2fpg - Revision history

OCA at 09:24, 14 February 2024

2024-02-14T09:24:48Z

← Older revision		Revision as of 09:24, 14 February 2024
Line 3:		Line 3:
	<StructureSection load='2fpg' size='340' side='right'caption='[[2fpg]], [[Resolution\|resolution]] 2.96Å' scene=''>		<StructureSection load='2fpg' size='340' side='right'caption='[[2fpg]], [[Resolution\|resolution]] 2.96Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2fpg]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Pig Pig~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FPG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FPG FirstGlance]. <br>		<table><tr><td colspan='2'>[[2fpg]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FPG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FPG FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GDP:GUANOSINE-5~~-~~DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>~~, ~~<scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2.96Å</td></tr>
	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em~~;~~'>[[1euc\|1euc]], [[1eud\|1eud]], [[2fp4\|2fp4]], [[2fpi\|2fpi]], [[2fpp\|2fpp]]</div>~~</td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~SUCLG1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=9823 PIG]), SUCLG2 ([https~~:~~//www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=~~5~~&id=9823 PIG])</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_(GDP-forming) Succinate--CoA ligase (GDP-forming)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.4 6.2.1.4]~~ </~~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=2fpg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fpg OCA], [https://pdbe.org/2fpg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fpg RCSB], [https://www.ebi.ac.uk/pdbsum/2fpg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fpg 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=2fpg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fpg OCA], [https://pdbe.org/2fpg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fpg RCSB], [https://www.ebi.ac.uk/pdbsum/2fpg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fpg ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/SUCA_PIG SUCA_PIG]] Catalyzes the ATP- or GTP-dependent ligation of succinate and CoA to form succinyl-CoA. The nature of the beta subunit determines the nucleotide specificity (By similarity). [[https://www.uniprot.org/uniprot/SUCB2_PIG SUCB2_PIG]] Catalyzes the GTP-dependent ligation of succinate and CoA to form succinyl-CoA (By similarity).		[https://www.uniprot.org/uniprot/SUCB2_PIG SUCB2_PIG] Catalyzes the GTP-dependent ligation of succinate and CoA to form succinyl-CoA (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 22:		Line 20:
	</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=2fpg 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=2fpg ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Two isoforms of succinyl-CoA synthetase exist in mammals, one specific for ATP and the other for GTP. The GTP-specific form of pig succinyl-CoA synthetase has been crystallized in the presence of GTP and the structure determined to 2.1 A resolution. GTP is bound in the ATP-grasp domain, where interactions of the guanine base with a glutamine residue (Gln-20beta) and with backbone atoms provide the specificity. The gamma-phosphate interacts with the side chain of an arginine residue (Arg-54beta) and with backbone amide nitrogen atoms, leading to tight interactions between the gamma-phosphate and the protein. This contrasts with the structures of ATP bound to other members of the family of ATP-grasp proteins where the gamma-phosphate is exposed, free to react with the other substrate. To test if GDP would interact with GTP-specific succinyl-CoA synthetase in the same way that ADP interacts with other members of the family of ATP-grasp proteins, the structure of GDP bound to GTP-specific succinyl-CoA synthetase was also determined. A comparison of the conformations of GTP and GDP shows that the bases adopt the same position but that changes in conformation of the ribose moieties and the alpha- and beta-phosphates allow the gamma-phosphate to interact with the arginine residue and amide nitrogen atoms in GTP, while the beta-phosphate interacts with these residues in GDP. The complex of GTP with succinyl-CoA synthetase shows that the enzyme is able to protect GTP from hydrolysis when the active-site histidine residue is not in position to be phosphorylated.

	Interactions of GTP with the ATP-grasp domain of GTP-specific succinyl-CoA synthetase.,Fraser ME, Hayakawa K, Hume MS, Ryan DG, Brownie ER J Biol Chem. 2006 Apr 21;281(16):11058-65. Epub 2006 Feb 15. PMID:16481318<ref>PMID:16481318</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 2fpg" style="background-color:#fffaf0;"></div>~~

	==See Also==		==See Also==
	*[[Succinyl-CoA synthetase 3D structures\|Succinyl-CoA synthetase 3D structures]]		*[[Succinyl-CoA synthetase 3D structures\|Succinyl-CoA synthetase 3D structures]]
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Pig~~]]		[[Category: Sus scrofa]]
	[[Category: Fraser~~, M E]]~~		[[Category: Fraser ME]]
	~~[[Category: Active site histidine residue]]~~
	~~[[Category: Ligase~~]]

OCA at 15:31, 3 March 2021

2021-03-03T15:31:05Z

← Older revision		Revision as of 15:31, 3 March 2021
Line 1:		Line 1:

	==Crystal structure of pig GTP-specific succinyl-CoA synthetase in complex with GDP==		==Crystal structure of pig GTP-specific succinyl-CoA synthetase in complex with GDP==
	<StructureSection load='2fpg' size='340' side='right' caption='[[2fpg]], [[Resolution\|resolution]] 2.96Å' scene=''>		<StructureSection load='2fpg' size='340' side='right'caption='[[2fpg]], [[Resolution\|resolution]] 2.96Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2fpg]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Pig Pig]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FPG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2FPG FirstGlance]. <br>		<table><tr><td colspan='2'>[[2fpg]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pig Pig]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FPG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FPG FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1euc\|1euc]], [[1eud\|1eud]], [[2fp4\|2fp4]], [[2fpi\|2fpi]], [[2fpp\|2fpp]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1euc\|1euc]], [[1eud\|1eud]], [[2fp4\|2fp4]], [[2fpi\|2fpi]], [[2fpp\|2fpp]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SUCLG1 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 PIG]), SUCLG2 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 PIG])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SUCLG1 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 PIG]), SUCLG2 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 PIG])</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_(GDP-forming) Succinate--CoA ligase (GDP-forming)], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.4 6.2.1.4] </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_(GDP-forming) Succinate--CoA ligase (GDP-forming)], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.4 6.2.1.4] </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=2fpg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fpg OCA], [~~http~~://pdbe.org/2fpg PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2fpg RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2fpg PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2fpg 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=2fpg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fpg OCA], [https://pdbe.org/2fpg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fpg RCSB], [https://www.ebi.ac.uk/pdbsum/2fpg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fpg ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/SUCA_PIG SUCA_PIG]] Catalyzes the ATP- or GTP-dependent ligation of succinate and CoA to form succinyl-CoA. The nature of the beta subunit determines the nucleotide specificity (By similarity). [[~~http~~://www.uniprot.org/uniprot/SUCB2_PIG SUCB2_PIG]] Catalyzes the GTP-dependent ligation of succinate and CoA to form succinyl-CoA (By similarity).		[[https://www.uniprot.org/uniprot/SUCA_PIG SUCA_PIG]] Catalyzes the ATP- or GTP-dependent ligation of succinate and CoA to form succinyl-CoA. The nature of the beta subunit determines the nucleotide specificity (By similarity). [[https://www.uniprot.org/uniprot/SUCB2_PIG SUCB2_PIG]] Catalyzes the GTP-dependent ligation of succinate and CoA to form succinyl-CoA (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fp/2fpg_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/fp/2fpg_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 31:		Line 31:
	</div>		</div>
	<div class="pdbe-citations 2fpg" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2fpg" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Succinyl-CoA synthetase 3D structures\|Succinyl-CoA synthetase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Large Structures]]
	[[Category: Pig]]		[[Category: Pig]]
	[[Category: Fraser, M E]]		[[Category: Fraser, M E]]
	[[Category: Active site histidine residue]]		[[Category: Active site histidine residue]]
	[[Category: Ligase]]		[[Category: Ligase]]

OCA at 07:42, 18 October 2017

2017-10-18T07:42:36Z

← Older revision		Revision as of 07:42, 18 October 2017
Line 1:		Line 1:

	==Crystal structure of pig GTP-specific succinyl-CoA synthetase in complex with GDP==		==Crystal structure of pig GTP-specific succinyl-CoA synthetase in complex with GDP==
	<StructureSection load='2fpg' size='340' side='right' caption='[[2fpg]], [[Resolution\|resolution]] 2.96Å' scene=''>		<StructureSection load='2fpg' size='340' side='right' caption='[[2fpg]], [[Resolution\|resolution]] 2.96Å' scene=''>
Line 7:		Line 8:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SUCLG1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 PIG]), SUCLG2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 PIG])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SUCLG1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 PIG]), SUCLG2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 PIG])</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_(GDP-forming) Succinate--CoA ligase (GDP-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.4 6.2.1.4] </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_(GDP-forming) Succinate--CoA ligase (GDP-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.4 6.2.1.4] </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=2fpg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fpg OCA], [http://pdbe.org/2fpg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2fpg RCSB], [http://www.ebi.ac.uk/pdbsum/2fpg 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=2fpg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fpg OCA], [http://pdbe.org/2fpg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2fpg RCSB], [http://www.ebi.ac.uk/pdbsum/2fpg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2fpg ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 30:		Line 31:
	</div>		</div>
	<div class="pdbe-citations 2fpg" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2fpg" style="background-color:#fffaf0;"></div>

	~~==See Also==~~
	*[[Succinyl-CoA synthetase\|Succinyl-CoA synthetase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 16:07, 7 February 2016

2016-02-07T16:07:37Z

← Older revision		Revision as of 16:07, 7 February 2016
Line 19:		Line 19:
	<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=2fpg ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 03:04, 10 September 2015

2015-09-10T03:04:42Z

← Older revision		Revision as of 03:04, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2fpg' size='340' side='right' caption='[[2fpg]], [[Resolution\|resolution]] 2.96Å' scene=''>		<StructureSection load='2fpg' size='340' side='right' caption='[[2fpg]], [[Resolution\|resolution]] 2.96Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2fpg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Sus_scrofa Sus scrofa~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FPG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FPG FirstGlance]. <br>		<table><tr><td colspan='2'>[[2fpg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pig Pig]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FPG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FPG FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1euc\|1euc]], [[1eud\|1eud]], [[2fp4\|2fp4]], [[2fpi\|2fpi]], [[2fpp\|2fpp]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1euc\|1euc]], [[1eud\|1eud]], [[2fp4\|2fp4]], [[2fpi\|2fpi]], [[2fpp\|2fpp]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SUCLG1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 ~~Sus scrofa~~]), SUCLG2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 ~~Sus scrofa~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SUCLG1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 PIG]), SUCLG2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 PIG])</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_(GDP-forming) Succinate--CoA ligase (GDP-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.4 6.2.1.4] </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_(GDP-forming) Succinate--CoA ligase (GDP-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.4 6.2.1.4] </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=2fpg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fpg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2fpg RCSB], [http://www.ebi.ac.uk/pdbsum/2fpg 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=2fpg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fpg OCA], [http://pdbe.org/2fpg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2fpg RCSB], [http://www.ebi.ac.uk/pdbsum/2fpg 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 2fpg" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 36:		Line 37:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Sus scrofa~~]]		[[Category: Pig]]
	[[Category: Fraser, M E]]		[[Category: Fraser, M E]]
	[[Category: Active site histidine residue]]		[[Category: Active site histidine residue]]
	[[Category: Ligase]]		[[Category: Ligase]]

OCA at 16:31, 24 December 2014

2014-12-24T16:31:17Z

← Older revision		Revision as of 16:31, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2fpg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FPG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FPG FirstGlance]. <br>		<table><tr><td colspan='2'>[[2fpg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FPG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FPG FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1euc\|1euc]], [[1eud\|1eud]], [[2fp4\|2fp4]], [[2fpi\|2fpi]], [[2fpp\|2fpp]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1euc\|1euc]], [[1eud\|1eud]], [[2fp4\|2fp4]], [[2fpi\|2fpi]], [[2fpp\|2fpp]]</td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SUCLG1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 Sus scrofa]), SUCLG2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 Sus scrofa])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SUCLG1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 Sus scrofa]), SUCLG2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 Sus scrofa])</td></tr>
	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Succinate--CoA_ligase_(GDP-forming) Succinate--CoA ligase (GDP-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.4 6.2.1.4] </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_(GDP-forming) Succinate--CoA ligase (GDP-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.4 6.2.1.4] </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=2fpg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fpg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2fpg RCSB], [http://www.ebi.ac.uk/pdbsum/2fpg 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=2fpg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fpg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2fpg RCSB], [http://www.ebi.ac.uk/pdbsum/2fpg PDBsum]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/SUCA_PIG SUCA_PIG]] Catalyzes the ATP- or GTP-dependent ligation of succinate and CoA to form succinyl-CoA. The nature of the beta subunit determines the nucleotide specificity (By similarity). [[http://www.uniprot.org/uniprot/SUCB2_PIG SUCB2_PIG]] Catalyzes the GTP-dependent ligation of succinate and CoA to form succinyl-CoA (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 35:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Sus scrofa]]		[[Category: Sus scrofa]]
	[[Category: Fraser, M E.]]		[[Category: Fraser, M E]]
	[[Category: Active site histidine residue]]		[[Category: Active site histidine residue]]
	[[Category: Ligase]]		[[Category: Ligase]]

OCA at 09:28, 29 September 2014

2014-09-29T09:28:41Z

← Older revision		Revision as of 09:28, 29 September 2014
Line 1:		Line 1:
	[[Image:~~2fpg~~.~~png~~\|~~left~~\|~~200px~~]]		==Crystal structure of pig GTP-specific succinyl-CoA synthetase in complex with GDP==
			<StructureSection load='2fpg' size='340' side='right' caption='[[2fpg]], [[Resolution\|resolution]] 2.96Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2fpg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FPG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2FPG FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1euc\|1euc]], [[1eud\|1eud]], [[2fp4\|2fp4]], [[2fpi\|2fpi]], [[2fpp\|2fpp]]</td></tr>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SUCLG1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 Sus scrofa]), SUCLG2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9823 Sus scrofa])</td></tr>
			<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Succinate--CoA_ligase_(GDP-forming) Succinate--CoA ligase (GDP-forming)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.4 6.2.1.4] </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=2fpg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fpg OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2fpg RCSB], [http://www.ebi.ac.uk/pdbsum/2fpg 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/fp/2fpg_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 ==
			Two isoforms of succinyl-CoA synthetase exist in mammals, one specific for ATP and the other for GTP. The GTP-specific form of pig succinyl-CoA synthetase has been crystallized in the presence of GTP and the structure determined to 2.1 A resolution. GTP is bound in the ATP-grasp domain, where interactions of the guanine base with a glutamine residue (Gln-20beta) and with backbone atoms provide the specificity. The gamma-phosphate interacts with the side chain of an arginine residue (Arg-54beta) and with backbone amide nitrogen atoms, leading to tight interactions between the gamma-phosphate and the protein. This contrasts with the structures of ATP bound to other members of the family of ATP-grasp proteins where the gamma-phosphate is exposed, free to react with the other substrate. To test if GDP would interact with GTP-specific succinyl-CoA synthetase in the same way that ADP interacts with other members of the family of ATP-grasp proteins, the structure of GDP bound to GTP-specific succinyl-CoA synthetase was also determined. A comparison of the conformations of GTP and GDP shows that the bases adopt the same position but that changes in conformation of the ribose moieties and the alpha- and beta-phosphates allow the gamma-phosphate to interact with the arginine residue and amide nitrogen atoms in GTP, while the beta-phosphate interacts with these residues in GDP. The complex of GTP with succinyl-CoA synthetase shows that the enzyme is able to protect GTP from hydrolysis when the active-site histidine residue is not in position to be phosphorylated.

	~~{{STRUCTURE_2fpg\| PDB=2fpg \| SCENE= }}~~		Interactions of GTP with the ATP-grasp domain of GTP-specific succinyl-CoA synthetase.,Fraser ME, Hayakawa K, Hume MS, Ryan DG, Brownie ER J Biol Chem. 2006 Apr 21;281(16):11058-65. Epub 2006 Feb 15. PMID:16481318<ref>PMID:16481318</ref>

	~~===Crystal structure~~ of ~~pig GTP-specific succinyl-CoA synthetase in complex with GDP===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_16481318}}~~

	~~==About this Structure==~~
	~~[[2fpg]] is a 2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Sus_scrofa Sus scrofa]~~. ~~Full crystallographic information is available from [http://oca.weizmann.ac.il~~/~~oca-bin/ocashort?id=2FPG OCA].~~

	==See Also==		==See Also==
	*[[Succinyl-CoA synthetase\|Succinyl-CoA synthetase]]		*[[Succinyl-CoA synthetase\|Succinyl-CoA synthetase]]
			== References ==
	==~~Reference~~==		<references/>
	<~~ref group="xtra">PMID:016481318<~~/~~ref~~><~~references group="xtra"~~/>		__TOC__
			</StructureSection>
	[[Category: Sus scrofa]]		[[Category: Sus scrofa]]
	[[Category: Fraser, M E.]]		[[Category: Fraser, M E.]]
	[[Category: Active site histidine residue]]		[[Category: Active site histidine residue]]
	[[Category: Ligase]]		[[Category: Ligase]]

OCA at 07:10, 20 October 2012

2012-10-20T07:10:30Z

← Older revision		Revision as of 07:10, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
	[[2fpg]] is a 2 chain structure ~~of [[Succinyl-CoA synthetase]]~~ with sequence from [http://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FPG OCA].		[[2fpg]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FPG OCA].

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

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

2012-07-25T15:29:44Z

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

← Older revision	Revision as of 15:29, 25 July 2012
(No difference)

OCA at 15:29, 25 July 2012

2012-07-25T15:29:43Z

← Older revision		Revision as of 15:29, 25 July 2012
Line 1:		Line 1:
	~~{{Seed}}~~
	[[Image:2fpg.png\|left\|200px]]		[[Image:2fpg.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2fpg", 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_2fpg\| PDB=2fpg \| SCENE= }}		{{STRUCTURE_2fpg\| PDB=2fpg \| SCENE= }}

	===Crystal structure of pig GTP-specific succinyl-CoA synthetase in complex with GDP===		===Crystal structure of pig GTP-specific succinyl-CoA synthetase in complex with GDP===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_16481318}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 16481318 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_16481318}}		{{ABSTRACT_PUBMED_16481318}}

	==About this Structure==		==About this Structure==
	~~2FPG~~ is a 2 ~~chains~~ structure of ~~sequences~~ from [http://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FPG OCA].		[[2fpg]] is a 2 chain structure of [[Succinyl-CoA synthetase]] with sequence from [http://en.wikipedia.org/wiki/Sus_scrofa Sus scrofa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FPG OCA].

			==See Also==
			*[[Succinyl-CoA synthetase\|Succinyl-CoA synthetase]]

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~16481318~~</ref><references group="xtra"/>		<ref group="xtra">PMID:016481318</ref><references group="xtra"/>
	[[Category: Sus scrofa]]		[[Category: Sus scrofa]]
	[[Category: Fraser, M E.]]		[[Category: Fraser, M E.]]
	[[Category: Active site histidine residue]]		[[Category: Active site histidine residue]]
			[[Category: Ligase]]
	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Mon Feb 16 14:59:40 2009''~~