7ecr - Revision history

OCA at 16:50, 29 November 2023

2023-11-29T16:50:49Z

←Older revision		Revision as of 16:50, 29 November 2023
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	<StructureSection load='7ecr' size='340' side='right'caption='[[7ecr]], [[Resolution\|resolution]] 1.73Å' scene=''>		<StructureSection load='7ecr' size='340' side='right'caption='[[7ecr]], [[Resolution\|resolution]] 1.73Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7ecr]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ECR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ECR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7ecr]] 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=7ECR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ECR FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A2R:[(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL+[(2R,3S,4R,5R)-3,4,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYL+DIHYDROGEN+DIPHOSPHATE'>A2R</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</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]] 1.73Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[5xvx\|5xvx]]</div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A2R:[(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL+[(2R,3S,4R,5R)-3,4,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYL+DIHYDROGEN+DIPHOSPHATE'>A2R</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</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=7ecr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ecr OCA], [https://pdbe.org/7ecr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ecr RCSB], [https://www.ebi.ac.uk/pdbsum/7ecr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ecr 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=7ecr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ecr OCA], [https://pdbe.org/7ecr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ecr RCSB], [https://www.ebi.ac.uk/pdbsum/7ecr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ecr 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 17:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 7ecr" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7ecr" 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

2022-02-23T08:36:02Z

←Older revision		Revision as of 08:36, 23 February 2022
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	==Crystal Structure of Aspergillus terreus Glutamate Dehydrogenase (AtGDH) Complexed With Succinate and ADP-ribose==		==Crystal Structure of Aspergillus terreus Glutamate Dehydrogenase (AtGDH) Complexed With Succinate and ADP-ribose==
-	<StructureSection load='7ecr' size='340' side='right'caption='[[7ecr]]' scene=''>	+	<StructureSection load='7ecr' size='340' side='right'caption='[[7ecr]], [[Resolution\|resolution]] 1.73Å' 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=7ECR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ECR FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7ecr]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7ECR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7ECR 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=7ecr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ecr OCA], [https://pdbe.org/7ecr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ecr RCSB], [https://www.ebi.ac.uk/pdbsum/7ecr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ecr 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=A2R:[(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL+[(2R,3S,4R,5R)-3,4,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYL+DIHYDROGEN+DIPHOSPHATE'>A2R</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[5xvx\|5xvx]]</div></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=7ecr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ecr OCA], [https://pdbe.org/7ecr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ecr RCSB], [https://www.ebi.ac.uk/pdbsum/7ecr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ecr 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 7ecr" 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

2021-12-08T09:54:51Z

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

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

OCA at 04:29, 7 April 2021

2021-04-07T04:29:10Z

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

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

	Authors:		Authors:

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

2021-03-24T05:23:02Z

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

←Older revision

Revision as of 05:23, 24 March 2021

OCA: New page: '''Unreleased structure''' The entry 7ecr is ON HOLD Authors: Description: Category: Unreleased Structures

2021-03-24T05:23:01Z

New page: '''Unreleased structure''' The entry 7ecr is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7ecr is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]