This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


3syi

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (13:12, 14 March 2024) (edit) (undo)
 
Line 3: Line 3:
<StructureSection load='3syi' size='340' side='right'caption='[[3syi]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
<StructureSection load='3syi' size='340' side='right'caption='[[3syi]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[3syi]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Acif2 Acif2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3SYI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SYI FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[3syi]] 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=3SYI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3SYI FirstGlance]. <br>
-
</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=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]] 2.2001&#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]], [[3sx6|3sx6]], [[3sxi|3sxi]], [[3sy4|3sy4]], [[3sz0|3sz0]], [[3szc|3szc]], [[3szf|3szf]]</div></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=SO4:SULFATE+ION'>SO4</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=3syi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3syi OCA], [https://pdbe.org/3syi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3syi RCSB], [https://www.ebi.ac.uk/pdbsum/3syi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3syi ProSAT]</span></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=3syi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3syi OCA], [https://pdbe.org/3syi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3syi RCSB], [https://www.ebi.ac.uk/pdbsum/3syi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3syi ProSAT]</span></td></tr>
</table>
</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 (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<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 3syi" style="background-color:#fffaf0;"></div>
+
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Acif2]]
+
[[Category: Acidithiobacillus ferrooxidans ATCC 23270]]
[[Category: Large Structures]]
[[Category: Large Structures]]
-
[[Category: Cherney, M M]]
+
[[Category: Cherney MM]]
-
[[Category: James, M N.G]]
+
[[Category: James MNG]]
-
[[Category: Weiner, J H]]
+
[[Category: Weiner JH]]
-
[[Category: Zhang, Y]]
+
[[Category: Zhang Y]]
-
[[Category: Complex with sulfide]]
+
-
[[Category: Integral monotopic membrane protein]]
+
-
[[Category: Oxidoreductase]]
+
-
[[Category: Ser126ala variant]]
+
-
[[Category: Sulfide:quinone oxidoreductase]]
+

Current revision

Crystal structure of sulfide:quinone oxidoreductase Ser126Ala variant from Acidithiobacillus ferrooxidans using 7.0 keV diffraction data

PDB ID 3syi

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3syi"
Personal tools