2yx9 - Revision history

OCA at 09:09, 25 October 2023

OCA — Wed, 25 Oct 2023 09:09:56 GMT

←Older revision		Revision as of 09:09, 25 October 2023
Line 3:		Line 3:
	<StructureSection load='2yx9' size='340' side='right'caption='[[2yx9]], [[Resolution\|resolution]] 1.68Å' scene=''>		<StructureSection load='2yx9' size='340' side='right'caption='[[2yx9]], [[Resolution\|resolution]] 1.68Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2yx9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"achromobacter_globiformis"_(conn_1928)_bergey_et_al._1930 "achromobacter~~ globiformis~~" (conn 1928) bergey et al. 1930~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YX9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YX9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2yx9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arthrobacter_globiformis Arthrobacter globiformis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YX9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YX9 FirstGlance]. <br>
-	</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>~~</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]] 1.68Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=DPQ:(S)-2-AMINO-3-(4-HYDROXY-3-OXOCYCLOHEXA-1,4-DIENYL)PROPANOIC+ACID'>DPQ</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=DPQ:(S)-2-AMINO-3-(4-HYDROXY-3-OXOCYCLOHEXA-1,4-DIENYL)PROPANOIC+ACID'>DPQ</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1iu7\|1iu7]]</div></td></tr>~~	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Oxidoreductase Oxidoreductase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.21 and 1.4.3.22 1.4.3.21 and 1.4.3.22] </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=2yx9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yx9 OCA], [https://pdbe.org/2yx9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yx9 RCSB], [https://www.ebi.ac.uk/pdbsum/2yx9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yx9 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=2yx9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yx9 OCA], [https://pdbe.org/2yx9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yx9 RCSB], [https://www.ebi.ac.uk/pdbsum/2yx9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yx9 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/PAOX_ARTGO PAOX_ARTGO]
	== 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: Arthrobacter globiformis]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Oxidoreductase]]~~	+	[[Category: Murakawa T]]
-	[[Category: Murakawa, T]]	+	[[Category: Okajima T]]
-	[[Category: Okajima, T]]	+	[[Category: Tanizawa K]]
-	[[Category: Tanizawa, K]]	+	[[Category: Yamaguchi H]]
-	[[Category: Yamaguchi, H]]	+
-	~~[[Category: Biogenesis]]~~	+
-	~~[[Category: Cofactor]]~~	+
-	~~[[Category: Copper]]~~	+
-	~~[[Category: Ltq]]~~	+
-	~~[[Category: Lysine tyrosylquinone]]~~	+
-	~~[[Category: Topaquinone]]~~	+
-	~~[[Category: Tpq~~]]	+

OCA at 07:10, 10 November 2021

OCA — Wed, 10 Nov 2021 07:10:38 GMT

←Older revision		Revision as of 07:10, 10 November 2021
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	<StructureSection load='2yx9' size='340' side='right'caption='[[2yx9]], [[Resolution\|resolution]] 1.68Å' scene=''>		<StructureSection load='2yx9' size='340' side='right'caption='[[2yx9]], [[Resolution\|resolution]] 1.68Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2yx9]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"achromobacter_globiformis"_(conn_1928)_bergey_et_al._1930 "achromobacter globiformis" (conn 1928) bergey et al. 1930]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YX9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=2YX9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2yx9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"achromobacter_globiformis"_(conn_1928)_bergey_et_al._1930 "achromobacter globiformis" (conn 1928) bergey et al. 1930]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YX9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YX9 FirstGlance]. <br>
	</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></td></tr>		</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></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DPQ:(S)-2-AMINO-3-(4-HYDROXY-3-OXOCYCLOHEXA-1,4-DIENYL)PROPANOIC+ACID'>DPQ</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DPQ:(S)-2-AMINO-3-(4-HYDROXY-3-OXOCYCLOHEXA-1,4-DIENYL)PROPANOIC+ACID'>DPQ</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iu7\|1iu7]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1iu7\|1iu7]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Oxidoreductase Oxidoreductase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.21 and 1.4.3.22 1.4.3.21 and 1.4.3.22] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Oxidoreductase Oxidoreductase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.21 and 1.4.3.22 1.4.3.21 and 1.4.3.22] </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=2yx9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yx9 OCA], [~~http~~://pdbe.org/2yx9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2yx9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2yx9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2yx9 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=2yx9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yx9 OCA], [https://pdbe.org/2yx9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yx9 RCSB], [https://www.ebi.ac.uk/pdbsum/2yx9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yx9 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 29:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 2yx9" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2yx9" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Copper amine oxidase 3D structures\|Copper amine oxidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 13:07, 22 July 2020

OCA — Wed, 22 Jul 2020 13:07:13 GMT

←Older revision		Revision as of 13:07, 22 July 2020
Line 1:		Line 1:

	==Crystal structure of D298K copper amine oxidase from Arthrobacter globiformis==		==Crystal structure of D298K copper amine oxidase from Arthrobacter globiformis==
-	<StructureSection load='2yx9' size='340' side='right' caption='[[2yx9]], [[Resolution\|resolution]] 1.68Å' scene=''>	+	<StructureSection load='2yx9' size='340' side='right'caption='[[2yx9]], [[Resolution\|resolution]] 1.68Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2yx9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"achromobacter_globiformis"_(conn_1928)_bergey_et_al._1930 "achromobacter globiformis" (conn 1928) bergey et al. 1930]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YX9 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2YX9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2yx9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"achromobacter_globiformis"_(conn_1928)_bergey_et_al._1930 "achromobacter globiformis" (conn 1928) bergey et al. 1930]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YX9 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=2YX9 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></td></tr>	+	</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></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DPQ:(S)-2-AMINO-3-(4-HYDROXY-3-OXOCYCLOHEXA-1,4-DIENYL)PROPANOIC+ACID'>DPQ</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DPQ:(S)-2-AMINO-3-(4-HYDROXY-3-OXOCYCLOHEXA-1,4-DIENYL)PROPANOIC+ACID'>DPQ</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iu7\|1iu7]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iu7\|1iu7]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Oxidoreductase Oxidoreductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.21 and 1.4.3.22 1.4.3.21 and 1.4.3.22] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Oxidoreductase Oxidoreductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.21 and 1.4.3.22 1.4.3.21 and 1.4.3.22] </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=2yx9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yx9 OCA], [http://pdbe.org/2yx9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2yx9 RCSB], [http://www.ebi.ac.uk/pdbsum/2yx9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2yx9 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=2yx9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yx9 OCA], [http://pdbe.org/2yx9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2yx9 RCSB], [http://www.ebi.ac.uk/pdbsum/2yx9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2yx9 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Murakawa, T]]		[[Category: Murakawa, T]]

OCA at 09:36, 17 October 2018

OCA — Wed, 17 Oct 2018 09:36:38 GMT

←Older revision		Revision as of 09:36, 17 October 2018
Line 1:		Line 1:
		+
	==Crystal structure of D298K copper amine oxidase from Arthrobacter globiformis==		==Crystal structure of D298K copper amine oxidase from Arthrobacter globiformis==
	<StructureSection load='2yx9' size='340' side='right' caption='[[2yx9]], [[Resolution\|resolution]] 1.68Å' scene=''>		<StructureSection load='2yx9' size='340' side='right' caption='[[2yx9]], [[Resolution\|resolution]] 1.68Å' scene=''>
Line 7:		Line 8:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iu7\|1iu7]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iu7\|1iu7]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Oxidoreductase Oxidoreductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.21 and 1.4.3.22 1.4.3.21 and 1.4.3.22] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Oxidoreductase Oxidoreductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.21 and 1.4.3.22 1.4.3.21 and 1.4.3.22] </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=2yx9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yx9 OCA], [http://pdbe.org/2yx9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2yx9 RCSB], [http://www.ebi.ac.uk/pdbsum/2yx9 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=2yx9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yx9 OCA], [http://pdbe.org/2yx9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2yx9 RCSB], [http://www.ebi.ac.uk/pdbsum/2yx9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2yx9 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yx/2yx9_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yx/2yx9_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 39:		Line 40:
	[[Category: Biogenesis]]		[[Category: Biogenesis]]
	[[Category: Cofactor]]		[[Category: Cofactor]]
		+	[[Category: Copper]]
	[[Category: Ltq]]		[[Category: Ltq]]
	[[Category: Lysine tyrosylquinone]]		[[Category: Lysine tyrosylquinone]]
	[[Category: Topaquinone]]		[[Category: Topaquinone]]
	[[Category: Tpq]]		[[Category: Tpq]]

OCA at 16:02, 9 February 2016

OCA — Tue, 09 Feb 2016 16:02:10 GMT

←Older revision		Revision as of 16:02, 9 February 2016
Line 2:		Line 2:
	<StructureSection load='2yx9' size='340' side='right' caption='[[2yx9]], [[Resolution\|resolution]] 1.68Å' scene=''>		<StructureSection load='2yx9' size='340' side='right' caption='[[2yx9]], [[Resolution\|resolution]] 1.68Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2yx9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Arthrobacter_globiformis Arthrobacter~~ globiformis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YX9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2YX9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2yx9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"achromobacter_globiformis"_(conn_1928)_bergey_et_al._1930 "achromobacter globiformis" (conn 1928) bergey et al. 1930]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YX9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2YX9 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></td></tr>		</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></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DPQ:(S)-2-AMINO-3-(4-HYDROXY-3-OXOCYCLOHEXA-1,4-DIENYL)PROPANOIC+ACID'>DPQ</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DPQ:(S)-2-AMINO-3-(4-HYDROXY-3-OXOCYCLOHEXA-1,4-DIENYL)PROPANOIC+ACID'>DPQ</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iu7\|1iu7]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iu7\|1iu7]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Oxidoreductase Oxidoreductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.21 and 1.4.3.22 1.4.3.21 and 1.4.3.22] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Oxidoreductase Oxidoreductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.21 and 1.4.3.22 1.4.3.21 and 1.4.3.22] </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=2yx9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yx9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2yx9 RCSB], [http://www.ebi.ac.uk/pdbsum/2yx9 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=2yx9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yx9 OCA], [http://pdbe.org/2yx9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2yx9 RCSB], [http://www.ebi.ac.uk/pdbsum/2yx9 PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 17:		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=2yx9 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 27:		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 2yx9" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Arthrobacter globiformis]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Murakawa, T]]		[[Category: Murakawa, T]]

OCA at 09:52, 20 January 2015

OCA — Tue, 20 Jan 2015 09:52:08 GMT

←Older revision		Revision as of 09:52, 20 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2yx9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arthrobacter_globiformis Arthrobacter globiformis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YX9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2YX9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2yx9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arthrobacter_globiformis Arthrobacter globiformis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YX9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2YX9 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene><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></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DPQ:(S)-2-AMINO-3-(4-HYDROXY-3-OXOCYCLOHEXA-1,4-DIENYL)PROPANOIC+ACID'>DPQ</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DPQ:(S)-2-AMINO-3-(4-HYDROXY-3-OXOCYCLOHEXA-1,4-DIENYL)PROPANOIC+ACID'>DPQ</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iu7\|1iu7]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iu7\|1iu7]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Oxidoreductase Oxidoreductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.21 and 1.4.3.22 1.4.3.21 and 1.4.3.22] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Oxidoreductase Oxidoreductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.21 and 1.4.3.22 1.4.3.21 and 1.4.3.22] </span></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=2yx9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yx9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2yx9 RCSB], [http://www.ebi.ac.uk/pdbsum/2yx9 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=2yx9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yx9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2yx9 RCSB], [http://www.ebi.ac.uk/pdbsum/2yx9 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 33:		Line 33:
	[[Category: Arthrobacter globiformis]]		[[Category: Arthrobacter globiformis]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
-	[[Category: Murakawa, T.]]	+	[[Category: Murakawa, T]]
-	[[Category: Okajima, T.]]	+	[[Category: Okajima, T]]
-	[[Category: Tanizawa, K.]]	+	[[Category: Tanizawa, K]]
-	[[Category: Yamaguchi, H.]]	+	[[Category: Yamaguchi, H]]
	[[Category: Biogenesis]]		[[Category: Biogenesis]]
	[[Category: Cofactor]]		[[Category: Cofactor]]
	[[Category: Ltq]]		[[Category: Ltq]]
	[[Category: Lysine tyrosylquinone]]		[[Category: Lysine tyrosylquinone]]
-	[[Category: Oxidoreductase]]
	[[Category: Topaquinone]]		[[Category: Topaquinone]]
	[[Category: Tpq]]		[[Category: Tpq]]

OCA at 05:41, 2 October 2014

OCA — Thu, 02 Oct 2014 05:41:16 GMT

←Older revision		Revision as of 05:41, 2 October 2014
Line 1:		Line 1:
-	[[~~Image:~~2yx9.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of D298K copper amine oxidase from Arthrobacter globiformis==
		+	<StructureSection load='2yx9' size='340' side='right' caption='[[2yx9]], [[Resolution\|resolution]] 1.68Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2yx9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arthrobacter_globiformis Arthrobacter globiformis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YX9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2YX9 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DPQ:(S)-2-AMINO-3-(4-HYDROXY-3-OXOCYCLOHEXA-1,4-DIENYL)PROPANOIC+ACID'>DPQ</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1iu7\|1iu7]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Oxidoreductase Oxidoreductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.21 and 1.4.3.22 1.4.3.21 and 1.4.3.22] </span></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=2yx9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yx9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2yx9 RCSB], [http://www.ebi.ac.uk/pdbsum/2yx9 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/yx/2yx9_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 ==
		+	The biogenesis of the topaquinone (TPQ) cofactor of copper amine oxidase (CAO) is self-catalyzed and requires copper and molecular oxygen. A dopaquinone intermediate has been proposed to undergo 1,4-addition of a copper-associated water molecule to form the reduced form of TPQ (TPQ(red)), followed by facile oxidation by O(2) to yield the mature TPQ (TPQ(ox)). In this study, we have incorporated a lysine residue in the active site of Arthrobacter globiformis CAO (AGAO) by site-directed mutagenesis to produce D298K-AGAO. The X-ray crystal structure of D298K-AGAO at 1.7-A resolution revealed that a covalent linkage formed between the epsilon-amino side chain of Lys298 and the C2 position of a dopaquinone derived from Tyr382, a precursor to TPQ(ox). We assigned the species as an iminoquinone tautomer (LTI) of lysine tyrosylquinone (LTQ), the organic cofactor of lysyl oxidase (LOX). The time course of the formation of LTI at pH 6.8 was followed by UV/vis and resonance Raman spectroscopies. In the early phase of the reaction, an LTQ-like intermediate was observed. This intermediate then slowly converted to LTI in an isosbestic manner. Not only is the presence of a dopaquinone intermediate in the TPQ biogenesis confirmed, but it also provides strong support for the proposed intermediacy of a dopaquinone in the biogenesis of LTQ in LOX. Further, this study indicates that the dopaquinone intermediate in AGAO is mobile and can swing from the copper site into the active-site wedge to react with Lys298.

-	~~{{STRUCTURE_2yx9\| PDB=2yx9 \| SCENE= }}~~	+	Trapping of a dopaquinone intermediate in the TPQ cofactor biogenesis in a copper-containing amine oxidase from Arthrobacter globiformis.,Moore RH, Spies MA, Culpepper MB, Murakawa T, Hirota S, Okajima T, Tanizawa K, Mure M J Am Chem Soc. 2007 Sep 19;129(37):11524-34. Epub 2007 Aug 23. PMID:17715921<ref>PMID:17715921</ref>

-	~~===Crystal structure~~ of ~~D298K copper amine oxidase from Arthrobacter globiformis===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17715921}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2yx9]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Arthrobacter_globiformis Arthrobacter globiformis]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2YX9 OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:017715921<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Arthrobacter globiformis]]		[[Category: Arthrobacter globiformis]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA: Protected "2yx9" [edit=sysop:move=sysop]

OCA — Mon, 07 Jan 2013 19:07:28 GMT

Protected "2yx9" [edit=sysop:move=sysop]

←Older revision

Revision as of 19:07, 7 January 2013

OCA at 19:07, 7 January 2013

OCA — Mon, 07 Jan 2013 19:07:25 GMT

←Older revision		Revision as of 19:07, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2yx9.png\|left\|200px]]		[[Image:2yx9.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2yx9", 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_2yx9\| PDB=2yx9 \| SCENE= }}		{{STRUCTURE_2yx9\| PDB=2yx9 \| SCENE= }}

	===Crystal structure of D298K copper amine oxidase from Arthrobacter globiformis===		===Crystal structure of D298K copper amine oxidase from Arthrobacter globiformis===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17715921}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17715921 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17715921}}		{{ABSTRACT_PUBMED_17715921}}

	==About this Structure==		==About this Structure==
-	~~2YX9~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Arthrobacter_globiformis Arthrobacter globiformis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YX9 OCA].	+	[[2yx9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arthrobacter_globiformis Arthrobacter globiformis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YX9 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17715921~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017715921</ref><references group="xtra"/>
	[[Category: Arthrobacter globiformis]]		[[Category: Arthrobacter globiformis]]
		+	[[Category: Oxidoreductase]]
	[[Category: Murakawa, T.]]		[[Category: Murakawa, T.]]
	[[Category: Okajima, T.]]		[[Category: Okajima, T.]]
Line 31:		Line 20:
	[[Category: Biogenesis]]		[[Category: Biogenesis]]
	[[Category: Cofactor]]		[[Category: Cofactor]]
-	[[Category: Copper]]
	[[Category: Ltq]]		[[Category: Ltq]]
	[[Category: Lysine tyrosylquinone]]		[[Category: Lysine tyrosylquinone]]
Line 37:		Line 25:
	[[Category: Topaquinone]]		[[Category: Topaquinone]]
	[[Category: Tpq]]		[[Category: Tpq]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 11:01:32 2009''

OCA at 09:01, 17 February 2009

OCA — Tue, 17 Feb 2009 09:01:33 GMT

←Older revision		Revision as of 09:01, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2YX9 is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Arthrobacter_globiformis Arthrobacter globiformis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YX9 OCA].	+	2YX9 is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Arthrobacter_globiformis Arthrobacter globiformis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YX9 OCA].

	==Reference==		==Reference==
-	Trapping of a dopaquinone intermediate in the TPQ cofactor biogenesis in a copper-containing amine oxidase from Arthrobacter globiformis., Moore RH, Spies MA, Culpepper MB, Murakawa T, Hirota S, Okajima T, Tanizawa K, Mure M, J Am Chem Soc. 2007 Sep 19;129(37):11524-34. Epub 2007 Aug 23. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/17715921 17715921]~~	+	<ref group="xtra">PMID:17715921</ref><references group="xtra"/>
	[[Category: Arthrobacter globiformis]]		[[Category: Arthrobacter globiformis]]
-	[[Category: Single protein]]
	[[Category: Murakawa, T.]]		[[Category: Murakawa, T.]]
	[[Category: Okajima, T.]]		[[Category: Okajima, T.]]
Line 39:		Line 38:
	[[Category: Tpq]]		[[Category: Tpq]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Jul 28 15~~:02:~~04 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 11:01:32 2009''