is a molybdoenzyme catalyzing the hydroxylation of nicotinate to 6-hydroxynicotinate. Reactivity of NDH critically depends on the presence of labile (nonselenocysteine) selenium with an as-yet-unidentified form and function. We have determined the crystal structure of NDH and analyzed its active site by multiple wavelengths anomalous dispersion methods. We show that selenium is bound as a terminal Mo=Se ligand to molybdenum and that it occupies the position of the terminal sulfido ligand in other molybdenum hydroxylases. The role of selenium in catalysis has been assessed by model calculations, which indicate an acceleration of the critical hydride transfer from the substrate to the selenido ligand in the course of substrate hydroxylation when compared with an active site containing a sulfido ligand. The MoO(OH)Se active site of NDH shows a novel type of utilization and reactivity of selenium in nature.
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===Crystal structure of nicotinate dehydrogenase===
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The Mo-Se active site of nicotinate dehydrogenase.,Wagener N, Pierik AJ, Ibdah A, Hille R, Dobbek H Proc Natl Acad Sci U S A. 2009 Jul 7;106(27):11055-60. Epub 2009 Jun 22. PMID:19549881<ref>PMID:19549881</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_19549881}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 3hrd" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 19549881 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_19549881}}
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__TOC__
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</StructureSection>
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==About this Structure==
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3HRD is a 8 chains structure of sequences from [http://en.wikipedia.org/wiki/Eubacterium_barkeri Eubacterium barkeri]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HRD OCA].
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==Reference==
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<ref group="xtra">PMID:19549881</ref><references group="xtra"/>
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[[Category: Eubacterium barkeri]]
[[Category: Eubacterium barkeri]]
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[[Category: Dobbek, H.]]
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[[Category: Large Structures]]
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[[Category: Hille, R.]]
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[[Category: Dobbek H]]
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[[Category: Pierik, A J.]]
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[[Category: Hille R]]
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[[Category: Wagener, N.]]
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[[Category: Pierik AJ]]
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[[Category: 2fe-2]]
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[[Category: Wagener N]]
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[[Category: Iron]]
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[[Category: Iron-sulfur]]
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[[Category: Metal-binding]]
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[[Category: Oxidoreductase]]
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[[Category: Selenium ligand]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 22 20:52:00 2009''
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Current revision

Crystal structure of nicotinate dehydrogenase

PDB ID 3hrd

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OCA

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