1nyk

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[[Image:1nyk.jpg|left|200px]]
 
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==Crystal Structure of the Rieske protein from Thermus thermophilus==
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The line below this paragraph, containing "STRUCTURE_1nyk", creates the "Structure Box" on the page.
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<StructureSection load='1nyk' size='340' side='right'caption='[[1nyk]], [[Resolution|resolution]] 1.31&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'>[[1nyk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NYK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NYK 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]] 1.31&#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=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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{{STRUCTURE_1nyk| PDB=1nyk | 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=1nyk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nyk OCA], [https://pdbe.org/1nyk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1nyk RCSB], [https://www.ebi.ac.uk/pdbsum/1nyk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1nyk ProSAT]</span></td></tr>
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</table>
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'''Crystal Structure of the Rieske protein from Thermus thermophilus'''
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== Function ==
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[https://www.uniprot.org/uniprot/Q5SGZ9_THET8 Q5SGZ9_THET8]
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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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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/ny/1nyk_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1nyk 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 ==
The structure of the soluble Rieske protein from Thermus thermophilus has been determined at a resolution of 1.3 A at pH 8.5 using multiwavelength anomalous dispersion (MAD) techniques. This is the first report of a Rieske protein from a menaquinone-utilizing organism. The structure shows an overall fold similar to previously reported Rieske proteins. A novel feature of this crystal form appears to be a shared hydrogen between the His-134 imidazole ring ligated to Fe2 of the [2Fe-2S] cluster and its symmetry partner, His-134', one being formally an imidazolate anion, Fe2-(His-134)N(epsilon)(-)...H-N(epsilon')(His-134')-Fe2', in which crystallographic C(2) axes pass equidistant between N(epsilon)...N(epsilon') and normal to the line defined by N(epsilon)...N(epsilon'). This provides evidence for a stable, oxidized cluster with a His(-) ligand and lends support to a previously proposed mechanism of coupled proton and electron transfer. A detailed comparison of the Thermus Rieske protein with six other Rieske and Rieske-type proteins indicates: (a) The cluster binding domain is tightly conserved. (b) The 3-D structure of the 10 beta-strand fold is conserved, even among the most divergent proteins. (c) There is an approximately linear relation between acid-pH redox potential and number of H-bonds to the cluster. (d) These proteins have two faces, one points into the larger complex (bc(1), b(6)f, or other), is involved in the proton coupled electron transfer function, and is highly conserved. The second is oriented toward the solvent and shows wide variation in charge, sequence, length, hydrophobicity, and secondary elements in the loops that connect the beta-sheets.
The structure of the soluble Rieske protein from Thermus thermophilus has been determined at a resolution of 1.3 A at pH 8.5 using multiwavelength anomalous dispersion (MAD) techniques. This is the first report of a Rieske protein from a menaquinone-utilizing organism. The structure shows an overall fold similar to previously reported Rieske proteins. A novel feature of this crystal form appears to be a shared hydrogen between the His-134 imidazole ring ligated to Fe2 of the [2Fe-2S] cluster and its symmetry partner, His-134', one being formally an imidazolate anion, Fe2-(His-134)N(epsilon)(-)...H-N(epsilon')(His-134')-Fe2', in which crystallographic C(2) axes pass equidistant between N(epsilon)...N(epsilon') and normal to the line defined by N(epsilon)...N(epsilon'). This provides evidence for a stable, oxidized cluster with a His(-) ligand and lends support to a previously proposed mechanism of coupled proton and electron transfer. A detailed comparison of the Thermus Rieske protein with six other Rieske and Rieske-type proteins indicates: (a) The cluster binding domain is tightly conserved. (b) The 3-D structure of the 10 beta-strand fold is conserved, even among the most divergent proteins. (c) There is an approximately linear relation between acid-pH redox potential and number of H-bonds to the cluster. (d) These proteins have two faces, one points into the larger complex (bc(1), b(6)f, or other), is involved in the proton coupled electron transfer function, and is highly conserved. The second is oriented toward the solvent and shows wide variation in charge, sequence, length, hydrophobicity, and secondary elements in the loops that connect the beta-sheets.
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==About this Structure==
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High-resolution structure of the soluble, respiratory-type Rieske protein from Thermus thermophilus: analysis and comparison.,Hunsicker-Wang LM, Heine A, Chen Y, Luna EP, Todaro T, Zhang YM, Williams PA, McRee DE, Hirst J, Stout CD, Fee JA Biochemistry. 2003 Jun 24;42(24):7303-17. PMID:12809486<ref>PMID:12809486</ref>
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1NYK is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NYK OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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High-resolution structure of the soluble, respiratory-type Rieske protein from Thermus thermophilus: analysis and comparison., Hunsicker-Wang LM, Heine A, Chen Y, Luna EP, Todaro T, Zhang YM, Williams PA, McRee DE, Hirst J, Stout CD, Fee JA, Biochemistry. 2003 Jun 24;42(24):7303-17. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12809486 12809486]
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</div>
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[[Category: Single protein]]
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<div class="pdbe-citations 1nyk" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Thermus thermophilus]]
[[Category: Thermus thermophilus]]
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[[Category: Chen, Y.]]
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[[Category: Chen Y]]
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[[Category: Fee, J A.]]
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[[Category: Fee JA]]
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[[Category: Heine, A.]]
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[[Category: Heine A]]
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[[Category: Hirst, J.]]
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[[Category: Hirst J]]
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[[Category: Hunsicker-Wang, L M.]]
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[[Category: Hunsicker-Wang LM]]
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[[Category: Luna, E P.]]
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[[Category: Luna EP]]
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[[Category: McRee, D E.]]
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[[Category: McRee DE]]
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[[Category: Stout, C D.]]
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[[Category: Stout CD]]
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[[Category: Todaro, T.]]
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[[Category: Todaro T]]
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[[Category: Williams, P A.]]
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[[Category: Williams PA]]
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[[Category: Zhang, Y M.]]
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[[Category: Zhang YM]]
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[[Category: Beta barrel]]
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[[Category: Iron sulfur cluster]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 03:08:28 2008''
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Current revision

Crystal Structure of the Rieske protein from Thermus thermophilus

PDB ID 1nyk

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