6yei - Revision history

OCA at 13:25, 24 January 2024

OCA — Wed, 24 Jan 2024 13:25:12 GMT

←Older revision		Revision as of 13:25, 24 January 2024
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	<StructureSection load='6yei' size='340' side='right'caption='[[6yei]], [[Resolution\|resolution]] 2.02Å' scene=''>		<StructureSection load='6yei' size='340' side='right'caption='[[6yei]], [[Resolution\|resolution]] 2.02Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6yei]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Arath Arath~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YEI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6YEI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6yei]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YEI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YEI FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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]] 2.02Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6yeh\|6yeh]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GDH1, At5g18170, MRG7.13 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</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=6yei FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yei OCA], [https://pdbe.org/6yei PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yei RCSB], [https://www.ebi.ac.uk/pdbsum/6yei PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yei ProSAT]</span></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glutamate_dehydrogenase_(NAD(P)(+)) Glutamate dehydrogenase (NAD(P)(+))], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.1.3 1.4.1.3] </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=6yei FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yei OCA], [~~http~~://pdbe.org/6yei PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6yei RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6yei PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6yei ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/DHE1_ARATH DHE1_ARATH]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6yei" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6yei" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Glutamate dehydrogenase 3D structures\|Glutamate dehydrogenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Arath~~]]	+	[[Category: Arabidopsis thaliana]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Grzechowiak, M]]	+	[[Category: Grzechowiak M]]
-	[[Category: Jaskolski, M]]	+	[[Category: Jaskolski M]]
-	[[Category: Ruszkowski, M]]	+	[[Category: Ruszkowski M]]
-	~~[[Category: 2-oxoglutarate]]~~	+
-	~~[[Category: Amino acid metabolism]]~~	+
-	~~[[Category: Glutamate dehydrogenase]]~~	+
-	~~[[Category: Nad]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 11:48, 22 July 2020

OCA — Wed, 22 Jul 2020 11:48:24 GMT

←Older revision		Revision as of 11:48, 22 July 2020
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	==Arabidopsis thaliana glutamate dehydrogenase isoform 1 in complex with NAD==		==Arabidopsis thaliana glutamate dehydrogenase isoform 1 in complex with NAD==
-	<StructureSection load='6yei' size='340' side='right'caption='[[6yei]]' scene=''>	+	<StructureSection load='6yei' size='340' side='right'caption='[[6yei]], [[Resolution\|resolution]] 2.02Å' 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=6YEI OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6YEI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6yei]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YEI OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6YEI FirstGlance]. <br>
-	</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=6yei FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yei OCA], [http://pdbe.org/6yei PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6yei RCSB], [http://www.ebi.ac.uk/pdbsum/6yei PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6yei 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=AKG:2-OXOGLUTARIC+ACID'>AKG</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6yeh\|6yeh]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">GDH1, At5g18170, MRG7.13 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glutamate_dehydrogenase_(NAD(P)(+)) Glutamate dehydrogenase (NAD(P)(+))], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.1.3 1.4.1.3] </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=6yei FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yei OCA], [http://pdbe.org/6yei PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6yei RCSB], [http://www.ebi.ac.uk/pdbsum/6yei PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6yei ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Glutamate dehydrogenase (GDH) releases ammonia in a reversible NAD(P)(+)-dependent oxidative deamination of glutamate that yields 2-oxoglutarate (2OG). In current perception, GDH contributes to Glu homeostasis and plays a significant role at the junction of carbon and nitrogen assimilation pathways. GDHs are members of a superfamily of ELFV (Glu/Leu/Phe/Val) amino acid dehydrogenases and are subdivided into three subclasses, based on coenzyme specificity: NAD(+)-specific, NAD(+)/NADP(+) dual-specific, and NADP(+)-specific. We determined in this work that the mitochondrial AtGDH1 isozyme from A. thaliana is NAD(+)-specific. Altogether, A. thaliana expresses three GDH isozymes (AtGDH1-3) targeted to mitochondria, of which AtGDH2 has an extra EF-hand motif and is stimulated by calcium. Our enzymatic assays of AtGDH1 established that its sensitivity to calcium is negligible. In vivo the AtGDH1-3 enzymes form homo- and heterohexamers of varied composition. We solved the crystal structure of recombinant AtGDH1 in the apo-form and in complex with NAD(+) at 2.59 and 2.03 A resolution, respectively. We demonstrate also that both in the apo form and in 1:1 complex with NAD(+), it forms D 3-symmetric homohexamers. A subunit of AtGDH1 consists of domain I, which is involved in hexamer formation and substrate binding, and of domain II which binds coenzyme. Most of the subunits in our crystal structures, including those in NAD(+) complex, are in open conformation, with domain II forming a large (albeit variable) angle with domain I. One of the subunits of the AtGDH1-NAD(+) hexamer contains a serendipitous 2OG molecule in the active site, causing a dramatic ( approximately 25 degrees ) closure of the domains. We provide convincing evidence that the N-terminal peptide preceding domain I is a mitochondrial targeting signal, with a predicted cleavage site for mitochondrial processing peptidase (MPP) at Leu17-Leu18 that is followed by an unexpected potassium coordination site (Ser27, Ile30). We also identified several MPD [(+/-)-2-methyl-2,4-pentanediol] binding sites with conserved sequence. Although AtGDH1 is insensitive to MPD in our assays, the observation of druggable sites opens a potential for non-competitive herbicide design.
		+
		+	Structural Studies of Glutamate Dehydrogenase (Isoform 1) From Arabidopsis thaliana, an Important Enzyme at the Branch-Point Between Carbon and Nitrogen Metabolism.,Grzechowiak M, Sliwiak J, Jaskolski M, Ruszkowski M Front Plant Sci. 2020 Jun 5;11:754. doi: 10.3389/fpls.2020.00754. eCollection, 2020. PMID:32655590<ref>PMID:32655590</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6yei" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Arath]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Grzechowiak M]]	+	[[Category: Grzechowiak, M]]
-	[[Category: Jaskolski M]]	+	[[Category: Jaskolski, M]]
-	[[Category: Ruszkowski M]]	+	[[Category: Ruszkowski, M]]
		+	[[Category: 2-oxoglutarate]]
		+	[[Category: Amino acid metabolism]]
		+	[[Category: Glutamate dehydrogenase]]
		+	[[Category: Nad]]
		+	[[Category: Oxidoreductase]]

OCA at 05:52, 20 May 2020

OCA — Wed, 20 May 2020 05:52:52 GMT

←Older revision		Revision as of 05:52, 20 May 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6yei ~~is ON HOLD~~	+	==Arabidopsis thaliana glutamate dehydrogenase isoform 1 in complex with NAD==
-		+	<StructureSection load='6yei' size='340' side='right'caption='[[6yei]]' scene=''>
-	~~Authors~~: ~~Ruszkowski~~, M., ~~Grzechowiak~~, M., ~~Jaskolski~~, M.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YEI OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6YEI FirstGlance]. <br>
-	~~Description: Arabidopsis thaliana glutamate dehydrogenase isoform 1 in complex with NAD~~	+	</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=6yei FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yei OCA], [http://pdbe.org/6yei PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6yei RCSB], [http://www.ebi.ac.uk/pdbsum/6yei PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6yei ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Ruszkowski,~~ M]]	+	__TOC__
-	[[Category: ~~Grzechowiak,~~ M]]	+	</StructureSection>
-	[[Category: ~~Jaskolski,~~ M]]	+	[[Category: Large Structures]]
		+	[[Category: Grzechowiak M]]
		+	[[Category: Jaskolski M]]
		+	[[Category: Ruszkowski M]]

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

OCA — Wed, 01 Apr 2020 07:44:52 GMT

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

←Older revision

Revision as of 07:44, 1 April 2020

OCA: New page: '''Unreleased structure''' The entry 6yei is ON HOLD Authors: Ruszkowski, M., Grzechowiak, M., Jaskolski, M. Description: Arabidopsis thaliana glutamate dehydrogenase isoform 1 in comp...

OCA — Wed, 01 Apr 2020 07:44:50 GMT

New page: '''Unreleased structure''' The entry 6yei is ON HOLD Authors: Ruszkowski, M., Grzechowiak, M., Jaskolski, M. Description: Arabidopsis thaliana glutamate dehydrogenase isoform 1 in comp...

New page

'''Unreleased structure'''

The entry 6yei is ON HOLD

Authors: Ruszkowski, M., Grzechowiak, M., Jaskolski, M.

Description: Arabidopsis thaliana glutamate dehydrogenase isoform 1 in complex with NAD
[[Category: Unreleased Structures]]
[[Category: Ruszkowski, M]]
[[Category: Grzechowiak, M]]
[[Category: Jaskolski, M]]