3t2k: Difference between revisions

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-[[Image:3t2k.jpg|left|200px]]
-<!--
+==Crystal structure of sulfide:quinone oxidoreductase Cys128Ala variant from Acidithiobacillus ferrooxidans with bound trisulfane==
-The line below this paragraph, containing "STRUCTURE_3t2k", creates the "Structure Box" on the page.
+<StructureSection load='3t2k' size='340' side='right'caption='[[3t2k]], [[Resolution|resolution]] 2.35&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'>[[3t2k]] 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=3T2K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3T2K 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]] 2.3501&#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=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=S3H:TRISULFANE'>S3H</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_3t2k|  PDB=3t2k  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3t2k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t2k OCA], [https://pdbe.org/3t2k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3t2k RCSB], [https://www.ebi.ac.uk/pdbsum/3t2k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3t2k 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>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Sulfide:quinone oxidoreductase (SQR) is a peripheral membrane protein that catalyzes the oxidation of sulfide species to elemental sulfur. The enzymatic reaction proceeds in two steps. The electrons from sulfides are transferred first to the enzyme cofactor, FAD, which, in turn, passes them onto the quinone pool in the membrane. Several wild-type SQR structures have been reported recently. However, the enzymatic mechanism of SQR has not been fully delineated. In order to understand the role of the catalytically essential residues in the enzymatic mechanism of SQR we produced a number of variants of the conserved residues in the catalytic site including the cysteine triad of SQR from the acidophilic, chemolithotrophic bacterium Acidithiobacillus ferrooxidans. These were structurally characterized and their activities for each reaction step were determined. In addition, the crystal structures of the wild-type SQR with sodium selenide and gold(I) cyanide have been determined. Previously we proposed a mechanism for the reduction of sulfides to elemental sulfur involving nucleophilic attack of Cys356 on C(4A) atom of FAD. Here we also consider an alternative anionic radical mechanism by direct electron transfer from Cys356 to the isoalloxazine ring of FAD.
-===Crystal structure of sulfide:quinone oxidoreductase Cys128Ala variant from Acidithiobacillus ferrooxidans with bound trisulfane===
+Structure-activity characterization of sulfide:quinone oxidoreductase variants.,Cherney MM, Zhang Y, James MN, Weiner JH J Struct Biol. 2012 Apr 19. PMID:22542586<ref>PMID:22542586</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3t2k" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_22542586}}, adds the Publication Abstract to the page
+*[[Quinone reductase 3D structures|Quinone reductase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 22542586 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_22542586}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Acidithiobacillus ferrooxidans ATCC 23270]]
-[[3t2k]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Acidithiobacillus_ferrooxidans Acidithiobacillus ferrooxidans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T2K OCA].
+[[Category: Large Structures]]
+[[Category: Cherney MM]]
-==Reference==
+[[Category: James MNG]]
-<ref group="xtra">PMID:022542586</ref><references group="xtra"/>
+[[Category: Weiner JH]]
-[[Category: Acidithiobacillus ferrooxidans]]
+[[Category: Zhang Y]]
-[[Category: Cherney, M M.]]
-[[Category: James, M N.G.]]
-[[Category: Weiner, J H.]]
-[[Category: Zhang, Y.]]
-[[Category: Complex with trisulfane]]
-[[Category: Cys128ala variant]]
-[[Category: Integral monotopic membrane protein]]
-[[Category: Oxidoreductase]]
-[[Category: Sulfide:quinone oxidoreductase]]