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| | ==Crystal structure of sulfide:quinone oxidoreductase from Acidithiobacillus ferrooxidans in complex with gold (I) cyanide== | | ==Crystal structure of sulfide:quinone oxidoreductase from Acidithiobacillus ferrooxidans in complex with gold (I) cyanide== |
| - | <StructureSection load='3szc' size='340' side='right' caption='[[3szc]], [[Resolution|resolution]] 2.20Å' scene=''> | + | <StructureSection load='3szc' size='340' side='right'caption='[[3szc]], [[Resolution|resolution]] 2.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3szc]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Acif2 Acif2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SZC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3SZC FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3szc]] 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=3SZC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SZC FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AU:GOLD+ION'>AU</scene>, <scene name='pdbligand=DCQ:2-DECYL-5,6-DIMETHOXY-3-METHYLCYCLOHEXA-2,5-DIENE-1,4-DIONE'>DCQ</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=H2S:HYDROSULFURIC+ACID'>H2S</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.2Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3kpg|3kpg]], [[3kpi|3kpi]], [[3kpk|3kpk]], [[3hyv|3hyv]], [[3hyw|3hyw]], [[3hyx|3hyx]], [[3sx6|3sx6]], [[3sxi|3sxi]], [[3sy4|3sy4]], [[3syi|3syi]], [[3sz0|3sz0]], [[3szf|3szf]], [[3szw|3szw]], [[3t0k|3t0k]], [[3t14|3t14]], [[3t2k|3t2k]], [[3t2y|3t2y]], [[3t2z|3t2z]], [[3t31|3t31]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AU:GOLD+ION'>AU</scene>, <scene name='pdbligand=DCQ:2-DECYL-5,6-DIMETHOXY-3-METHYLCYCLOHEXA-2,5-DIENE-1,4-DIONE'>DCQ</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=H2S:HYDROSULFURIC+ACID'>H2S</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">AFE_1792 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243159 ACIF2])</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=3szc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3szc OCA], [https://pdbe.org/3szc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3szc RCSB], [https://www.ebi.ac.uk/pdbsum/3szc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3szc ProSAT]</span></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=3szc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3szc OCA], [http://pdbe.org/3szc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3szc RCSB], [http://www.ebi.ac.uk/pdbsum/3szc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3szc ProSAT]</span></td></tr> | + | |
| | </table> | | </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;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Acif2]] | + | [[Category: Acidithiobacillus ferrooxidans ATCC 23270]] |
| - | [[Category: Cherney, M M]] | + | [[Category: Large Structures]] |
| - | [[Category: James, M N.G]] | + | [[Category: Cherney MM]] |
| - | [[Category: Weiner, J H]] | + | [[Category: James MNG]] |
| - | [[Category: Zhang, Y]] | + | [[Category: Weiner JH]] |
| - | [[Category: Integral monotopic membrane protein]] | + | [[Category: Zhang Y]] |
| - | [[Category: Oxidoreductase]]
| + | |
| - | [[Category: Sulfide:quinone oxidoreductase]]
| + | |
| Structural highlights
3szc is a 1 chain structure with sequence from Acidithiobacillus ferrooxidans ATCC 23270. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 2.2Å |
| Ligands: | , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
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.[1] [2]
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.
Structure-activity characterization of sulfide:quinone oxidoreductase variants.,Cherney MM, Zhang Y, James MN, Weiner JH J Struct Biol. 2012 Apr 19. PMID:22542586[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Cherney MM, Zhang Y, Solomonson M, Weiner JH, James MN. Crystal structure of sulfide:quinone oxidoreductase from Acidithiobacillus ferrooxidans: insights into sulfidotrophic respiration and detoxification. J Mol Biol. 2010 Apr 30;398(2):292-305. Epub 2010 Mar 19. PMID:20303979 doi:10.1016/j.jmb.2010.03.018
- ↑ Cherney MM, Zhang Y, James MN, Weiner JH. Structure-activity characterization of sulfide:quinone oxidoreductase variants. J Struct Biol. 2012 Apr 19. PMID:22542586 doi:10.1016/j.jsb.2012.04.007
- ↑ Cherney MM, Zhang Y, James MN, Weiner JH. Structure-activity characterization of sulfide:quinone oxidoreductase variants. J Struct Biol. 2012 Apr 19. PMID:22542586 doi:10.1016/j.jsb.2012.04.007
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