6no0 - Revision history

OCA at 11:43, 13 November 2019

OCA — Wed, 13 Nov 2019 11:43:32 GMT

←Older revision		Revision as of 11:43, 13 November 2019
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	<StructureSection load='6no0' size='340' side='right'caption='[[6no0]], [[Resolution\|resolution]] 2.21Å' scene=''>		<StructureSection load='6no0' size='340' side='right'caption='[[6no0]], [[Resolution\|resolution]] 2.21Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6no0]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NO0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NO0 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6no0]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Blahn Blahn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NO0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NO0 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SCSb ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=478820 BLAHN])</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=6no0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6no0 OCA], [http://pdbe.org/6no0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6no0 RCSB], [http://www.ebi.ac.uk/pdbsum/6no0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6no0 ProSAT]</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=6no0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6no0 OCA], [http://pdbe.org/6no0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6no0 RCSB], [http://www.ebi.ac.uk/pdbsum/6no0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6no0 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Succinyl-CoA synthetase (SCS) catalyzes the only step of the tricarboxylic acid cycle that leads to substrate-level phosphorylation. Some forms of SCS are specific for ADP/ATP or for GDP/GTP, while others can bind all of these nucleotides, generally with different affinities. The theory of `gatekeeper' residues has been proposed to explain the nucleotide-specificity. Gatekeeper residues lie outside the binding site and create specific electrostatic interactions with incoming nucleotides to determine whether the nucleotides can enter the binding site. To test this theory, the crystal structure of the nucleotide-binding domain in complex with Mg(2+)-ADP was determined, as well as the structures of four proteins with single mutations, K46betaE, K114betaD, V113betaL and L227betaF, and one with two mutations, K46betaE/K114betaD. The crystal structures show that the enzyme is specific for ADP/ATP because of interactions between the nucleotide and the binding site. Nucleotide-specificity is provided by hydrogen-bonding interactions between the adenine base and Gln20beta, Gly111beta and Val113beta. The O atom of the side chain of Gln20beta interacts with N6 of ADP, while the side-chain N atom interacts with the carbonyl O atom of Gly111beta. It is the different conformations of the backbone at Gln20beta, of the side chain of Gln20beta and of the linker that make the enzyme ATP-specific. This linker connects the two subdomains of the ATP-grasp fold and interacts differently with adenine and guanine bases. The mutant proteins have similar conformations, although the L227betaF mutant shows structural changes that disrupt the binding site for the magnesium ion. Although the K46betaE/K114betaD double mutant of Blastocystis hominis SCS binds GTP better than ATP according to kinetic assays, only the complex with Mg(2+)-ADP was obtained.
		+
		+	ATP-specificity of succinyl-CoA synthetase from Blastocystis hominis.,Huang J, Nguyen VH, Hamblin KA, Maytum R, van der Giezen M, Fraser ME Acta Crystallogr D Struct Biol. 2019 Jul 1;75(Pt 7):647-659. doi:, 10.1107/S2059798319007976. Epub 2019 Jun 26. PMID:31282474<ref>PMID:31282474</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6no0" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Blahn]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Fraser, M E]]		[[Category: Fraser, M E]]

OCA at 10:46, 17 July 2019

OCA — Wed, 17 Jul 2019 10:46:45 GMT

←Older revision		Revision as of 10:46, 17 July 2019
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-	'''Unreleased structure'''

-	~~The entry 6no0 is ON HOLD until Paper Publication~~	+	==ADP bound to ATP-grasp fold of Blastocystis hominis succinyl-CoA synthetase==
-		+	<StructureSection load='6no0' size='340' side='right'caption='[[6no0]], [[Resolution\|resolution]] 2.21Å' scene=''>
-	~~Authors: Huang, J., Fraser, M.E.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6no0]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NO0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NO0 FirstGlance]. <br>
-	~~Description:~~ ADP bound to ATP-grasp fold of Blastocystis hominis succinyl-CoA synthetase	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<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=6no0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6no0 OCA], [http://pdbe.org/6no0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6no0 RCSB], [http://www.ebi.ac.uk/pdbsum/6no0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6no0 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Fraser, M E]]
	[[Category: Huang, J]]		[[Category: Huang, J]]
-	[[Category: ~~Fraser, M.E~~]]	+	[[Category: Complex]]
		+	[[Category: Ligase]]

OCA at 07:35, 13 February 2019

OCA — Wed, 13 Feb 2019 07:35:13 GMT

←Older revision		Revision as of 07:35, 13 February 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6no0 is ON HOLD	+	The entry 6no0 is ON HOLD until Paper Publication

	Authors: Huang, J., Fraser, M.E.		Authors: Huang, J., Fraser, M.E.

OCA: Protected "6no0" [edit=sysop:move=sysop]

OCA — Wed, 30 Jan 2019 06:39:50 GMT

Protected "6no0" [edit=sysop:move=sysop]

←Older revision

Revision as of 06:39, 30 January 2019

OCA: New page: '''Unreleased structure''' The entry 6no0 is ON HOLD Authors: Huang, J., Fraser, M.E. Description: ADP bound to ATP-grasp fold of Blastocystis hominis succinyl-CoA synthetase [[Categor...

OCA — Wed, 30 Jan 2019 06:39:48 GMT

New page: '''Unreleased structure''' The entry 6no0 is ON HOLD Authors: Huang, J., Fraser, M.E. Description: ADP bound to ATP-grasp fold of Blastocystis hominis succinyl-CoA synthetase [[Categor...

New page

'''Unreleased structure'''

The entry 6no0 is ON HOLD

Authors: Huang, J., Fraser, M.E.

Description: ADP bound to ATP-grasp fold of Blastocystis hominis succinyl-CoA synthetase
[[Category: Unreleased Structures]]
[[Category: Huang, J]]
[[Category: Fraser, M.E]]