3kpk: Difference between revisions

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-{{Seed}}
-[[Image:3kpk.png|left|200px]]
-<!--
+==Crystal structure of sulfide:quinone oxidoreductase from Acidithiobacillus ferrooxidans, C160A mutant==
-The line below this paragraph, containing "STRUCTURE_3kpk", creates the "Structure Box" on the page.
+<StructureSection load='3kpk' size='340' side='right'caption='[[3kpk]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3kpk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Acidithiobacillus_ferrooxidans_ATCC_23270 Acidithiobacillus ferrooxidans ATCC 23270]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KPK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3KPK FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.05&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=H2S:HYDROSULFURIC+ACID'>H2S</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=PGR:R-1,2-PROPANEDIOL'>PGR</scene></td></tr>
-{{STRUCTURE_3kpk|  PDB=3kpk  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3kpk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3kpk OCA], [https://pdbe.org/3kpk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3kpk RCSB], [https://www.ebi.ac.uk/pdbsum/3kpk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3kpk ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SQRD_ACIF2 SQRD_ACIF2] Catalyzes the oxidation of hydrogen sulfide, with the help of a quinone. Consecutive reaction cycles lead to the accumulation of a polysulfide product on the active site Cys residues; these products are released when they exceed a critical length, typically as cyclooctasulfur.<ref>PMID:20303979</ref> <ref>PMID:22542586</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/kp/3kpk_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=3kpk ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Sulfide:quinone oxidoreductase from the acidophilic and chemolithotrophic bacterium Acidithiobacillus ferrooxidans was expressed in Escherichia coli and crystallized, and its X-ray molecular structure was determined to 2.3 A resolution for native unbound protein in space group P4(2)2(1)2 . The decylubiquinone-bound structure and the Cys160Ala variant structure were subsequently determined to 2.3 A and 2.05 A resolutions, respectively, in space group P6(2)22 . The enzymatic reaction catalyzed by sulfide:quinone oxidoreductase includes the oxidation of sulfide compounds H(2)S, HS(-), and S(2-) to soluble polysulfide chains or to elemental sulfur in the form of octasulfur rings; these oxidations are coupled to the reduction of ubiquinone or menaquinone. The enzyme comprises two tandem Rossmann fold domains and a flexible C-terminal domain encompassing two amphipathic helices that are thought to provide for membrane anchoring. The second amphipathic helix unwinds and changes its orientation in the hexagonal crystal form. The protein forms a dimer that could be inserted into the membrane to a depth of approximately 20 A. It has an endogenous flavin adenine dinucleotide (FAD) cofactor that is noncovalently bound in the N-terminal domain. Several wide channels connect the FAD cofactor to the exterior of the protein molecule; some of the channels would provide access to the membrane. The ubiquinone molecule is bound in one of these channels; its benzoquinone ring is stacked between the aromatic rings of two conserved Phe residues, and it closely approaches the isoalloxazine moiety of the FAD cofactor. Two active-site cysteine residues situated on the re side of the FAD cofactor form a branched polysulfide bridge. Cys356 disulfide acts as a nucleophile that attacks the C4A atom of the FAD cofactor in electron transfer reaction. The third essential cysteine Cys128 is not modified in these structures; its role is likely confined to the release of the polysulfur product.
-===Crystal structure of sulfide:quinone oxidoreductase from Acidithiobacillus ferrooxidans, C160A mutant===
+Crystal structure of sulfide:quinone oxidoreductase from Acidithiobacillus ferrooxidans: insights into sulfidotrophic respiration and detoxification.,Cherney MM, Zhang Y, Solomonson M, Weiner JH, James MN J Mol Biol. 2010 Apr 30;398(2):292-305. Epub 2010 Mar 19. PMID:20303979<ref>PMID:20303979</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_20303979}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 3kpk" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 20303979 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_20303979}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Acidithiobacillus ferrooxidans ATCC 23270]]
-KPK is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Acidithiobacillus_ferrooxidans_atcc_23270 Acidithiobacillus ferrooxidans atcc 23270]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3KPK OCA].
+[[Category: Large Structures]]
+[[Category: Cherney MM]]
-==Reference==
+[[Category: James MNG]]
-<ref group="xtra">PMID:20303979</ref><references group="xtra"/>
+[[Category: Solomonson M]]
-[[Category: Acidithiobacillus ferrooxidans atcc 23270]]
+[[Category: Weiner JH]]
-[[Category: Cherney, M M.]]
+[[Category: Zhang Y]]
-[[Category: James, M N.G.]]
-[[Category: Solomonson, M.]]
-[[Category: Weiner, J H.]]
-[[Category: Zhang, Y.]]
-[[Category: C160a mutant]]
-[[Category: Oxidoreductase]]
-[[Category: Oxidoreductase]]
-[[Category: Sulfide:quinone oxidoreductase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 28 11:21:29 2010''