6koe - Revision history

OCA at 10:38, 22 November 2023

2023-11-22T10:38:28Z

←Older revision		Revision as of 10:38, 22 November 2023
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	<StructureSection load='6koe' size='340' side='right'caption='[[6koe]], [[Resolution\|resolution]] 3.75Å' scene=''>		<StructureSection load='6koe' size='340' side='right'caption='[[6koe]], [[Resolution\|resolution]] 3.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6koe]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~"vibrio_subtilis"_ehrenberg_1835 "vibrio~~ subtilis~~" ehrenberg 1835~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KOE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6KOE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6koe]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KOE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KOE FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=CU:COPPER+(II)+ION'~~>~~CU</scene>, <scene name='pdbligand=HEA:HEME~~-~~A'>HEA</scene>~~, ~~<scene name='pdbligand=HQO:2-HEPTYL-4-HYDROXY+QUINOLINE+N-OXIDE'>HQO</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]] 3.75Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~UNK~~:~~UNKNOWN~~'>~~UNK~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=HEA:HEME-A'>HEA</scene>, <scene name='pdbligand=HQO:2-HEPTYL-4-HYDROXY+QUINOLINE+N-OXIDE'>HQO</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td><~~td class="sblockDat">[[6kob\|6kob]]</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=6koe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6koe OCA], [https://pdbe.org/6koe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6koe RCSB], [https://www.ebi.ac.uk/pdbsum/6koe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6koe ProSAT]</span></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td><td class="sblockDat">qoxB, B4122_4931, B4417_2140, ETA10_20065, ETK61_21170, ETL41_11350, SC09_contig4orf01211 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835]), qoxA, ETA10_20070, ETK61_21175, ETL41_11355 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835]), B4122_4930, B4417_2139, ETA10_20060, ETK61_21165, ETL41_11345, SC09_contig4orf01209 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</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=6koe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6koe OCA], [~~http~~://pdbe.org/6koe PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6koe RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6koe PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6koe ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~A0A2I7T8S1_BACIU A0A2I7T8S1_BACIU]~~] Catalyzes quinol oxidation with the concomitant reduction of oxygen to water. ~~Subunit II transfers the electrons from a quinol to the binuclear center of the catalytic subunit I~~.~~[PIRNR:PIRNR000292]~~	+	[https://www.uniprot.org/uniprot/QOX1_BACSU QOX1_BACSU] Catalyzes quinol oxidation with the concomitant reduction of oxygen to water. Major component for energy conversion during vegetative growth (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Vibrio~~ subtilis ~~ehrenberg 1835~~]]	+	[[Category: Bacillus subtilis]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ding, Z]]	+	[[Category: Ding Z]]
-	[[Category: Gennis~~, R B~~]]	+	[[Category: Gennis RB]]
-	[[Category: Li, J]]	+	[[Category: Li J]]
-	[[Category: Liu, B]]	+	[[Category: Liu B]]
-	[[Category: Xu, J]]	+	[[Category: Xu J]]
-	[[Category: Zhu, J]]	+	[[Category: Zhu J]]
-	~~[[Category: Complex]]~~	+
-	~~[[Category: Inhibitor]]~~	+
-	~~[[Category: Menaquinol oxidase]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Proton pumping~~]]	+

OCA at 16:37, 22 January 2020

2020-01-22T16:37:40Z

←Older revision		Revision as of 16:37, 22 January 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6koe is ~~ON HOLD until Paper~~ Publication	+	==X-ray Structure of the proton-pumping cytochrome aa3-600 menaquinol oxidase from Bacillus subtilis==
		+	<StructureSection load='6koe' size='340' side='right'caption='[[6koe]], [[Resolution\|resolution]] 3.75Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6koe]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KOE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6KOE FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=HEA:HEME-A'>HEA</scene>, <scene name='pdbligand=HQO:2-HEPTYL-4-HYDROXY+QUINOLINE+N-OXIDE'>HQO</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6kob\|6kob]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">qoxB, B4122_4931, B4417_2140, ETA10_20065, ETK61_21170, ETL41_11350, SC09_contig4orf01211 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835]), qoxA, ETA10_20070, ETK61_21175, ETL41_11355 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835]), B4122_4930, B4417_2139, ETA10_20060, ETK61_21165, ETL41_11345, SC09_contig4orf01209 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</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=6koe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6koe OCA], [http://pdbe.org/6koe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6koe RCSB], [http://www.ebi.ac.uk/pdbsum/6koe PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6koe ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/A0A2I7T8S1_BACIU A0A2I7T8S1_BACIU]] Catalyzes quinol oxidation with the concomitant reduction of oxygen to water. Subunit II transfers the electrons from a quinol to the binuclear center of the catalytic subunit I.[PIRNR:PIRNR000292]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Virtually all proton-pumping terminal respiratory oxygen reductases are members of the heme-copper oxidoreductase superfamily. Most of these enzymes use reduced cytochrome c as a source of electrons, but a group of enzymes have evolved to directly oxidize membrane-bound quinols, usually menaquinol or ubiquinol. All of the quinol oxidases have an additional transmembrane helix (TM0) in subunit I that is not present in the related cytochrome c oxidases. The current work reports the 3.6-A-resolution X-ray structure of the cytochrome aa 3 -600 menaquinol oxidase from Bacillus subtilis containing 1 equivalent of menaquinone. The structure shows that TM0 forms part of a cleft to accommodate the menaquinol-7 substrate. Crystals which have been soaked with the quinol-analog inhibitor HQNO (N-oxo-2-heptyl-4-hydroxyquinoline) or 3-iodo-HQNO reveal a single binding site where the inhibitor forms hydrogen bonds to amino acid residues shown previously by spectroscopic methods to interact with the semiquinone state of menaquinone, a catalytic intermediate.

-	~~Authors~~:	+	Structure of the cytochrome aa 3 -600 heme-copper menaquinol oxidase bound to inhibitor HQNO shows TM0 is part of the quinol binding site.,Xu J, Ding Z, Liu B, Yi SM, Li J, Zhang Z, Liu Y, Li J, Liu L, Zhou A, Gennis RB, Zhu J Proc Natl Acad Sci U S A. 2020 Jan 14;117(2):872-876. doi:, 10.1073/pnas.1915013117. Epub 2019 Dec 30. PMID:31888984<ref>PMID:31888984</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6koe" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Vibrio subtilis ehrenberg 1835]]
		+	[[Category: Large Structures]]
		+	[[Category: Ding, Z]]
		+	[[Category: Gennis, R B]]
		+	[[Category: Li, J]]
		+	[[Category: Liu, B]]
		+	[[Category: Xu, J]]
		+	[[Category: Zhu, J]]
		+	[[Category: Complex]]
		+	[[Category: Inhibitor]]
		+	[[Category: Menaquinol oxidase]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Proton pumping]]

OCA at 06:36, 2 October 2019

2019-10-02T06:36:13Z

←Older revision		Revision as of 06:36, 2 October 2019
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6koe is ON HOLD	+	The entry 6koe is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6koe" [edit=sysop:move=sysop]

2019-08-14T14:58:58Z

Protected "6koe" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:58, 14 August 2019

OCA: New page: '''Unreleased structure''' The entry 6koe is ON HOLD Authors: Description: Category: Unreleased Structures

2019-08-14T14:58:56Z

New page: '''Unreleased structure''' The entry 6koe is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6koe is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]