1nyk

From Proteopedia

(Difference between revisions)

Current revision

Crystal Structure of the Rieske protein from Thermus thermophilus

Structural highlights

1nyk is a 2 chain structure with sequence from Thermus thermophilus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.31Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q5SGZ9_THET8

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

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.

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^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Hunsicker-Wang LM, Heine A, Chen Y, Luna EP, Todaro T, Zhang YM, Williams PA, McRee DE, Hirst J, Stout CD, Fee JA. High-resolution structure of the soluble, respiratory-type Rieske protein from Thermus thermophilus: analysis and comparison. Biochemistry. 2003 Jun 24;42(24):7303-17. PMID:12809486 doi:10.1021/bi0342719

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1nyk"

@@ Line 1: / Line 1: @@
 ==Crystal Structure of the Rieske protein from Thermus thermophilus==
-<StructureSection load='1nyk' size='340' side='right' caption='[[1nyk]], [[Resolution|resolution]] 1.31&Aring;' scene=''>
+<StructureSection load='1nyk' size='340' side='right'caption='[[1nyk]], [[Resolution|resolution]] 1.31&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1nyk]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NYK FirstGlance]. <br>
+<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>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+</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>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1nyk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1nyk OCA], [http://pdbe.org/1nyk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1nyk RCSB], [http://www.ebi.ac.uk/pdbsum/1nyk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1nyk ProSAT]</span></td></tr>
+<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>
+<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>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q5SGZ9_THET8 Q5SGZ9_THET8]
 == 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/ny/1nyk_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ny/1nyk_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 30: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
+[[Category: Large Structures]]
-[[Category: Chen, Y]]
+[[Category: Thermus thermophilus]]
-[[Category: Fee, J A]]
+[[Category: Chen Y]]
-[[Category: Heine, A]]
+[[Category: Fee JA]]
-[[Category: Hirst, J]]
+[[Category: Heine A]]
-[[Category: Hunsicker-Wang, L M]]
+[[Category: Hirst J]]
-[[Category: Luna, E P]]
+[[Category: Hunsicker-Wang LM]]
-[[Category: McRee, D E]]
+[[Category: Luna EP]]
-[[Category: Stout, C D]]
+[[Category: McRee DE]]
-[[Category: Todaro, T]]
+[[Category: Stout CD]]
-[[Category: Williams, P A]]
+[[Category: Todaro T]]
-[[Category: Zhang, Y M]]
+[[Category: Williams PA]]
-[[Category: Beta barrel]]
+[[Category: Zhang YM]]
-[[Category: Electron transport]]
-[[Category: Iron sulfur cluster]]

1nyk

From Proteopedia

Current revision

Crystal Structure of the Rieske protein from Thermus thermophilus

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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