3hyx - Revision history

OCA at 15:54, 1 November 2023

2023-11-01T15:54:48Z

←Older revision		Revision as of 15:54, 1 November 2023
Line 3:		Line 3:
	<StructureSection load='3hyx' size='340' side='right'caption='[[3hyx]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='3hyx' size='340' side='right'caption='[[3hyx]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== 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]] 2.9Å</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>		</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 ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 30:		Line 31:

	==See Also==		==See Also==
-	*[[Quinone reductase\|Quinone reductase]]	+	*[[Quinone reductase 3D structures\|Quinone reductase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 37:		Line 38:
	[[Category: Aquifex aeolicus]]		[[Category: Aquifex aeolicus]]
	[[Category: Large Structures]]		[[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~~]]	+

OCA at 10:52, 16 September 2020

2020-09-16T10:52:25Z

←Older revision		Revision as of 10:52, 16 September 2020
Line 1:		Line 1:

	==3-D X-Ray structure of the sulfide:quinone oxidoreductase from Aquifex aeolicus in complex with Aurachin C==		==3-D X-Ray structure of the sulfide:quinone oxidoreductase from Aquifex aeolicus in complex with Aurachin C==
-	<StructureSection load='3hyx' size='340' side='right' caption='[[3hyx]], [[Resolution\|resolution]] 2.90Å' scene=''>	+	<StructureSection load='3hyx' size='340' side='right'caption='[[3hyx]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== 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://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3HYX FirstGlance]. <br>	+	<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>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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='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>
	<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='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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3hyv\|3hyv]], [[3hyw\|3hyw]]</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'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/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>	+	<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>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 36:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Aquifex aeolicus]]		[[Category: Aquifex aeolicus]]
		+	[[Category: Large Structures]]
	[[Category: Ermler, U]]		[[Category: Ermler, U]]
	[[Category: Marcia, M]]		[[Category: Marcia, M]]

OCA at 08:03, 12 December 2018

2018-12-12T08:03:53Z

←Older revision		Revision as of 08:03, 12 December 2018
Line 13:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hy/3hyx_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hy/3hyx_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 09:29, 11 August 2016

2016-08-11T09:29:03Z

←Older revision		Revision as of 09:29, 11 August 2016
Line 1:		Line 1:
		+
	==3-D X-Ray structure of the sulfide:quinone oxidoreductase from Aquifex aeolicus in complex with Aurachin C==		==3-D X-Ray structure of the sulfide:quinone oxidoreductase from Aquifex aeolicus in complex with Aurachin C==
	<StructureSection load='3hyx' size='340' side='right' caption='[[3hyx]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='3hyx' size='340' side='right' caption='[[3hyx]], [[Resolution\|resolution]] 2.90Å' scene=''>
Line 6:		Line 7:
	<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='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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3hyv\|3hyv]], [[3hyw\|3hyw]]</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3hyx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hyx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3hyx RCSB], [http://www.ebi.ac.uk/pdbsum/3hyx PDBsum]</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=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>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 16:		Line 17:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3hyx ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 26:		Line 27:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3hyx" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 10:33, 20 January 2015

2015-01-20T10:33:28Z

←Older revision		Revision as of 10:33, 20 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== 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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HYX FirstGlance]. <br>		<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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HYX FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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>
-	<tr><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='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><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3hyv\|3hyv]], [[3hyw\|3hyw]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3hyv\|3hyv]], [[3hyw\|3hyw]]</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3hyx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hyx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3hyx RCSB], [http://www.ebi.ac.uk/pdbsum/3hyx PDBsum]</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=3hyx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hyx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3hyx RCSB], [http://www.ebi.ac.uk/pdbsum/3hyx PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Aquifex aeolicus]]		[[Category: Aquifex aeolicus]]
-	[[Category: Ermler, U.]]	+	[[Category: Ermler, U]]
-	[[Category: Marcia, M.]]	+	[[Category: Marcia, M]]
-	[[Category: Michel, H.]]	+	[[Category: Michel, H]]
-	[[Category: Peng, G H.]]	+	[[Category: Peng, G H]]
	[[Category: Flavoprotein]]		[[Category: Flavoprotein]]
	[[Category: Monotopic membrane protein]]		[[Category: Monotopic membrane protein]]

OCA at 12:29, 29 September 2014

2014-09-29T12:29:14Z

←Older revision		Revision as of 12:29, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~3hyx.~~png~~\|~~left~~\|200px]]	+	==3-D X-Ray structure of the sulfide:quinone oxidoreductase from Aquifex aeolicus in complex with Aurachin C==
		+	<StructureSection load='3hyx' size='340' side='right' caption='[[3hyx]], [[Resolution\|resolution]] 2.90Å' 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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HYX FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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><br>
		+	<tr><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><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3hyv\|3hyv]], [[3hyw\|3hyw]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3hyx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hyx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3hyx RCSB], [http://www.ebi.ac.uk/pdbsum/3hyx PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hy/3hyx_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== 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.

-	~~{{STRUCTURE_3hyx\| PDB=3hyx \| SCENE= }}~~	+	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<ref>PMID:19487671</ref>

-	~~===3-D X-Ray structure~~ of the ~~sulfide:quinone oxidoreductase from Aquifex aeolicus in complex with Aurachin C===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_19487671}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[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].~~	+

	==See Also==		==See Also==
	*[[Quinone reductase\|Quinone reductase]]		*[[Quinone reductase\|Quinone reductase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:019487671<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Aquifex aeolicus]]		[[Category: Aquifex aeolicus]]
	[[Category: Ermler, U.]]		[[Category: Ermler, U.]]

OCA at 18:50, 20 October 2012

2012-10-20T18:50:14Z

←Older revision		Revision as of 18:50, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3hyx]] is a 6 chain structure ~~of [[Quinone reductase]]~~ 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].	+	[[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].

	==See Also==		==See Also==

OCA: Protected "3hyx" [edit=sysop:move=sysop]

2012-07-27T05:23:21Z

Protected "3hyx" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:23, 27 July 2012

OCA at 05:23, 27 July 2012

2012-07-27T05:23:19Z

←Older revision		Revision as of 05:23, 27 July 2012
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-	~~{{Seed}}~~	+	[[Image:3hyx.png\|left\|200px]]
-	[[Image:3hyx.~~jpg~~\|left\|200px]]	+

-	<!--
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	{{STRUCTURE_3hyx\| PDB=3hyx \| SCENE= }}		{{STRUCTURE_3hyx\| PDB=3hyx \| SCENE= }}

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

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_19487671}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 19487671 is the PubMed ID number.
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	{{ABSTRACT_PUBMED_19487671}}		{{ABSTRACT_PUBMED_19487671}}

	==About this Structure==		==About this Structure==
-	~~3HYX~~ is a 6 ~~chains~~ structure of ~~sequences~~ 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].	+	[[3hyx]] is a 6 chain structure of [[Quinone reductase]] 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].
		+
		+	==See Also==
		+	*[[Quinone reductase\|Quinone reductase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~19487671~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:019487671</ref><references group="xtra"/>
	[[Category: Aquifex aeolicus]]		[[Category: Aquifex aeolicus]]
	[[Category: Ermler, U.]]		[[Category: Ermler, U.]]
Line 35:		Line 26:
	[[Category: Rossmann-fold domain]]		[[Category: Rossmann-fold domain]]
	[[Category: Sulfide oxidation]]		[[Category: Sulfide oxidation]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 15 08:38:53 2009''

OCA at 05:38, 15 July 2009

2009-07-15T05:38:55Z

←Older revision		Revision as of 05:38, 15 July 2009
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3hyx.jpg\|left\|200px]]

-	The ~~entry 3hyx~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3hyx", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3hyx\| PDB=3hyx \| SCENE= }}

-	~~Authors~~: ~~Marcia, M., Ermler, U., Peng, G.H., Michel, H.~~	+	===3-D X-Ray structure of the sulfide:quinone oxidoreductase from Aquifex aeolicus in complex with Aurachin C===

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

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 1 08:57:43 2009''	+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_19487671}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 19487671 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_19487671}}
		+
		+	==About this Structure==
		+	3HYX is a 6 chains structure of sequences 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].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:19487671</ref><references group="xtra"/>
		+	[[Category: Aquifex aeolicus]]
		+	[[Category: Ermler, U.]]
		+	[[Category: Marcia, M.]]
		+	[[Category: Michel, H.]]
		+	[[Category: Peng, G H.]]
		+	[[Category: Flavoprotein]]
		+	[[Category: Monotopic membrane protein]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Quinone reduction]]
		+	[[Category: Rossmann-fold domain]]
		+	[[Category: Sulfide oxidation]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 15 08:38:53 2009''