5xvi - Revision history

OCA at 08:15, 22 November 2023

2023-11-22T08:15:06Z

←Older revision		Revision as of 08:15, 22 November 2023
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	<StructureSection load='5xvi' size='340' side='right'caption='[[5xvi]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='5xvi' size='340' side='right'caption='[[5xvi]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xvi]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XVI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5XVI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xvi]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Aspergillus_niger Aspergillus niger]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XVI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XVI 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></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]] 2.8Å</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5xvi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xvi OCA], [~~http~~://pdbe.org/5xvi PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5xvi RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5xvi PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5xvi ProSAT]</span></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></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=5xvi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xvi OCA], [https://pdbe.org/5xvi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xvi RCSB], [https://www.ebi.ac.uk/pdbsum/5xvi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xvi ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/B6V7E4_ASPNG B6V7E4_ASPNG]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Aspergillus niger]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bhaumik, P]]	+	[[Category: Bhaumik P]]
-	[[Category: Prakash, P]]	+	[[Category: Prakash P]]
-	[[Category: Punekar~~, N S]]~~	+	[[Category: Punekar NS]]
-	~~[[Category: 2-oxoglutarate]]~~	+
-	~~[[Category: Allostery]]~~	+
-	~~[[Category: Aspergillus]]~~	+
-	~~[[Category: Dehydrogenase]]~~	+
-	~~[[Category: Glutamate]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 06:59, 14 October 2020

2020-10-14T06:59:34Z

←Older revision		Revision as of 06:59, 14 October 2020
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	==Crystal Structure of Aspergillus niger Apo- Glutamate Dehydrogenase==		==Crystal Structure of Aspergillus niger Apo- Glutamate Dehydrogenase==
-	<StructureSection load='5xvi' size='340' side='right' caption='[[5xvi]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='5xvi' size='340' side='right'caption='[[5xvi]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xvi]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XVI OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5XVI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xvi]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XVI OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5XVI FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></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></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=5xvi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xvi OCA], [http://pdbe.org/5xvi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xvi RCSB], [http://www.ebi.ac.uk/pdbsum/5xvi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xvi ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5xvi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xvi OCA], [http://pdbe.org/5xvi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xvi RCSB], [http://www.ebi.ac.uk/pdbsum/5xvi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xvi ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 16:
	</div>		</div>
	<div class="pdbe-citations 5xvi" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5xvi" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Glutamate dehydrogenase 3D structures\|Glutamate dehydrogenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Bhaumik, P]]		[[Category: Bhaumik, P]]
	[[Category: Prakash, P]]		[[Category: Prakash, P]]

OCA at 06:28, 9 May 2018

2018-05-09T06:28:41Z

←Older revision		Revision as of 06:28, 9 May 2018
Line 3:		Line 3:
	<StructureSection load='5xvi' size='340' side='right' caption='[[5xvi]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='5xvi' size='340' side='right' caption='[[5xvi]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xvi]] is a 6 chain structure ~~with sequence from [http://en.wikipedia.org/wiki/A._niger A. niger]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XVI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XVI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xvi]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XVI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XVI FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></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=5xvi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xvi OCA], [http://pdbe.org/5xvi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xvi RCSB], [http://www.ebi.ac.uk/pdbsum/5xvi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xvi 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=5xvi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xvi OCA], [http://pdbe.org/5xvi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xvi RCSB], [http://www.ebi.ac.uk/pdbsum/5xvi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xvi ProSAT]</span></td></tr>
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: A. niger]]
	[[Category: Bhaumik, P]]		[[Category: Bhaumik, P]]
	[[Category: Prakash, P]]		[[Category: Prakash, P]]

OCA at 07:07, 28 March 2018

2018-03-28T07:07:56Z

←Older revision		Revision as of 07:07, 28 March 2018
Line 3:		Line 3:
	<StructureSection load='5xvi' size='340' side='right' caption='[[5xvi]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='5xvi' size='340' side='right' caption='[[5xvi]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xvi]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XVI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XVI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xvi]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/A._niger A. niger]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XVI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XVI FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></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=5xvi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xvi OCA], [http://pdbe.org/5xvi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xvi RCSB], [http://www.ebi.ac.uk/pdbsum/5xvi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xvi 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=5xvi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xvi OCA], [http://pdbe.org/5xvi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xvi RCSB], [http://www.ebi.ac.uk/pdbsum/5xvi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xvi ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Glutamate dehydrogenase (GDH) is a key enzyme connecting carbon and nitrogen metabolism in all living organisms. Despite extensive studies on GDHs from both prokaryotic and eukaryotic organisms in the last 40 years, the structural basis of the catalytic features of this enzyme remains incomplete. This study reports the structural basis of the GDH catalytic mechanism and allosteric behavior. We determined the first high-resolution crystal structures of glutamate dehydrogenase from the fungus Aspergillus niger (AnGDH), a unique NADP(+)-dependent allosteric enzyme that is forward inhibited by the formation of mixed disulfide. We determined the structures of the active enzyme in its apo form and in binary/ternary complexes with bound substrate (alpha- ketoglutarate), inhibitor (isophthalate), coenzyme (NADPH), or two reaction intermediates (alpha-iminoglutarate and 2-amino-2-hydroxyglutarate). The structure of the forward-inhibited enzyme (fiAnGDH) was also determined. The hexameric AnGDH had three open subunits at one side and three partially closed protomers at the other, a configuration not previously been reported. The AnGDH hexamers having subunits with different conformations indicated that its alpha-ketoglutarate-dependent homotropic cooperativity follows the Monod-Wyman-Changeux (MWC) model. Moreover, the position of the water attached to Asp154 and Gly153 defined the previously unresolved ammonium ion-binding pocket, and the binding site for the 2'-phosphate group of the coenzyme was also better defined by our structural data. Additional structural and mutagenesis experiments identified the residues essential for coenzyme recognition. This study reveals the structural features responsible for positioning alpha-ketoglutarate, NADPH, ammonium ion, and the reaction intermediates in the GDH active site.
		+
		+	Structural basis for the catalytic mechanism and alpha-ketoglutarate cooperativity of glutamate dehydrogenase.,Prakash P, Punekar NS, Bhaumik P J Biol Chem. 2018 Mar 14. pii: RA117.000149. doi: 10.1074/jbc.RA117.000149. PMID:29540480<ref>PMID:29540480</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5xvi" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: A. niger]]
	[[Category: Bhaumik, P]]		[[Category: Bhaumik, P]]
	[[Category: Prakash, P]]		[[Category: Prakash, P]]

OCA at 07:34, 21 March 2018

2018-03-21T07:34:38Z

←Older revision		Revision as of 07:34, 21 March 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5xvi is ~~ON HOLD until Paper Publication~~	+	==Crystal Structure of Aspergillus niger Apo- Glutamate Dehydrogenase==
-		+	<StructureSection load='5xvi' size='340' side='right' caption='[[5xvi]], [[Resolution\|resolution]] 2.80Å' scene=''>
-	~~Authors~~: ~~Prakash~~, P., ~~Punekar~~, N.S., ~~Bhaumik~~, P.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5xvi]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XVI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XVI FirstGlance]. <br>
-	~~Description: Crystal Structure of Aspergillus niger Apo-Glutamate Dehydrogenase~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=5xvi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xvi OCA], [http://pdbe.org/5xvi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xvi RCSB], [http://www.ebi.ac.uk/pdbsum/5xvi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xvi ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Bhaumik, P]]
	[[Category: Prakash, P]]		[[Category: Prakash, P]]
-	[[Category: Punekar, N.S]]	+	[[Category: Punekar, N S]]
-	[[Category: ~~Bhaumik, P~~]]	+	[[Category: 2-oxoglutarate]]
		+	[[Category: Allostery]]
		+	[[Category: Aspergillus]]
		+	[[Category: Dehydrogenase]]
		+	[[Category: Glutamate]]
		+	[[Category: Oxidoreductase]]

OCA at 05:06, 15 February 2018

2018-02-15T05:06:15Z

←Older revision		Revision as of 05:06, 15 February 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5xvi is ON HOLD	+	The entry 5xvi is ON HOLD until Paper Publication

	Authors: Prakash, P., Punekar, N.S., Bhaumik, P.		Authors: Prakash, P., Punekar, N.S., Bhaumik, P.
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	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Prakash, P]]		[[Category: Prakash, P]]
-	[[Category: Bhaumik, P]]
	[[Category: Punekar, N.S]]		[[Category: Punekar, N.S]]
		+	[[Category: Bhaumik, P]]

OCA at 05:29, 17 January 2018

2018-01-17T05:29:26Z

←Older revision		Revision as of 05:29, 17 January 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5xvi is ON HOLD ~~until Paper Publication~~	+	The entry 5xvi is ON HOLD

	Authors: Prakash, P., Punekar, N.S., Bhaumik, P.		Authors: Prakash, P., Punekar, N.S., Bhaumik, P.

OCA: Protected "5xvi" [edit=sysop:move=sysop]

2017-09-27T15:49:40Z

Protected "5xvi" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:49, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5xvi is ON HOLD until Paper Publication Authors: Prakash, P., Punekar, N.S., Bhaumik, P. Description: Crystal Structure of Aspergillus niger Apo-Gl...

2017-09-27T15:49:39Z

New page: '''Unreleased structure''' The entry 5xvi is ON HOLD until Paper Publication Authors: Prakash, P., Punekar, N.S., Bhaumik, P. Description: Crystal Structure of Aspergillus niger Apo-Gl...

New page

'''Unreleased structure'''

The entry 5xvi is ON HOLD until Paper Publication

Authors: Prakash, P., Punekar, N.S., Bhaumik, P.

Description: Crystal Structure of Aspergillus niger Apo-Glutamate Dehydrogenase
[[Category: Unreleased Structures]]
[[Category: Prakash, P]]
[[Category: Bhaumik, P]]
[[Category: Punekar, N.S]]