3ehb - Revision history

OCA at 15:21, 1 November 2023

OCA — Wed, 01 Nov 2023 15:21:27 GMT

←Older revision		Revision as of 15:21, 1 November 2023
Line 3:		Line 3:
	<StructureSection load='3ehb' size='340' side='right'caption='[[3ehb]], [[Resolution\|resolution]] 2.32Å' scene=''>		<StructureSection load='3ehb' size='340' side='right'caption='[[3ehb]], [[Resolution\|resolution]] 2.32Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ehb]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_17741 Atcc 17741~~] and [https://en.wikipedia.org/wiki/~~Lk3_transgenic_mice Lk3 transgenic mice~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EHB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EHB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ehb]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [https://en.wikipedia.org/wiki/Paracoccus_denitrificans Paracoccus denitrificans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EHB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EHB FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=HEA:HEME-A'>HEA</scene>, <scene name='pdbligand=LDA:LAURYL+DIMETHYLAMINE-N-OXIDE'>LDA</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PER:PEROXIDE+ION'>PER</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]] 2.32Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ar1\|1ar1]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=HEA:HEME-A'>HEA</scene>, <scene name='pdbligand=LDA:LAURYL+DIMETHYLAMINE-N-OXIDE'>LDA</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PER:PEROXIDE+ION'>PER</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Cytochrome-c_oxidase Cytochrome-c oxidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.9.3.1 1.9.3.1] </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=3ehb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ehb OCA], [https://pdbe.org/3ehb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ehb RCSB], [https://www.ebi.ac.uk/pdbsum/3ehb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ehb 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=3ehb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ehb OCA], [https://pdbe.org/3ehb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ehb RCSB], [https://www.ebi.ac.uk/pdbsum/3ehb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ehb ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/COX1B_PARDE COX1B_PARDE]] Subunit I and II form the functional core of the enzyme complex. Electrons originating in cytochrome c are transferred via heme a and Cu(A) to the binuclear center formed by heme a3 and Cu(B). This cytochrome c oxidase shows proton pump activity across the membrane in addition to the electron transfer. [[https://www.uniprot.org/uniprot/COX2_PARDE COX2_PARDE]] Subunits I and II form the functional core of the enzyme complex. Electrons originating in cytochrome c are transferred via heme a and Cu(A) to the binuclear center formed by heme a3 and Cu(B).	+	[https://www.uniprot.org/uniprot/COX1B_PARDE COX1B_PARDE] Subunit I and II form the functional core of the enzyme complex. Electrons originating in cytochrome c are transferred via heme a and Cu(A) to the binuclear center formed by heme a3 and Cu(B). This cytochrome c oxidase shows proton pump activity across the membrane in addition to the electron transfer.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 17741]]
-	[[Category: Cytochrome-c oxidase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lk3 transgenic mice~~]]	+	[[Category: Mus musculus]]
-	[[Category: ~~Koepke, J~~]]	+	[[Category: Paracoccus denitrificans]]
-	[[Category: ~~Mueller, H~~]]	+	[[Category: Koepke J]]
-	[[Category: ~~Peng, G~~]]	+	[[Category: Mueller H]]
-	[[Category: ~~Cell inner membrane]]~~	+	[[Category: Peng G]]
-	~~[[Category: Cell membrane]]~~	+
-	~~[[Category: Copper]]~~	+
-	~~[[Category: Electron transfer]]~~	+
-	~~[[Category: Electron transport]]~~	+
-	~~[[Category: Heme]]~~	+
-	~~[[Category: Hydrogen ion transport]]~~	+
-	~~[[Category: Ion transport]]~~	+
-	~~[[Category: Iron]]~~	+
-	~~[[Category: Membrane]]~~	+
-	~~[[Category: Metal-binding]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Oxidoreductase-immune system complex]]~~	+
-	~~[[Category: Proton pumping]]~~	+
-	~~[[Category: Pyrrolidone carboxylic acid]]~~	+
-	~~[[Category: Respiratory chain]]~~	+
-	~~[[Category: Transmembrane]]~~	+
-	~~[[Category: Transport]]~~	+
-	~~[[Category: Water chain~~]]	+

OCA at 07:35, 10 November 2021

OCA — Wed, 10 Nov 2021 07:35:36 GMT

←Older revision		Revision as of 07:35, 10 November 2021
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	<StructureSection load='3ehb' size='340' side='right'caption='[[3ehb]], [[Resolution\|resolution]] 2.32Å' scene=''>		<StructureSection load='3ehb' size='340' side='right'caption='[[3ehb]], [[Resolution\|resolution]] 2.32Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ehb]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_17741 Atcc 17741] and [~~http~~://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EHB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3EHB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ehb]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_17741 Atcc 17741] and [https://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EHB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EHB FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=HEA:HEME-A'>HEA</scene>, <scene name='pdbligand=LDA:LAURYL+DIMETHYLAMINE-N-OXIDE'>LDA</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PER:PEROXIDE+ION'>PER</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=HEA:HEME-A'>HEA</scene>, <scene name='pdbligand=LDA:LAURYL+DIMETHYLAMINE-N-OXIDE'>LDA</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PER:PEROXIDE+ION'>PER</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ar1\|1ar1]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ar1\|1ar1]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Cytochrome-c_oxidase Cytochrome-c oxidase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.9.3.1 1.9.3.1] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Cytochrome-c_oxidase Cytochrome-c oxidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.9.3.1 1.9.3.1] </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=3ehb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ehb OCA], [~~http~~://pdbe.org/3ehb PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3ehb RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3ehb PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3ehb 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=3ehb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ehb OCA], [https://pdbe.org/3ehb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ehb RCSB], [https://www.ebi.ac.uk/pdbsum/3ehb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ehb ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/COX1B_PARDE COX1B_PARDE]] Subunit I and II form the functional core of the enzyme complex. Electrons originating in cytochrome c are transferred via heme a and Cu(A) to the binuclear center formed by heme a3 and Cu(B). This cytochrome c oxidase shows proton pump activity across the membrane in addition to the electron transfer. [[~~http~~://www.uniprot.org/uniprot/COX2_PARDE COX2_PARDE]] Subunits I and II form the functional core of the enzyme complex. Electrons originating in cytochrome c are transferred via heme a and Cu(A) to the binuclear center formed by heme a3 and Cu(B).	+	[[https://www.uniprot.org/uniprot/COX1B_PARDE COX1B_PARDE]] Subunit I and II form the functional core of the enzyme complex. Electrons originating in cytochrome c are transferred via heme a and Cu(A) to the binuclear center formed by heme a3 and Cu(B). This cytochrome c oxidase shows proton pump activity across the membrane in addition to the electron transfer. [[https://www.uniprot.org/uniprot/COX2_PARDE COX2_PARDE]] Subunits I and II form the functional core of the enzyme complex. Electrons originating in cytochrome c are transferred via heme a and Cu(A) to the binuclear center formed by heme a3 and Cu(B).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 07:21, 7 August 2019

OCA — Wed, 07 Aug 2019 07:21:15 GMT

←Older revision		Revision as of 07:21, 7 August 2019
Line 1:		Line 1:

	==A D-Pathway Mutation Decouples the Paracoccus Denitrificans Cytochrome c Oxidase by Altering the side chain orientation of a distant, conserved Glutamate==		==A D-Pathway Mutation Decouples the Paracoccus Denitrificans Cytochrome c Oxidase by Altering the side chain orientation of a distant, conserved Glutamate==
-	<StructureSection load='3ehb' size='340' side='right' caption='[[3ehb]], [[Resolution\|resolution]] 2.32Å' scene=''>	+	<StructureSection load='3ehb' size='340' side='right'caption='[[3ehb]], [[Resolution\|resolution]] 2.32Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3ehb]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_17741 Atcc 17741] and [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EHB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EHB FirstGlance]. <br>		<table><tr><td colspan='2'>[[3ehb]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_17741 Atcc 17741] and [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EHB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EHB FirstGlance]. <br>
Line 15:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/eh/3ehb_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/eh/3ehb_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>
Line 30:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 3ehb" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3ehb" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Cytochrome c oxidase 3D structures\|Cytochrome c oxidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 36:		Line 39:
	[[Category: Atcc 17741]]		[[Category: Atcc 17741]]
	[[Category: Cytochrome-c oxidase]]		[[Category: Cytochrome-c oxidase]]
		+	[[Category: Large Structures]]
	[[Category: Lk3 transgenic mice]]		[[Category: Lk3 transgenic mice]]
	[[Category: Koepke, J]]		[[Category: Koepke, J]]

OCA at 09:11, 25 October 2017

OCA — Wed, 25 Oct 2017 09:11:58 GMT

←Older revision		Revision as of 09:11, 25 October 2017
Line 1:		Line 1:
		+
	==A D-Pathway Mutation Decouples the Paracoccus Denitrificans Cytochrome c Oxidase by Altering the side chain orientation of a distant, conserved Glutamate==		==A D-Pathway Mutation Decouples the Paracoccus Denitrificans Cytochrome c Oxidase by Altering the side chain orientation of a distant, conserved Glutamate==
	<StructureSection load='3ehb' size='340' side='right' caption='[[3ehb]], [[Resolution\|resolution]] 2.32Å' scene=''>		<StructureSection load='3ehb' size='340' side='right' caption='[[3ehb]], [[Resolution\|resolution]] 2.32Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ar1\|1ar1]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ar1\|1ar1]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytochrome-c_oxidase Cytochrome-c oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.9.3.1 1.9.3.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytochrome-c_oxidase Cytochrome-c oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.9.3.1 1.9.3.1] </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=3ehb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ehb OCA], [http://pdbe.org/3ehb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ehb RCSB], [http://www.ebi.ac.uk/pdbsum/3ehb 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=3ehb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ehb OCA], [http://pdbe.org/3ehb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ehb RCSB], [http://www.ebi.ac.uk/pdbsum/3ehb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ehb ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 29:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 3ehb" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3ehb" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Cytochrome c oxidase\|Cytochrome c oxidase]]
	== References ==		== References ==
	<references/>		<references/>
Line 44:		Line 42:
	[[Category: Cell inner membrane]]		[[Category: Cell inner membrane]]
	[[Category: Cell membrane]]		[[Category: Cell membrane]]
		+	[[Category: Copper]]
	[[Category: Electron transfer]]		[[Category: Electron transfer]]
	[[Category: Electron transport]]		[[Category: Electron transport]]

OCA at 12:23, 9 February 2016

OCA — Tue, 09 Feb 2016 12:23:53 GMT

←Older revision		Revision as of 12:23, 9 February 2016
Line 2:		Line 2:
	<StructureSection load='3ehb' size='340' side='right' caption='[[3ehb]], [[Resolution\|resolution]] 2.32Å' scene=''>		<StructureSection load='3ehb' size='340' side='right' caption='[[3ehb]], [[Resolution\|resolution]] 2.32Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ehb]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Mus_musculus Mus musculus~~] and [http://en.wikipedia.org/wiki/~~Paracoccus_denitrificans Paracoccus denitrificans~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EHB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EHB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ehb]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_17741 Atcc 17741] and [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EHB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EHB FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=HEA:HEME-A'>HEA</scene>, <scene name='pdbligand=LDA:LAURYL+DIMETHYLAMINE-N-OXIDE'>LDA</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PER:PEROXIDE+ION'>PER</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=HEA:HEME-A'>HEA</scene>, <scene name='pdbligand=LDA:LAURYL+DIMETHYLAMINE-N-OXIDE'>LDA</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PER:PEROXIDE+ION'>PER</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ar1\|1ar1]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ar1\|1ar1]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytochrome-c_oxidase Cytochrome-c oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.9.3.1 1.9.3.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytochrome-c_oxidase Cytochrome-c oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.9.3.1 1.9.3.1] </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=3ehb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ehb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ehb RCSB], [http://www.ebi.ac.uk/pdbsum/3ehb 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=3ehb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ehb OCA], [http://pdbe.org/3ehb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ehb RCSB], [http://www.ebi.ac.uk/pdbsum/3ehb PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 18:
	<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=3ehb ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 28:		Line 28:
	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 3ehb" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 17741]]
	[[Category: Cytochrome-c oxidase]]		[[Category: Cytochrome-c oxidase]]
-	[[Category: ~~Mus musculus]]~~	+	[[Category: Lk3 transgenic mice]]
-	~~[[Category: Paracoccus denitrificans~~]]	+
	[[Category: Koepke, J]]		[[Category: Koepke, J]]
	[[Category: Mueller, H]]		[[Category: Mueller, H]]

OCA at 06:47, 25 December 2014

OCA — Thu, 25 Dec 2014 06:47:47 GMT

←Older revision		Revision as of 06:47, 25 December 2014
Line 1:		Line 1:
-	[[~~Image:~~3ehb.~~png~~\|~~left~~\|200px]]	+	==A D-Pathway Mutation Decouples the Paracoccus Denitrificans Cytochrome c Oxidase by Altering the side chain orientation of a distant, conserved Glutamate==
		+	<StructureSection load='3ehb' size='340' side='right' caption='[[3ehb]], [[Resolution\|resolution]] 2.32Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3ehb]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [http://en.wikipedia.org/wiki/Paracoccus_denitrificans Paracoccus denitrificans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EHB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EHB FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=HEA:HEME-A'>HEA</scene>, <scene name='pdbligand=LDA:LAURYL+DIMETHYLAMINE-N-OXIDE'>LDA</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PER:PEROXIDE+ION'>PER</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1ar1\|1ar1]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytochrome-c_oxidase Cytochrome-c oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.9.3.1 1.9.3.1] </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=3ehb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ehb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ehb RCSB], [http://www.ebi.ac.uk/pdbsum/3ehb PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/COX1B_PARDE COX1B_PARDE]] Subunit I and II form the functional core of the enzyme complex. Electrons originating in cytochrome c are transferred via heme a and Cu(A) to the binuclear center formed by heme a3 and Cu(B). This cytochrome c oxidase shows proton pump activity across the membrane in addition to the electron transfer. [[http://www.uniprot.org/uniprot/COX2_PARDE COX2_PARDE]] Subunits I and II form the functional core of the enzyme complex. Electrons originating in cytochrome c are transferred via heme a and Cu(A) to the binuclear center formed by heme a3 and Cu(B).
		+	== 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/eh/3ehb_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 ==
		+	Asparagine 131, located near the cytoplasmic entrance of the D-pathway in subunit I of the Paracoccus denitrificans aa(3) cytochrome c oxidase, is a residue crucial for proton pumping. When replaced by an aspartate, the mutant enzyme is completely decoupled: while retaining full cytochrome c oxidation activity, it does not pump protons. The same phenotype is observed for two other substitutions at this position (N131E and N131C), whereas a conservative replacement by glutamine affects both activities of the enzyme. The N131D variant oxidase was crystallized and its structure was solved to 2.32-A resolution, revealing no significant overall change in the protein structure when compared with the wild type (WT), except for an alternative orientation of the E278 side chain in addition to its WT conformation. Moreover, remarkable differences in the crystallographically resolved chain of water molecules in the D-pathway are found for the variant: four water molecules that are observed in the water chain between N131 and E278 in the WT structure are not visible in the variant, indicating a higher mobility of these water molecules. Electrochemically induced Fourier transform infrared difference spectra of decoupled mutants confirm that the protonation state of E278 is unaltered by these mutations but indicate a distinct perturbation in the hydrogen-bonding environment of this residue. Furthermore, they suggest that the carboxylate side chain of the N131D mutant is deprotonated. These findings are discussed in terms of their mechanistic implications for proton routing through the D-pathway of cytochrome c oxidase.

-	~~{{STRUCTURE_3ehb\| PDB=3ehb \| SCENE= }}~~	+	A D-pathway mutation decouples the Paracoccus denitrificans cytochrome c oxidase by altering the side-chain orientation of a distant conserved glutamate.,Durr KL, Koepke J, Hellwig P, Muller H, Angerer H, Peng G, Olkhova E, Richter OM, Ludwig B, Michel H J Mol Biol. 2008 Dec 26;384(4):865-77. Epub 2008 Oct 9. PMID:18930738<ref>PMID:18930738</ref>

-	~~===A D-Pathway Mutation Decouples the Paracoccus Denitrificans Cytochrome c Oxidase by Altering the side chain orientation of a distant~~, ~~conserved Glutamate===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18930738}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3ehb]] is~~ a ~~4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Mus_musculus Mus musculus] and [http://en~~.~~wikipedia.org~~/~~wiki/Paracoccus_denitrificans Paracoccus denitrificans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EHB OCA].~~	+

	==See Also==		==See Also==
	*[[Cytochrome c oxidase\|Cytochrome c oxidase]]		*[[Cytochrome c oxidase\|Cytochrome c oxidase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:018930738<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Cytochrome-c oxidase]]		[[Category: Cytochrome-c oxidase]]
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
	[[Category: Paracoccus denitrificans]]		[[Category: Paracoccus denitrificans]]
-	[[Category: Koepke, J.]]	+	[[Category: Koepke, J]]
-	[[Category: Mueller, H.]]	+	[[Category: Mueller, H]]
-	[[Category: Peng, G.]]	+	[[Category: Peng, G]]
	[[Category: Cell inner membrane]]		[[Category: Cell inner membrane]]
	[[Category: Cell membrane]]		[[Category: Cell membrane]]

OCA at 13:49, 20 October 2012

OCA — Sat, 20 Oct 2012 13:49:36 GMT

←Older revision		Revision as of 13:49, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[3ehb]] is a 4 chain structure ~~of [[Cytochrome c oxidase]]~~ with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [http://en.wikipedia.org/wiki/Paracoccus_denitrificans Paracoccus denitrificans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EHB OCA].	+	[[3ehb]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [http://en.wikipedia.org/wiki/Paracoccus_denitrificans Paracoccus denitrificans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EHB OCA].

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

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

OCA — Thu, 26 Jul 2012 13:14:25 GMT

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

←Older revision

Revision as of 13:14, 26 July 2012

OCA at 13:14, 26 July 2012

OCA — Thu, 26 Jul 2012 13:14:23 GMT

←Older revision		Revision as of 13:14, 26 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:3ehb.png\|left\|200px]]		[[Image:3ehb.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3ehb", 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_3ehb\| PDB=3ehb \| SCENE= }}		{{STRUCTURE_3ehb\| PDB=3ehb \| SCENE= }}

	===A D-Pathway Mutation Decouples the Paracoccus Denitrificans Cytochrome c Oxidase by Altering the side chain orientation of a distant, conserved Glutamate===		===A D-Pathway Mutation Decouples the Paracoccus Denitrificans Cytochrome c Oxidase by Altering the side chain orientation of a distant, conserved Glutamate===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18930738}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18930738 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18930738}}		{{ABSTRACT_PUBMED_18930738}}

	==About this Structure==		==About this Structure==
-	~~3EHB~~ is a 4 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [http://en.wikipedia.org/wiki/Paracoccus_denitrificans Paracoccus denitrificans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EHB OCA].	+	[[3ehb]] is a 4 chain structure of [[Cytochrome c oxidase]] with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [http://en.wikipedia.org/wiki/Paracoccus_denitrificans Paracoccus denitrificans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EHB OCA].
		+
		+	==See Also==
		+	*[[Cytochrome c oxidase\|Cytochrome c oxidase]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18930738~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018930738</ref><references group="xtra"/>
	[[Category: Cytochrome-c oxidase]]		[[Category: Cytochrome-c oxidase]]
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
Line 32:		Line 23:
	[[Category: Cell inner membrane]]		[[Category: Cell inner membrane]]
	[[Category: Cell membrane]]		[[Category: Cell membrane]]
-	[[Category: Copper]]
	[[Category: Electron transfer]]		[[Category: Electron transfer]]
	[[Category: Electron transport]]		[[Category: Electron transport]]
Line 42:		Line 32:
	[[Category: Metal-binding]]		[[Category: Metal-binding]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
-	[[Category: Oxidoreductase/immune system complex]]	+	[[Category: Oxidoreductase-immune system complex]]
	[[Category: Proton pumping]]		[[Category: Proton pumping]]
	[[Category: Pyrrolidone carboxylic acid]]		[[Category: Pyrrolidone carboxylic acid]]
Line 49:		Line 39:
	[[Category: Transport]]		[[Category: Transport]]
	[[Category: Water chain]]		[[Category: Water chain]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 09:45:26 2009''

OCA at 07:45, 17 February 2009

OCA — Tue, 17 Feb 2009 07:45:27 GMT

←Older revision		Revision as of 07:45, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	3EHB is a ~~[[Protein complex]]~~ structure of sequences from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [http://en.wikipedia.org/wiki/Paracoccus_denitrificans Paracoccus denitrificans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EHB OCA].	+	3EHB is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [http://en.wikipedia.org/wiki/Paracoccus_denitrificans Paracoccus denitrificans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EHB OCA].

	==Reference==		==Reference==
-	A D-pathway mutation decouples the paracoccusdenitrificans cytochrome c oxidase by altering the side-chain orientation of a distant conserved glutamate., Durr KL, Koepke J, Hellwig P, Muller H, Angerer H, Peng G, Olkhova E, Richter OM, Ludwig B, Michel H, J Mol Biol. 2008 Dec 26;384(4):865-77. Epub 2008 Oct 9. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18930738 18930738]~~	+	<ref group="xtra">PMID:18930738</ref><references group="xtra"/>
	[[Category: Cytochrome-c oxidase]]		[[Category: Cytochrome-c oxidase]]
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
	[[Category: Paracoccus denitrificans]]		[[Category: Paracoccus denitrificans]]
-	[[Category: ~~Protein complex~~]]	+	[[Category: Koepke, J.]]
-	[[Category: ~~Pdbx_ordinal=~~, ~~<PDBx~~:~~audit_author~~.]]	+	[[Category: Mueller, H.]]
		+	[[Category: Peng, G.]]
	[[Category: Cell inner membrane]]		[[Category: Cell inner membrane]]
	[[Category: Cell membrane]]		[[Category: Cell membrane]]
Line 49:		Line 50:
	[[Category: Water chain]]		[[Category: Water chain]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Dec 10 20~~:22:~~19 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 09:45:26 2009''