1jkj - Revision history

OCA at 08:42, 16 August 2023

OCA — Wed, 16 Aug 2023 08:42:04 GMT

←Older revision		Revision as of 08:42, 16 August 2023
Line 3:		Line 3:
	<StructureSection load='1jkj' size='340' side='right'caption='[[1jkj]], [[Resolution\|resolution]] 2.35Å' scene=''>		<StructureSection load='1jkj' size='340' side='right'caption='[[1jkj]], [[Resolution\|resolution]] 2.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1jkj]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JKJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JKJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1jkj]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JKJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JKJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene~~></td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.35Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2scu\|2scu]], [[1cqi\|1cqi]], [[1cqj\|1cqj]], [[1euc\|1euc]], [[1eud\|1eud]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Succinate--CoA_ligase_(ADP-forming) Succinate--CoA ligase (ADP-forming)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.5 6.2.1.5] </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=1jkj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jkj OCA], [https://pdbe.org/1jkj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jkj RCSB], [https://www.ebi.ac.uk/pdbsum/1jkj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jkj 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=1jkj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jkj OCA], [https://pdbe.org/1jkj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jkj RCSB], [https://www.ebi.ac.uk/pdbsum/1jkj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jkj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/SUCD_ECOLI SUCD_ECOLI]] During aerobic metabolism it functions in the citric acid cycle, coupling the hydrolysis of succinyl-CoA to the synthesis of ATP and thus represents an important site of substrate-level phosphorylation. It can also function in the other direction for anabolic purposes, and this may be particularly important for providing succinyl-CoA during anaerobic growth when the oxidative route from 2-oxoglutarate is severely repressed. The alpha-subunit binds CoA, as well as ATP and catalyzes phosphoryl transfer to one of its histidine residues. The complete active site is probably located in the region of alpha-beta contact. [[https://www.uniprot.org/uniprot/SUCC_ECOLI SUCC_ECOLI]] During aerobic metabolism it functions in the citric acid cycle, coupling the hydrolysis of succinyl-CoA to the synthesis of ATP and thus represents an important site of substrate-level phosphorylation. It can also function in the other direction for anabolic purposes, and this may be particularly important for providing succinyl-CoA during anaerobic growth when the oxidative route from 2-oxoglutarate is severely repressed. The beta-subunit contains the attachment sites for succinate. The complete active site is probably located in the region of alpha-beta contact.	+	[https://www.uniprot.org/uniprot/SUCD_ECOLI SUCD_ECOLI] During aerobic metabolism it functions in the citric acid cycle, coupling the hydrolysis of succinyl-CoA to the synthesis of ATP and thus represents an important site of substrate-level phosphorylation. It can also function in the other direction for anabolic purposes, and this may be particularly important for providing succinyl-CoA during anaerobic growth when the oxidative route from 2-oxoglutarate is severely repressed. The alpha-subunit binds CoA, as well as ATP and catalyzes phosphoryl transfer to one of its histidine residues. The complete active site is probably located in the region of alpha-beta contact.
	== 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: ~~Bacillus~~ coli ~~migula 1895~~]]	+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Fraser~~, M E]]~~	+	[[Category: Fraser ME]]
-	~~[[Category: Atp-grasp fold]]~~	+
-	~~[[Category: Citric acid cycle]]~~	+
-	~~[[Category: Heterotetramer]]~~	+
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: Rossmann fold~~]]	+

OCA at 06:41, 11 August 2021

OCA — Wed, 11 Aug 2021 06:41:53 GMT

←Older revision		Revision as of 06:41, 11 August 2021
Line 3:		Line 3:
	<StructureSection load='1jkj' size='340' side='right'caption='[[1jkj]], [[Resolution\|resolution]] 2.35Å' scene=''>		<StructureSection load='1jkj' size='340' side='right'caption='[[1jkj]], [[Resolution\|resolution]] 2.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1jkj]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JKJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1JKJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1jkj]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JKJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1JKJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2scu\|2scu]], [[1cqi\|1cqi]], [[1cqj\|1cqj]], [[1euc\|1euc]], [[1eud\|1eud]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2scu\|2scu]], [[1cqi\|1cqi]], [[1cqj\|1cqj]], [[1euc\|1euc]], [[1eud\|1eud]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Succinate--CoA_ligase_(ADP-forming) Succinate--CoA ligase (ADP-forming)], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.5 6.2.1.5] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Succinate--CoA_ligase_(ADP-forming) Succinate--CoA ligase (ADP-forming)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.5 6.2.1.5] </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=1jkj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jkj OCA], [~~http~~://pdbe.org/1jkj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1jkj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1jkj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1jkj 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=1jkj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jkj OCA], [https://pdbe.org/1jkj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1jkj RCSB], [https://www.ebi.ac.uk/pdbsum/1jkj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1jkj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/SUCD_ECOLI SUCD_ECOLI]] During aerobic metabolism it functions in the citric acid cycle, coupling the hydrolysis of succinyl-CoA to the synthesis of ATP and thus represents an important site of substrate-level phosphorylation. It can also function in the other direction for anabolic purposes, and this may be particularly important for providing succinyl-CoA during anaerobic growth when the oxidative route from 2-oxoglutarate is severely repressed. The alpha-subunit binds CoA, as well as ATP and catalyzes phosphoryl transfer to one of its histidine residues. The complete active site is probably located in the region of alpha-beta contact. [[~~http~~://www.uniprot.org/uniprot/SUCC_ECOLI SUCC_ECOLI]] During aerobic metabolism it functions in the citric acid cycle, coupling the hydrolysis of succinyl-CoA to the synthesis of ATP and thus represents an important site of substrate-level phosphorylation. It can also function in the other direction for anabolic purposes, and this may be particularly important for providing succinyl-CoA during anaerobic growth when the oxidative route from 2-oxoglutarate is severely repressed. The beta-subunit contains the attachment sites for succinate. The complete active site is probably located in the region of alpha-beta contact.	+	[[https://www.uniprot.org/uniprot/SUCD_ECOLI SUCD_ECOLI]] During aerobic metabolism it functions in the citric acid cycle, coupling the hydrolysis of succinyl-CoA to the synthesis of ATP and thus represents an important site of substrate-level phosphorylation. It can also function in the other direction for anabolic purposes, and this may be particularly important for providing succinyl-CoA during anaerobic growth when the oxidative route from 2-oxoglutarate is severely repressed. The alpha-subunit binds CoA, as well as ATP and catalyzes phosphoryl transfer to one of its histidine residues. The complete active site is probably located in the region of alpha-beta contact. [[https://www.uniprot.org/uniprot/SUCC_ECOLI SUCC_ECOLI]] During aerobic metabolism it functions in the citric acid cycle, coupling the hydrolysis of succinyl-CoA to the synthesis of ATP and thus represents an important site of substrate-level phosphorylation. It can also function in the other direction for anabolic purposes, and this may be particularly important for providing succinyl-CoA during anaerobic growth when the oxidative route from 2-oxoglutarate is severely repressed. The beta-subunit contains the attachment sites for succinate. The complete active site is probably located in the region of alpha-beta contact.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 32:

	==See Also==		==See Also==
-	*[[Succinyl-CoA synthetase\|Succinyl-CoA synthetase]]	+	*[[Succinyl-CoA synthetase 3D structures\|Succinyl-CoA synthetase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:03, 6 November 2019

OCA — Wed, 06 Nov 2019 09:03:36 GMT

←Older revision		Revision as of 09:03, 6 November 2019
Line 1:		Line 1:

	==E. coli SCS==		==E. coli SCS==
-	<StructureSection load='1jkj' size='340' side='right' caption='[[1jkj]], [[Resolution\|resolution]] 2.35Å' scene=''>	+	<StructureSection load='1jkj' size='340' side='right'caption='[[1jkj]], [[Resolution\|resolution]] 2.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1jkj]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JKJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JKJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1jkj]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JKJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JKJ FirstGlance]. <br>
Line 30:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1jkj" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1jkj" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Succinyl-CoA synthetase\|Succinyl-CoA synthetase]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
		+	[[Category: Large Structures]]
	[[Category: Fraser, M E]]		[[Category: Fraser, M E]]
	[[Category: Atp-grasp fold]]		[[Category: Atp-grasp fold]]

OCA at 08:40, 17 January 2018

OCA — Wed, 17 Jan 2018 08:40:45 GMT

←Older revision		Revision as of 08:40, 17 January 2018
Line 1:		Line 1:
		+
	==E. coli SCS==		==E. coli SCS==
	<StructureSection load='1jkj' size='340' side='right' caption='[[1jkj]], [[Resolution\|resolution]] 2.35Å' scene=''>		<StructureSection load='1jkj' size='340' side='right' caption='[[1jkj]], [[Resolution\|resolution]] 2.35Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2scu\|2scu]], [[1cqi\|1cqi]], [[1cqj\|1cqj]], [[1euc\|1euc]], [[1eud\|1eud]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2scu\|2scu]], [[1cqi\|1cqi]], [[1cqj\|1cqj]], [[1euc\|1euc]], [[1eud\|1eud]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Succinate--CoA_ligase_(ADP-forming) Succinate--CoA ligase (ADP-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.5 6.2.1.5] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Succinate--CoA_ligase_(ADP-forming) Succinate--CoA ligase (ADP-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.5 6.2.1.5] </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=1jkj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jkj OCA], [http://pdbe.org/1jkj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1jkj RCSB], [http://www.ebi.ac.uk/pdbsum/1jkj 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=1jkj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jkj OCA], [http://pdbe.org/1jkj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1jkj RCSB], [http://www.ebi.ac.uk/pdbsum/1jkj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1jkj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jk/1jkj_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/jk/1jkj_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 29:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1jkj" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1jkj" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Succinyl-CoA synthetase\|Succinyl-CoA synthetase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 21:14, 8 February 2016

OCA — Mon, 08 Feb 2016 21:14:24 GMT

←Older revision		Revision as of 21:14, 8 February 2016
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=1jkj ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 15:27, 10 September 2015

OCA — Thu, 10 Sep 2015 15:27:30 GMT

←Older revision		Revision as of 15:27, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1jkj' size='340' side='right' caption='[[1jkj]], [[Resolution\|resolution]] 2.35Å' scene=''>		<StructureSection load='1jkj' size='340' side='right' caption='[[1jkj]], [[Resolution\|resolution]] 2.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1jkj]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JKJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JKJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1jkj]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JKJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JKJ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2scu\|2scu]], [[1cqi\|1cqi]], [[1cqj\|1cqj]], [[1euc\|1euc]], [[1eud\|1eud]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2scu\|2scu]], [[1cqi\|1cqi]], [[1cqj\|1cqj]], [[1euc\|1euc]], [[1eud\|1eud]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Succinate--CoA_ligase_(ADP-forming) Succinate--CoA ligase (ADP-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.5 6.2.1.5] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Succinate--CoA_ligase_(ADP-forming) Succinate--CoA ligase (ADP-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.5 6.2.1.5] </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=1jkj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jkj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1jkj RCSB], [http://www.ebi.ac.uk/pdbsum/1jkj 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=1jkj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jkj OCA], [http://pdbe.org/1jkj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1jkj RCSB], [http://www.ebi.ac.uk/pdbsum/1jkj PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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 1jkj" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Escherichia~~ coli]]	+	[[Category: Bacillus coli migula 1895]]
	[[Category: Fraser, M E]]		[[Category: Fraser, M E]]
	[[Category: Atp-grasp fold]]		[[Category: Atp-grasp fold]]

OCA at 02:11, 25 December 2014

OCA — Thu, 25 Dec 2014 02:11:49 GMT

←Older revision		Revision as of 02:11, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1jkj]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JKJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JKJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[1jkj]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JKJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JKJ FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2scu\|2scu]], [[1cqi\|1cqi]], [[1cqj\|1cqj]], [[1euc\|1euc]], [[1eud\|1eud]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2scu\|2scu]], [[1cqi\|1cqi]], [[1cqj\|1cqj]], [[1euc\|1euc]], [[1eud\|1eud]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Succinate--CoA_ligase_(ADP-forming) Succinate--CoA ligase (ADP-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.5 6.2.1.5] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Succinate--CoA_ligase_(ADP-forming) Succinate--CoA ligase (ADP-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.5 6.2.1.5] </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=1jkj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jkj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1jkj RCSB], [http://www.ebi.ac.uk/pdbsum/1jkj 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=1jkj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jkj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1jkj RCSB], [http://www.ebi.ac.uk/pdbsum/1jkj PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/SUCD_ECOLI SUCD_ECOLI]] During aerobic metabolism it functions in the citric acid cycle, coupling the hydrolysis of succinyl-CoA to the synthesis of ATP and thus represents an important site of substrate-level phosphorylation. It can also function in the other direction for anabolic purposes, and this may be particularly important for providing succinyl-CoA during anaerobic growth when the oxidative route from 2-oxoglutarate is severely repressed. The alpha-subunit binds CoA, as well as ATP and catalyzes phosphoryl transfer to one of its histidine residues. The complete active site is probably located in the region of alpha-beta contact. [[http://www.uniprot.org/uniprot/SUCC_ECOLI SUCC_ECOLI]] During aerobic metabolism it functions in the citric acid cycle, coupling the hydrolysis of succinyl-CoA to the synthesis of ATP and thus represents an important site of substrate-level phosphorylation. It can also function in the other direction for anabolic purposes, and this may be particularly important for providing succinyl-CoA during anaerobic growth when the oxidative route from 2-oxoglutarate is severely repressed. The beta-subunit contains the attachment sites for succinate. The complete active site is probably located in the region of alpha-beta contact.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Fraser, M E.]]	+	[[Category: Fraser, M E]]
	[[Category: Atp-grasp fold]]		[[Category: Atp-grasp fold]]
	[[Category: Citric acid cycle]]		[[Category: Citric acid cycle]]

OCA at 13:56, 28 September 2014

OCA — Sun, 28 Sep 2014 13:56:10 GMT

←Older revision		Revision as of 13:56, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1jkj.~~png~~\|~~left~~\|200px]]	+	==E. coli SCS==
		+	<StructureSection load='1jkj' size='340' side='right' caption='[[1jkj]], [[Resolution\|resolution]] 2.35Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1jkj]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JKJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1JKJ FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=COA:COENZYME+A'>COA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2scu\|2scu]], [[1cqi\|1cqi]], [[1cqj\|1cqj]], [[1euc\|1euc]], [[1eud\|1eud]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Succinate--CoA_ligase_(ADP-forming) Succinate--CoA ligase (ADP-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.5 6.2.1.5] </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=1jkj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jkj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1jkj RCSB], [http://www.ebi.ac.uk/pdbsum/1jkj 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/jk/1jkj_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 ==
		+	Succinyl-CoA synthetase catalyzes the reversible reaction succinyl-CoA + NDP + P(i) <--> succinate + CoA + NTP (N denoting adenosine or guanosine). The enzyme consists of two different subunits, designated alpha and beta. During the reaction, a histidine residue of the alpha-subunit is transiently phosphorylated. This histidine residue interacts with Glu 208 alpha at site I in the structures of phosphorylated and dephosphorylated Escherichia coli SCS. We postulated that Glu 197 beta, a residue in the nucleotide-binding domain, would provide similar stabilization of the histidine residue during the actual phosphorylation/dephosphorylation by nucleotide at site II. In this work, these two glutamate residues have been mutated individually to aspartate or glutamine. Glu 197 beta has been additionally mutated to alanine. The mutant proteins were tested for their ability to be phosphorylated in the forward or reverse direction. The aspartate mutant proteins can be phosphorylated in either direction, while the E208 alpha Q mutant protein can only be phosphorylated by NTP, and the E197 beta Q mutant protein can only be phosphorylated by succinyl-CoA and P(i). These results demonstrate that the length of the side chain at these positions is not critical, but that the charge is. Most significantly, the E197 beta A mutant protein could not be phosphorylated in either direction. Its crystal structure shows large differences from the wild-type enzyme in the conformation of two residues of the alpha-subunit, Cys 123 alpha-Pro 124 alpha. We postulate that in this conformation, the protein cannot productively bind succinyl-CoA for phosphorylation via succinyl-CoA and P(i).

-	~~{{STRUCTURE_1jkj\| PDB=1jkj \| SCENE= }}~~	+	Two glutamate residues, Glu 208 alpha and Glu 197 beta, are crucial for phosphorylation and dephosphorylation of the active-site histidine residue in succinyl-CoA synthetase.,Fraser ME, Joyce MA, Ryan DG, Wolodko WT Biochemistry. 2002 Jan 15;41(2):537-46. PMID:11781092<ref>PMID:11781092</ref>

-	~~===E. coli SCS===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_11781092}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1jkj]] is~~ a ~~4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Escherichia_coli Escherichia coli]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1JKJ OCA].~~	+

	==See Also==		==See Also==
	*[[Succinyl-CoA synthetase\|Succinyl-CoA synthetase]]		*[[Succinyl-CoA synthetase\|Succinyl-CoA synthetase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:011781092<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
	[[Category: Fraser, M E.]]		[[Category: Fraser, M E.]]

OCA at 11:30, 20 October 2012

OCA — Sat, 20 Oct 2012 11:30:02 GMT

←Older revision		Revision as of 11:30, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1jkj]] is a 4 chain structure ~~of [[Succinyl-CoA synthetase]]~~ with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JKJ OCA].	+	[[1jkj]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1JKJ OCA].

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

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

OCA — Thu, 26 Jul 2012 05:35:36 GMT

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

←Older revision

Revision as of 05:35, 26 July 2012