3sxi: Difference between revisions

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[[Image:3sxi.png|left|200px]]
==Crystal structure of sulfide:quinone oxidoreductase Cys128Ala variant from Acidithiobacillus ferrooxidans complexed with decylubiquinone==
<StructureSection load='3sxi' size='340' side='right' caption='[[3sxi]], [[Resolution|resolution]] 2.18&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3sxi]] 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=3SXI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3SXI FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3kpg|3kpg]], [[3kpi|3kpi]], [[3kpk|3kpk]], [[3sx6|3sx6]], [[3sy4|3sy4]], [[3syi|3syi]], [[3sz0|3sz0]], [[3szc|3szc]], [[3szf|3szf]]</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=920 Acidithiobacillus ferrooxidans])</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=3sxi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3sxi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3sxi RCSB], [http://www.ebi.ac.uk/pdbsum/3sxi PDBsum]</span></td></tr>
</table>
<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.


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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>
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{{STRUCTURE_3sxi|  PDB=3sxi  |  SCENE=  }}


===Crystal structure of sulfide:quinone oxidoreductase Cys128Ala variant from Acidithiobacillus ferrooxidans complexed with decylubiquinone===
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 
</div>
 
== References ==
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{{ABSTRACT_PUBMED_22542586}}
 
==About this Structure==
[[3sxi]] 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=3SXI OCA].
 
==Reference==
<ref group="xtra">PMID:022542586</ref><references group="xtra"/>
[[Category: Acidithiobacillus ferrooxidans]]
[[Category: Acidithiobacillus ferrooxidans]]
[[Category: Cherney, M M.]]
[[Category: Cherney, M M]]
[[Category: James, M N.G.]]
[[Category: James, M N.G]]
[[Category: Weiner, J H.]]
[[Category: Weiner, J H]]
[[Category: Zhang, Y.]]
[[Category: Zhang, Y]]
[[Category: Complex with sulfide]]
[[Category: Complex with sulfide]]
[[Category: Cys128ala variant]]
[[Category: Cys128ala variant]]

Revision as of 12:52, 4 January 2015

Crystal structure of sulfide:quinone oxidoreductase Cys128Ala variant from Acidithiobacillus ferrooxidans complexed with decylubiquinoneCrystal structure of sulfide:quinone oxidoreductase Cys128Ala variant from Acidithiobacillus ferrooxidans complexed with decylubiquinone

Structural highlights

3sxi is a 1 chain structure with sequence from Acidithiobacillus ferrooxidans. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:, , , ,
Gene:AFE_1792 (Acidithiobacillus ferrooxidans)
Resources:FirstGlance, OCA, RCSB, PDBsum

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[1]

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

References

  1. ↑ 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

3sxi, resolution 2.18Å

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