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3hrd
From Proteopedia
(Difference between revisions)
(New page: '''Unreleased structure''' The entry 3hrd is ON HOLD Authors: Wagener, N., Pierik, A.J., Hille, R., Dobbek, H. Description: Crystal structure of nicotinate dehydrogenase ''Page seeded...) |
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| - | '''Unreleased structure''' | ||
| - | + | ==Crystal structure of nicotinate dehydrogenase== | |
| + | <StructureSection load='3hrd' size='340' side='right'caption='[[3hrd]], [[Resolution|resolution]] 2.20Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <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> | ||
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2Å</td></tr> | ||
| + | <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> | ||
| + | <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> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [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> | ||
| + | == Evolutionary Conservation == | ||
| + | [[Image:Consurf_key_small.gif|200px|right]] | ||
| + | Check<jmol> | ||
| + | <jmolCheckbox> | ||
| + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hr/3hrd_consurf.spt"</scriptWhenChecked> | ||
| + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
| + | <text>to colour the structure by Evolutionary Conservation</text> | ||
| + | </jmolCheckbox> | ||
| + | </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]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | 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. | ||
| - | + | 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> | |
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | + | </div> | |
| - | + | <div class="pdbe-citations 3hrd" style="background-color:#fffaf0;"></div> | |
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Eubacterium barkeri]] | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Dobbek H]] | ||
| + | [[Category: Hille R]] | ||
| + | [[Category: Pierik AJ]] | ||
| + | [[Category: Wagener N]] | ||
Current revision
Crystal structure of nicotinate dehydrogenase
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