7ect - Revision history

OCA at 16:50, 29 November 2023

OCA — Wed, 29 Nov 2023 16:50:54 GMT

←Older revision		Revision as of 16:50, 29 November 2023
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	<StructureSection load='7ect' size='340' side='right'caption='[[7ect]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='7ect' size='340' side='right'caption='[[7ect]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7ect]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ECT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ECT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7ect]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_terreus Aspergillus terreus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ECT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ECT FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</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]] 2.9Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></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=7ect FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ect OCA], [https://pdbe.org/7ect PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ect RCSB], [https://www.ebi.ac.uk/pdbsum/7ect PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ect 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=7ect FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ect OCA], [https://pdbe.org/7ect PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ect RCSB], [https://www.ebi.ac.uk/pdbsum/7ect PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ect ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/T2D1F5_ASPTE T2D1F5_ASPTE]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 16:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 7ect" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7ect" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Glutamate dehydrogenase 3D structures\|Glutamate dehydrogenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Aspergillus terreus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bhaumik, P]]	+	[[Category: Bhaumik P]]
-	[[Category: Godsora~~, B K.J~~]]	+	[[Category: Godsora BKJ]]
-	[[Category: Prakash, P]]	+	[[Category: Prakash P]]
-	[[Category: Punekar~~, N S]]~~	+	[[Category: Punekar NS]]
-	~~[[Category: Allostery]]~~	+
-	~~[[Category: Aspergillus]]~~	+
-	~~[[Category: Enzyme mechanism]]~~	+
-	~~[[Category: Glutamate dehydrogenase]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 08:36, 23 February 2022

OCA — Wed, 23 Feb 2022 08:36:04 GMT

←Older revision		Revision as of 08:36, 23 February 2022
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	==Crystal Structure of Aspergillus terreus Glutamate Dehydrogenase (AtGDH) Complexed With Tartrate and NADPH==		==Crystal Structure of Aspergillus terreus Glutamate Dehydrogenase (AtGDH) Complexed With Tartrate and NADPH==
-	<StructureSection load='7ect' size='340' side='right'caption='[[7ect]]' scene=''>	+	<StructureSection load='7ect' size='340' side='right'caption='[[7ect]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ECT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ECT FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7ect]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ECT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ECT FirstGlance]. <br>
-	</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=7ect FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ect OCA], [https://pdbe.org/7ect PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ect RCSB], [https://www.ebi.ac.uk/pdbsum/7ect PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ect ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></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=7ect FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ect OCA], [https://pdbe.org/7ect PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ect RCSB], [https://www.ebi.ac.uk/pdbsum/7ect PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ect ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Glutamate dehydrogenase (GDH) is a salient metabolic enzyme which catalyzes the NAD(+) - or NADP(+) -dependent reversible conversion of alpha-ketoglutarate (AKG) to l-glutamate; and thereby connects the carbon and nitrogen metabolism cycles in all living organisms. The function of GDH is extensively regulated by both metabolites (citrate, succinate, etc.) and non-metabolites (ATP, NADH, etc.) but sufficient molecular evidences are lacking to rationalize the inhibitory effects by the metabolites. We have expressed and purified NADP(+) -dependent Aspergillus terreus GDH (AtGDH) in recombinant form. Succinate, malonate, maleate, fumarate, and tartrate independently inhibit the activity of AtGDH to different extents. The crystal structures of AtGDH complexed with the dicarboxylic acid metabolites and the coenzyme NADPH have been determined. Although AtGDH structures are not complexed with substrate; surprisingly, they acquire super closed conformation like previously reported for substrate and coenzyme bound catalytically competent Aspergillus niger GDH (AnGDH). These dicarboxylic acid metabolites partially occupy the same binding pocket as substrate; but interact with varying polar interactions and the coenzyme NADPH binds to the Domain-II of AtGDH. The low inhibition potential of tartrate as compared to other dicarboxylic acid metabolites is due to its weaker interactions of carboxylate groups with AtGDH. Our results suggest that the length of carbon skeleton and positioning of the carboxylate groups of inhibitors between two conserved lysine residues at the GDH active site might be the determinants of their inhibitory potency. Molecular details on the dicarboxylic acid metabolites bound AtGDH active site architecture presented here would be applicable to GDHs in general.
		+
		+	Molecular insights into the inhibition of glutamate dehydrogenase by the dicarboxylic acid metabolites.,Godsora BKJ, Prakash P, Punekar NS, Bhaumik P Proteins. 2021 Nov 8. doi: 10.1002/prot.26276. PMID:34748226<ref>PMID:34748226</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7ect" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bhaumik P]]	+	[[Category: Bhaumik, P]]
-	[[Category: Godsora ~~BKJ~~]]	+	[[Category: Godsora, B K.J]]
-	[[Category: Prakash P]]	+	[[Category: Prakash, P]]
-	[[Category: Punekar NS]]	+	[[Category: Punekar, N S]]
		+	[[Category: Allostery]]
		+	[[Category: Aspergillus]]
		+	[[Category: Enzyme mechanism]]
		+	[[Category: Glutamate dehydrogenase]]
		+	[[Category: Oxidoreductase]]

OCA at 09:54, 8 December 2021

OCA — Wed, 08 Dec 2021 09:54:52 GMT

←Older revision		Revision as of 09:54, 8 December 2021
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-	'''Unreleased structure'''

-	~~The entry~~ 7ect ~~is ON HOLD until Paper Publication~~	+	==Crystal Structure of Aspergillus terreus Glutamate Dehydrogenase (AtGDH) Complexed With Tartrate and NADPH==
-		+	<StructureSection load='7ect' size='340' side='right'caption='[[7ect]]' scene=''>
-	~~Authors~~: ~~Godsora~~, B.K.J., ~~Prakash, P~~., ~~Punekar, N~~.S., ~~Bhaumik~~, P.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ECT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ECT FirstGlance]. <br>
-	~~Description: Crystal Structure of Aspergillus terreus Glutamate Dehydrogenase (AtGDH) Complexed With Tartrate and NADPH~~	+	</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=7ect FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ect OCA], [https://pdbe.org/7ect PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ect RCSB], [https://www.ebi.ac.uk/pdbsum/7ect PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ect ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Prakash,~~ P]]	+	__TOC__
-	[[Category: ~~Punekar, N.S~~]]	+	</StructureSection>
-	[[Category: ~~Godsora, B.K.J~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Bhaumik, P~~]]	+	[[Category: Bhaumik P]]
		+	[[Category: Godsora BKJ]]
		+	[[Category: Prakash P]]
		+	[[Category: Punekar NS]]

OCA at 04:29, 7 April 2021

OCA — Wed, 07 Apr 2021 04:29:15 GMT

←Older revision		Revision as of 04:29, 7 April 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7ect is ON HOLD	+	The entry 7ect is ON HOLD until Paper Publication

	Authors: Godsora, B.K.J., Prakash, P., Punekar, N.S., Bhaumik, P.		Authors: Godsora, B.K.J., Prakash, P., Punekar, N.S., Bhaumik, P.

OCA: Protected "7ect" [edit=sysop:move=sysop]

OCA — Wed, 24 Mar 2021 05:23:13 GMT

Protected "7ect" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:23, 24 March 2021

OCA: New page: '''Unreleased structure''' The entry 7ect is ON HOLD Authors: Godsora, B.K.J., Prakash, P., Punekar, N.S., Bhaumik, P. Description: Crystal Structure of Aspergillus terreus Glutamate D...

OCA — Wed, 24 Mar 2021 05:23:12 GMT

New page: '''Unreleased structure''' The entry 7ect is ON HOLD Authors: Godsora, B.K.J., Prakash, P., Punekar, N.S., Bhaumik, P. Description: Crystal Structure of Aspergillus terreus Glutamate D...

New page

'''Unreleased structure'''

The entry 7ect is ON HOLD

Authors: Godsora, B.K.J., Prakash, P., Punekar, N.S., Bhaumik, P.

Description: Crystal Structure of Aspergillus terreus Glutamate Dehydrogenase (AtGDH) Complexed With Tartrate and NADPH
[[Category: Unreleased Structures]]
[[Category: Prakash, P]]
[[Category: Punekar, N.S]]
[[Category: Godsora, B.K.J]]
[[Category: Bhaumik, P]]