1upp - Revision history

OCA at 13:18, 9 May 2024

OCA — Thu, 09 May 2024 13:18:28 GMT

←Older revision		Revision as of 13:18, 9 May 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1upp]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Spinacia_oleracea Spinacia oleracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UPP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UPP FirstGlance]. <br>		<table><tr><td colspan='2'>[[1upp]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Spinacia_oleracea Spinacia oleracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UPP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UPP 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=CAP:~~2~~-CARBOXYARABINITOL-1,5-DIPHOSPHATE'>CAP</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]] 2.3Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~KCX~~:~~LYSINE~~+~~NZ-CARBOXYLIC+ACID~~'>~~KCX~~</scene><~~/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=CAP:2-CARBOXYARABINITOL-1,5-DIPHOSPHATE'>CAP</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</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;~~'>~~[[1aa1\|1aa1]], [[1aus\|1aus]], [[1ir1\|1ir1]], [[1rbo\|1rbo]], [[1rco\|1rco]], [[1rcx\|1rcx]], [[1rxo\|1rxo]], [[1upm\|1upm]], [[8ruc\|8ruc]]~~</~~div~~><~~/td></tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/Ribulose-bisphosphate_carboxylase Ribulose-bisphosphate carboxylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.39 4.1.1.39]~~ </~~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=1upp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1upp OCA], [https://pdbe.org/1upp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1upp RCSB], [https://www.ebi.ac.uk/pdbsum/1upp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1upp 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=1upp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1upp OCA], [https://pdbe.org/1upp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1upp RCSB], [https://www.ebi.ac.uk/pdbsum/1upp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1upp ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/RBL_SPIOL RBL_SPIOL]] RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate in the photorespiration process. Both reactions occur simultaneously and in competition at the same active site.[HAMAP-Rule:MF_01338] [[https://www.uniprot.org/uniprot/RBS2_SPIOL RBS2_SPIOL]] RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate. Both reactions occur simultaneously and in competition at the same active site.	+	[https://www.uniprot.org/uniprot/RBS2_SPIOL RBS2_SPIOL] RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate. Both reactions occur simultaneously and in competition at the same active site.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ribulose-bisphosphate carboxylase]]
	[[Category: Spinacia oleracea]]		[[Category: Spinacia oleracea]]
-	[[Category: Andersson, I]]	+	[[Category: Andersson I]]
-	[[Category: Karkehabadi, S]]	+	[[Category: Karkehabadi S]]
-	[[Category: Taylor~~, T C]]~~	+	[[Category: Taylor TC]]
-	~~[[Category: Carbon-carbon]]~~	+
-	~~[[Category: Carbon-dioxide fixation]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Photosynthesis~~]]	+

OCA at 06:15, 6 October 2021

OCA — Wed, 06 Oct 2021 06:15:45 GMT

OCA at 13:20, 1 January 2020

OCA — Wed, 01 Jan 2020 13:20:31 GMT

←Older revision		Revision as of 13:20, 1 January 2020
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	==SPINACH RUBISCO IN COMPLEX WITH 2-CARBOXYARABINITOL 2 BISPHOSPHATE and Calcium.==		==SPINACH RUBISCO IN COMPLEX WITH 2-CARBOXYARABINITOL 2 BISPHOSPHATE and Calcium.==
-	<StructureSection load='1upp' size='340' side='right' caption='[[1upp]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='1upp' size='340' side='right'caption='[[1upp]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1upp]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Spinacia_oleracea Spinacia oleracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UPP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UPP FirstGlance]. <br>		<table><tr><td colspan='2'>[[1upp]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Spinacia_oleracea Spinacia oleracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UPP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UPP FirstGlance]. <br>
Line 33:		Line 33:

	==See Also==		==See Also==
-	*[[RuBisCO\|RuBisCO]]	+	*[[RuBisCO 3D structures\|RuBisCO 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Ribulose-bisphosphate carboxylase]]		[[Category: Ribulose-bisphosphate carboxylase]]
	[[Category: Spinacia oleracea]]		[[Category: Spinacia oleracea]]

OCA at 08:09, 28 March 2018

OCA — Wed, 28 Mar 2018 08:09:58 GMT

←Older revision		Revision as of 08:09, 28 March 2018
Line 1:		Line 1:
-	==SPINACH RUBISCO IN COMPLEX WITH 2-CARBOXYARABINITOL 2 BISPHOSPHATE ~~AND CALCIUM~~.==	+
		+	==SPINACH RUBISCO IN COMPLEX WITH 2-CARBOXYARABINITOL 2 BISPHOSPHATE and Calcium.==
	<StructureSection load='1upp' size='340' side='right' caption='[[1upp]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='1upp' size='340' side='right' caption='[[1upp]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1upp]] is a 8 chain structure with sequence from ~~[http://en.wikipedia.org/wiki/Spiol Spiol] and~~ [http://en.wikipedia.org/wiki/Spinacia_oleracea Spinacia oleracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UPP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UPP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1upp]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Spinacia_oleracea Spinacia oleracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UPP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UPP 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=CAP:2-CARBOXYARABINITOL-1,5-DIPHOSPHATE'>CAP</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=CAP:2-CARBOXYARABINITOL-1,5-DIPHOSPHATE'>CAP</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1aa1\|1aa1]], [[1aus\|1aus]], [[1ir1\|1ir1]], [[1rbo\|1rbo]], [[1rco\|1rco]], [[1rcx\|1rcx]], [[1rxo\|1rxo]], [[1upm\|1upm]], [[8ruc\|8ruc]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1aa1\|1aa1]], [[1aus\|1aus]], [[1ir1\|1ir1]], [[1rbo\|1rbo]], [[1rco\|1rco]], [[1rcx\|1rcx]], [[1rxo\|1rxo]], [[1upm\|1upm]], [[8ruc\|8ruc]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribulose-bisphosphate_carboxylase Ribulose-bisphosphate carboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.39 4.1.1.39] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribulose-bisphosphate_carboxylase Ribulose-bisphosphate carboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.39 4.1.1.39] </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=1upp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1upp OCA], [http://pdbe.org/1upp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1upp RCSB], [http://www.ebi.ac.uk/pdbsum/1upp 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=1upp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1upp OCA], [http://pdbe.org/1upp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1upp RCSB], [http://www.ebi.ac.uk/pdbsum/1upp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1upp ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/up/1upp_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/up/1upp_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>
	</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=1upp ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	[[Category: Ribulose-bisphosphate carboxylase]]		[[Category: Ribulose-bisphosphate carboxylase]]
	[[Category: Spinacia oleracea]]		[[Category: Spinacia oleracea]]
-	[[Category: Spiol]]
	[[Category: Andersson, I]]		[[Category: Andersson, I]]
	[[Category: Karkehabadi, S]]		[[Category: Karkehabadi, S]]

OCA at 07:14, 11 September 2015

OCA — Fri, 11 Sep 2015 07:14:01 GMT

←Older revision		Revision as of 07:14, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1upp' size='340' side='right' caption='[[1upp]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='1upp' size='340' side='right' caption='[[1upp]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1upp]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Spinacia_oleracea Spinacia oleracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UPP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UPP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1upp]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Spiol Spiol] and [http://en.wikipedia.org/wiki/Spinacia_oleracea Spinacia oleracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UPP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UPP 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=CAP:2-CARBOXYARABINITOL-1,5-DIPHOSPHATE'>CAP</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=CAP:2-CARBOXYARABINITOL-1,5-DIPHOSPHATE'>CAP</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1aa1\|1aa1]], [[1aus\|1aus]], [[1ir1\|1ir1]], [[1rbo\|1rbo]], [[1rco\|1rco]], [[1rcx\|1rcx]], [[1rxo\|1rxo]], [[1upm\|1upm]], [[8ruc\|8ruc]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1aa1\|1aa1]], [[1aus\|1aus]], [[1ir1\|1ir1]], [[1rbo\|1rbo]], [[1rco\|1rco]], [[1rcx\|1rcx]], [[1rxo\|1rxo]], [[1upm\|1upm]], [[8ruc\|8ruc]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribulose-bisphosphate_carboxylase Ribulose-bisphosphate carboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.39 4.1.1.39] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribulose-bisphosphate_carboxylase Ribulose-bisphosphate carboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.39 4.1.1.39] </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=1upp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1upp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1upp RCSB], [http://www.ebi.ac.uk/pdbsum/1upp 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=1upp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1upp OCA], [http://pdbe.org/1upp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1upp RCSB], [http://www.ebi.ac.uk/pdbsum/1upp PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 29:		Line 29:
	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 1upp" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 38:		Line 39:
	[[Category: Ribulose-bisphosphate carboxylase]]		[[Category: Ribulose-bisphosphate carboxylase]]
	[[Category: Spinacia oleracea]]		[[Category: Spinacia oleracea]]
		+	[[Category: Spiol]]
	[[Category: Andersson, I]]		[[Category: Andersson, I]]
	[[Category: Karkehabadi, S]]		[[Category: Karkehabadi, S]]

OCA at 13:05, 25 December 2014

OCA — Thu, 25 Dec 2014 13:05:18 GMT

←Older revision		Revision as of 13:05, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1upp]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Spinacia_oleracea Spinacia oleracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UPP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UPP FirstGlance]. <br>		<table><tr><td colspan='2'>[[1upp]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Spinacia_oleracea Spinacia oleracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UPP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UPP FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CAP:2-CARBOXYARABINITOL-1,5-DIPHOSPHATE'>CAP</scene><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=CAP:2-CARBOXYARABINITOL-1,5-DIPHOSPHATE'>CAP</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1aa1\|1aa1]], [[1aus\|1aus]], [[1ir1\|1ir1]], [[1rbo\|1rbo]], [[1rco\|1rco]], [[1rcx\|1rcx]], [[1rxo\|1rxo]], [[1upm\|1upm]], [[8ruc\|8ruc]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1aa1\|1aa1]], [[1aus\|1aus]], [[1ir1\|1ir1]], [[1rbo\|1rbo]], [[1rco\|1rco]], [[1rcx\|1rcx]], [[1rxo\|1rxo]], [[1upm\|1upm]], [[8ruc\|8ruc]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribulose-bisphosphate_carboxylase Ribulose-bisphosphate carboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.39 4.1.1.39] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribulose-bisphosphate_carboxylase Ribulose-bisphosphate carboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.39 4.1.1.39] </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=1upp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1upp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1upp RCSB], [http://www.ebi.ac.uk/pdbsum/1upp 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=1upp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1upp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1upp RCSB], [http://www.ebi.ac.uk/pdbsum/1upp PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RBL_SPIOL RBL_SPIOL]] RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate in the photorespiration process. Both reactions occur simultaneously and in competition at the same active site.[HAMAP-Rule:MF_01338] [[http://www.uniprot.org/uniprot/RBS2_SPIOL RBS2_SPIOL]] RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate. Both reactions occur simultaneously and in competition at the same active site.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 38:
	[[Category: Ribulose-bisphosphate carboxylase]]		[[Category: Ribulose-bisphosphate carboxylase]]
	[[Category: Spinacia oleracea]]		[[Category: Spinacia oleracea]]
-	[[Category: Andersson, I.]]	+	[[Category: Andersson, I]]
-	[[Category: Karkehabadi, S.]]	+	[[Category: Karkehabadi, S]]
-	[[Category: Taylor, T C.]]	+	[[Category: Taylor, T C]]
	[[Category: Carbon-carbon]]		[[Category: Carbon-carbon]]
	[[Category: Carbon-dioxide fixation]]		[[Category: Carbon-dioxide fixation]]

OCA at 22:03, 28 September 2014

OCA — Sun, 28 Sep 2014 22:03:15 GMT

←Older revision		Revision as of 22:03, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1upp.~~png~~\|~~left~~\|200px]]	+	==SPINACH RUBISCO IN COMPLEX WITH 2-CARBOXYARABINITOL 2 BISPHOSPHATE AND CALCIUM.==
		+	<StructureSection load='1upp' size='340' side='right' caption='[[1upp]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1upp]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Spinacia_oleracea Spinacia oleracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UPP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UPP FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CAP:2-CARBOXYARABINITOL-1,5-DIPHOSPHATE'>CAP</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1aa1\|1aa1]], [[1aus\|1aus]], [[1ir1\|1ir1]], [[1rbo\|1rbo]], [[1rco\|1rco]], [[1rcx\|1rcx]], [[1rxo\|1rxo]], [[1upm\|1upm]], [[8ruc\|8ruc]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Ribulose-bisphosphate_carboxylase Ribulose-bisphosphate carboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.39 4.1.1.39] </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=1upp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1upp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1upp RCSB], [http://www.ebi.ac.uk/pdbsum/1upp 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/up/1upp_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 ==
		+	Rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase) catalyses CO(2) assimilation in biology. A prerequisite for catalysis is an activation process, whereby an active site lysine is selectively carbamylated. The carbamyl group is then stablised by a metal ion, which in vivo is Mg(2+). Other divalent metal ions can replace Mg(2+) as activators in vitro, but the nature of the metal ion strongly influences the catalytic activity of the enzyme and has a differential effect on the ratio of the carboxylation reaction and the competing oxygenation reaction. Biochemical studies show that calcium promotes carbamylation but not catalysis. To investigate the role of the metal in catalysis, we have determined two structures of the enzyme complexed with Ca(2+) and the transition state analogue 2-carboxy-D-arbinitol-1,5-bisphosphate (2CABP). One of the complexes was prepared by soaking 2CABP into crystals of the enzyme-Ca(2+)-product complex, while the other was obtained by cocrystallising the enzyme with calcium and 2CABP under activating conditions. The two crystals belong to different space groups, and one was merohedrally twinned. Both complexes show very similar three-dimensional features. The enzyme is carbamylated at Lys201, and requisite loops close over the bound ligands in the active site, shielding them from the solvent in a manner similar to the corresponding complex with Mg(2+). However, there are subtle differences that could explain the particular role of Ca(2+) in these processes. The larger radius of the calcium ion and its reduced Lewis-acid character causes a significant increase in the required proton hop distance between the C3 proton and the carbamate on Lys201 in the calcium complex. This alone could explain the inability of calcium to sustain catalysis in Rubisco. Similar effects are also expected on subsequent proton transfer steps in the catalytic cycle. Here we also discuss the effect of metal substitution on the dynamics of the ligands around the metal ion.

-	~~{{STRUCTURE_1upp\| PDB=1upp \| SCENE= }}~~	+	Calcium supports loop closure but not catalysis in Rubisco.,Karkehabadi S, Taylor TC, Andersson I J Mol Biol. 2003 Nov 14;334(1):65-73. PMID:14596800<ref>PMID:14596800</ref>

-	~~===SPINACH RUBISCO IN COMPLEX WITH 2-CARBOXYARABINITOL 2 BISPHOSPHATE AND CALCIUM.===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_14596800}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1upp]] is~~ a ~~8 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Spinacia_oleracea Spinacia oleracea]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1UPP OCA].~~	+

	==See Also==		==See Also==
	*[[RuBisCO\|RuBisCO]]		*[[RuBisCO\|RuBisCO]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:014596800<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Ribulose-bisphosphate carboxylase]]		[[Category: Ribulose-bisphosphate carboxylase]]
	[[Category: Spinacia oleracea]]		[[Category: Spinacia oleracea]]

OCA at 17:01, 20 October 2012

OCA — Sat, 20 Oct 2012 17:01:20 GMT

←Older revision		Revision as of 17:01, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1upp]] is a 8 chain structure ~~of [[RuBisCO]]~~ with sequence from [http://en.wikipedia.org/wiki/Spinacia_oleracea Spinacia oleracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UPP OCA].	+	[[1upp]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Spinacia_oleracea Spinacia oleracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UPP OCA].

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

OCA: Protected "1upp" [edit=sysop:move=sysop]

OCA — Thu, 26 Jul 2012 23:34:22 GMT

Protected "1upp" [edit=sysop:move=sysop]

←Older revision

Revision as of 23:34, 26 July 2012

OCA at 23:34, 26 July 2012

OCA — Thu, 26 Jul 2012 23:34:21 GMT

←Older revision		Revision as of 23:34, 26 July 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1upp.png\|left\|200px]]		[[Image:1upp.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1upp", 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_1upp\| PDB=1upp \| SCENE= }}		{{STRUCTURE_1upp\| PDB=1upp \| SCENE= }}

	===SPINACH RUBISCO IN COMPLEX WITH 2-CARBOXYARABINITOL 2 BISPHOSPHATE AND CALCIUM.===		===SPINACH RUBISCO IN COMPLEX WITH 2-CARBOXYARABINITOL 2 BISPHOSPHATE AND CALCIUM.===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_14596800}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 14596800 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_14596800}}		{{ABSTRACT_PUBMED_14596800}}

	==About this Structure==		==About this Structure==
-	~~1UPP~~ is a 8 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Spinacia_oleracea Spinacia oleracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UPP OCA].	+	[[1upp]] is a 8 chain structure of [[RuBisCO]] with sequence from [http://en.wikipedia.org/wiki/Spinacia_oleracea Spinacia oleracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UPP OCA].
		+
		+	==See Also==
		+	*[[RuBisCO\|RuBisCO]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~14596800~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:014596800</ref><references group="xtra"/>
	[[Category: Ribulose-bisphosphate carboxylase]]		[[Category: Ribulose-bisphosphate carboxylase]]
	[[Category: Spinacia oleracea]]		[[Category: Spinacia oleracea]]
Line 34:		Line 25:
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
	[[Category: Photosynthesis]]		[[Category: Photosynthesis]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 16:56:29 2009''

←Older revision		Revision as of 06:15, 6 October 2021
Line 3:		Line 3:
	<StructureSection load='1upp' size='340' side='right'caption='[[1upp]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='1upp' size='340' side='right'caption='[[1upp]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1upp]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Spinacia_oleracea Spinacia oleracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UPP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1UPP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1upp]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Spinacia_oleracea Spinacia oleracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UPP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UPP 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=CAP:2-CARBOXYARABINITOL-1,5-DIPHOSPHATE'>CAP</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=CAP:2-CARBOXYARABINITOL-1,5-DIPHOSPHATE'>CAP</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1aa1\|1aa1]], [[1aus\|1aus]], [[1ir1\|1ir1]], [[1rbo\|1rbo]], [[1rco\|1rco]], [[1rcx\|1rcx]], [[1rxo\|1rxo]], [[1upm\|1upm]], [[8ruc\|8ruc]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1aa1\|1aa1]], [[1aus\|1aus]], [[1ir1\|1ir1]], [[1rbo\|1rbo]], [[1rco\|1rco]], [[1rcx\|1rcx]], [[1rxo\|1rxo]], [[1upm\|1upm]], [[8ruc\|8ruc]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Ribulose-bisphosphate_carboxylase Ribulose-bisphosphate carboxylase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.39 4.1.1.39] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Ribulose-bisphosphate_carboxylase Ribulose-bisphosphate carboxylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.39 4.1.1.39] </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=1upp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1upp OCA], [~~http~~://pdbe.org/1upp PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1upp RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1upp PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1upp 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=1upp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1upp OCA], [https://pdbe.org/1upp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1upp RCSB], [https://www.ebi.ac.uk/pdbsum/1upp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1upp ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/RBL_SPIOL RBL_SPIOL]] RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate in the photorespiration process. Both reactions occur simultaneously and in competition at the same active site.[HAMAP-Rule:MF_01338] [[~~http~~://www.uniprot.org/uniprot/RBS2_SPIOL RBS2_SPIOL]] RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate. Both reactions occur simultaneously and in competition at the same active site.	+	[[https://www.uniprot.org/uniprot/RBL_SPIOL RBL_SPIOL]] RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate in the photorespiration process. Both reactions occur simultaneously and in competition at the same active site.[HAMAP-Rule:MF_01338] [[https://www.uniprot.org/uniprot/RBS2_SPIOL RBS2_SPIOL]] RuBisCO catalyzes two reactions: the carboxylation of D-ribulose 1,5-bisphosphate, the primary event in carbon dioxide fixation, as well as the oxidative fragmentation of the pentose substrate. Both reactions occur simultaneously and in competition at the same active site.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]