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.

3hyx

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

3-D X-Ray structure of the sulfide:quinone oxidoreductase from Aquifex aeolicus in complex with Aurachin C

Structural highlights

3hyx is a 6 chain structure with sequence from Aquifex aeolicus. This structure supersedes the now removed PDB entry 3h29. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.9Å
Ligands:	, , , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SQRD_AQUAE 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]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Sulfide:quinone oxidoreductase (SQR) is a flavoprotein with homologues in all domains of life except plants. It plays a physiological role both in sulfide detoxification and in energy transduction. We isolated the protein from native membranes of the hyperthermophilic bacterium Aquifex aeolicus, and we determined its X-ray structure in the "as-purified," substrate-bound, and inhibitor-bound forms at resolutions of 2.3, 2.0, and 2.9 A, respectively. The structure is composed of 2 Rossmann domains and 1 attachment domain, with an overall monomeric architecture typical of disulfide oxidoreductase flavoproteins. A. aeolicus SQR is a surprisingly trimeric, periplasmic integral monotopic membrane protein that inserts about 12 A into the lipidic bilayer through an amphipathic helix-turn-helix tripodal motif. The quinone is located in a channel that extends from the si side of the FAD to the membrane. The quinone ring is sandwiched between the conserved amino acids Phe-385 and Ile-346, and it is possibly protonated upon reduction via Glu-318 and/or neighboring water molecules. Sulfide polymerization occurs on the re side of FAD, where the invariant Cys-156 and Cys-347 appear to be covalently bound to polysulfur fragments. The structure suggests that FAD is covalently linked to the polypeptide in an unusual way, via a disulfide bridge between the 8-methyl group and Cys-124. The applicability of this disulfide bridge for transferring electrons from sulfide to FAD, 2 mechanisms for sulfide polymerization and channeling of the substrate, S(2-), and of the product, S(n), in and out of the active site are discussed.

The structure of Aquifex aeolicus sulfide:quinone oxidoreductase, a basis to understand sulfide detoxification and respiration.,Marcia M, Ermler U, Peng G, Michel H Proc Natl Acad Sci U S A. 2009 Jun 1. PMID:19487671^[3]

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

References

↑ Nübel T, Klughammer C, Huber R, Hauska G, Schütz M. Sulfide:quinone oxidoreductase in membranes of the hyperthermophilic bacterium Aquifex aeolicus (VF5). Arch Microbiol. 2000 Apr;173(4):233-44. PMID:10816041 doi:10.1007/s002030000135
↑ Marcia M, Ermler U, Peng G, Michel H. The structure of Aquifex aeolicus sulfide:quinone oxidoreductase, a basis to understand sulfide detoxification and respiration. Proc Natl Acad Sci U S A. 2009 Jun 1. PMID:19487671
↑ Marcia M, Ermler U, Peng G, Michel H. The structure of Aquifex aeolicus sulfide:quinone oxidoreductase, a basis to understand sulfide detoxification and respiration. Proc Natl Acad Sci U S A. 2009 Jun 1. PMID:19487671

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3hyx"

@@ Line 3: / Line 3: @@
 <StructureSection load='3hyx' size='340' side='right'caption='[[3hyx]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3hyx]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3h29 3h29]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HYX OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3HYX FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3hyx]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Aquifex_aeolicus Aquifex aeolicus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3h29 3h29]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HYX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HYX FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AUK:1-HYDROXY-2-METHYL-3-[(2E,6E)-3,7,11-TRIMETHYLDODECA-2,6,10-TRIEN-1-YL]QUINOLIN-4(1H)-ONE'>AUK</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=PS9:OCTATHIOCANE'>PS9</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]] 2.9&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSS:S-MERCAPTOCYSTEINE'>CSS</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AUK:1-HYDROXY-2-METHYL-3-[(2E,6E)-3,7,11-TRIMETHYLDODECA-2,6,10-TRIEN-1-YL]QUINOLIN-4(1H)-ONE'>AUK</scene>, <scene name='pdbligand=CSS:S-MERCAPTOCYSTEINE'>CSS</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=PS9:OCTATHIOCANE'>PS9</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">[[3hyv|3hyv]], [[3hyw|3hyw]]</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=3hyx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hyx OCA], [https://pdbe.org/3hyx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hyx RCSB], [https://www.ebi.ac.uk/pdbsum/3hyx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hyx ProSAT]</span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=3hyx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hyx OCA], [http://pdbe.org/3hyx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3hyx RCSB], [http://www.ebi.ac.uk/pdbsum/3hyx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3hyx ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/SQRD_AQUAE SQRD_AQUAE] 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:10816041</ref> <ref>PMID:19487671</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 30: / Line 31: @@
 ==See Also==
-*[[Quinone reductase|Quinone reductase]]
+*[[Quinone reductase 3D structures|Quinone reductase 3D structures]]
 == References ==
 <references/>
@@ Line 37: / Line 38: @@
 [[Category: Aquifex aeolicus]]
 [[Category: Large Structures]]
-[[Category: Ermler, U]]
+[[Category: Ermler U]]
-[[Category: Marcia, M]]
+[[Category: Marcia M]]
-[[Category: Michel, H]]
+[[Category: Michel H]]
-[[Category: Peng, G H]]
+[[Category: Peng GH]]
-[[Category: Flavoprotein]]
-[[Category: Monotopic membrane protein]]
-[[Category: Oxidoreductase]]
-[[Category: Quinone reduction]]
-[[Category: Rossmann-fold domain]]
-[[Category: Sulfide oxidation]]

3hyx

From Proteopedia

Current revision

3-D X-Ray structure of the sulfide:quinone oxidoreductase from Aquifex aeolicus in complex with Aurachin C

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox