3t31

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Current revision

Crystal structure of sulfide:quinone oxidoreductase from Acidithiobacillus ferrooxidans in complex with decylubiquinone

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 <StructureSection load='3t31' size='340' side='right'caption='[[3t31]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3t31]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Acif2 Acif2]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3kpg 3kpg]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T31 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3T31 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3t31]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Acidithiobacillus_ferrooxidans_ATCC_23270 Acidithiobacillus ferrooxidans ATCC 23270]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3kpg 3kpg]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3T31 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3T31 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</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]] 2.2999&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3kpg|3kpg]], [[3kpi|3kpi]], [[3kpk|3kpk]], [[3sxi|3sxi]], [[3sz0|3sz0]], [[3syi|3syi]], [[3sy4|3sy4]], [[3szc|3szc]], [[3szf|3szf]], [[3hyv|3hyv]], [[3hyw|3hyw]], [[3hyx|3hyx]], [[3t0k|3t0k]], [[3szw|3szw]], [[3h8l|3h8l]], [[3h8i|3h8i]], [[3t14|3t14]], [[3t2k|3t2k]], [[3t2z|3t2z]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">AFE_1792 ([https://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=3t31 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3t31 OCA], [https://pdbe.org/3t31 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3t31 RCSB], [https://www.ebi.ac.uk/pdbsum/3t31 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3t31 ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[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>
-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: 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>
-<div class="pdbe-citations 3t31" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Quinone reductase|Quinone reductase]]
+*[[Quinone reductase 3D structures|Quinone reductase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Acif2]]
+[[Category: Acidithiobacillus ferrooxidans ATCC 23270]]
 [[Category: Large Structures]]
-[[Category: Cherney, M M]]
+[[Category: Cherney MM]]
-[[Category: James, M N]]
+[[Category: James MN]]
-[[Category: Solomonson, M]]
+[[Category: Solomonson M]]
-[[Category: Weiner, J H]]
+[[Category: Weiner JH]]
-[[Category: Zhang, Y]]
+[[Category: Zhang Y]]
-[[Category: Acidithiobacillus ferrooxidan]]
-[[Category: Complex with decylubiquinone]]
-[[Category: Integral monotopic membrane protein]]
-[[Category: Oxidoreductase]]
-[[Category: Sulfide:quinone oxidoreductase]]

3t31

From Proteopedia

Current revision

Crystal structure of sulfide:quinone oxidoreductase from Acidithiobacillus ferrooxidans in complex with decylubiquinone

Structural highlights

Function

See Also

References

Contents

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