6dhk - Revision history

OCA at 14:34, 13 March 2024

OCA — Wed, 13 Mar 2024 14:34:27 GMT

←Older revision		Revision as of 14:34, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='6dhk' size='340' side='right'caption='[[6dhk]], [[Resolution\|resolution]] 3.50Å' scene=''>		<StructureSection load='6dhk' size='340' side='right'caption='[[6dhk]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dhk]] is a 12 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DHK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6DHK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dhk]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DHK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DHK FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ADP:ADENOSINE~~-5~~-DIPHOSPHATE'>ADP</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]] 3.5Å</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 Glutamate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.1.2 1.4.1.2]~~ </~~span~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></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=6dhk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dhk OCA], [~~http~~://pdbe.org/6dhk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6dhk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6dhk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6dhk 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=6dhk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dhk OCA], [https://pdbe.org/6dhk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dhk RCSB], [https://www.ebi.ac.uk/pdbsum/6dhk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dhk ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/DHE3_BOVIN DHE3_BOVIN] May be involved in learning and memory reactions by increasing the turnover of the excitatory neurotransmitter glutamate (By similarity).<ref>PMID:14659072</ref>
-	~~Glutamate dehydrogenase (GDH) is found in all organisms and catalyzes the reversible oxidative deamination of L-glutamate to 2-oxoglutarate~~. ~~Unlike GDH from bacteria, mammalian GDH exhibits negative cooperativity with respect to coenzyme, activation by ADP, and inhibition by GTP~~. Presented here are the structures of apo bovine GDH, bovine GDH complexed with ADP, and the R463A mutant form of human GDH (huGDH) that is insensitive to ADP activation. In the absence of active site ligands, the catalytic cleft is in ~~the open conformation,~~ and the hexamers form long polymers in the crystal cell with more interactions than found in the abortive complex crystals. This is consistent with the fact that ADP promotes aggregation in solution. ADP is shown to bind to the second, inhibitory, NADH site yet causes activation. The beta-phosphates of the bound ADP interact with R459 (R463 in huGDH) on the pivot helix. The structure of the ADP-resistant, R463A mutant of human GDH is identical to native GDH with the exception of the truncated side chain on the pivot helix. Together, these results strongly suggest that ADP activates by ~~facilitating~~ the ~~opening~~ of the catalytic cleft. From alignment of GDH from various sources, it is likely that the antenna evolved in the protista prior to the formation of purine regulatory sites. This suggests that there was some selective advantage of the antenna itself and that animals evolved new functions for GDH through the addition of allosteric regulation.	+
-		+
-	~~Structural studies on ADP activation of mammalian~~ glutamate ~~dehydrogenase and the evolution of regulation.,Banerjee S, Schmidt T, Fang J, Stanley CA, Smith TJ Biochemistry. 2003 Apr 1;42~~(12)~~:3446-56~~. ~~PMID:12653548~~<ref>PMID:~~12653548~~</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6dhk" style="background-color:#fffaf0;"></div~~>	+

	==See Also==		==See Also==
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	</StructureSection>		</StructureSection>
	[[Category: Bos taurus]]		[[Category: Bos taurus]]
-	[[Category: Glutamate dehydrogenase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Smith~~, T J]]~~	+	[[Category: Smith TJ]]
-	~~[[Category: Adp]]~~	+
-	~~[[Category: Dehydrogenase]]~~	+
-	~~[[Category: Glutamate]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 09:05, 11 November 2020

OCA — Wed, 11 Nov 2020 09:05:18 GMT

←Older revision		Revision as of 09:05, 11 November 2020
Line 1:		Line 1:

	==Bovine glutamate dehydrogenase complexed with ADP==		==Bovine glutamate dehydrogenase complexed with ADP==
-	<StructureSection load='6dhk' size='340' side='right' caption='[[6dhk]], [[Resolution\|resolution]] 3.50Å' scene=''>	+	<StructureSection load='6dhk' size='340' side='right'caption='[[6dhk]], [[Resolution\|resolution]] 3.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dhk]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DHK OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6DHK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dhk]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DHK OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6DHK 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></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></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 Glutamate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.1.2 1.4.1.2] </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 Glutamate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.1.2 1.4.1.2] </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=6dhk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dhk OCA], [http://pdbe.org/6dhk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dhk RCSB], [http://www.ebi.ac.uk/pdbsum/6dhk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dhk 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=6dhk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dhk OCA], [http://pdbe.org/6dhk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dhk RCSB], [http://www.ebi.ac.uk/pdbsum/6dhk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dhk ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 17:		Line 17:
	</div>		</div>
	<div class="pdbe-citations 6dhk" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6dhk" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Glutamate dehydrogenase 3D structures\|Glutamate dehydrogenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 23:		Line 26:
	[[Category: Bos taurus]]		[[Category: Bos taurus]]
	[[Category: Glutamate dehydrogenase]]		[[Category: Glutamate dehydrogenase]]
		+	[[Category: Large Structures]]
	[[Category: Smith, T J]]		[[Category: Smith, T J]]
	[[Category: Adp]]		[[Category: Adp]]

OCA at 07:19, 25 July 2018

OCA — Wed, 25 Jul 2018 07:19:46 GMT

←Older revision		Revision as of 07:19, 25 July 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6dhk is ~~ON HOLD~~	+	==Bovine glutamate dehydrogenase complexed with ADP==
		+	<StructureSection load='6dhk' size='340' side='right' caption='[[6dhk]], [[Resolution\|resolution]] 3.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6dhk]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DHK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DHK 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></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 Glutamate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.1.2 1.4.1.2] </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=6dhk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dhk OCA], [http://pdbe.org/6dhk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dhk RCSB], [http://www.ebi.ac.uk/pdbsum/6dhk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dhk ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Glutamate dehydrogenase (GDH) is found in all organisms and catalyzes the reversible oxidative deamination of L-glutamate to 2-oxoglutarate. Unlike GDH from bacteria, mammalian GDH exhibits negative cooperativity with respect to coenzyme, activation by ADP, and inhibition by GTP. Presented here are the structures of apo bovine GDH, bovine GDH complexed with ADP, and the R463A mutant form of human GDH (huGDH) that is insensitive to ADP activation. In the absence of active site ligands, the catalytic cleft is in the open conformation, and the hexamers form long polymers in the crystal cell with more interactions than found in the abortive complex crystals. This is consistent with the fact that ADP promotes aggregation in solution. ADP is shown to bind to the second, inhibitory, NADH site yet causes activation. The beta-phosphates of the bound ADP interact with R459 (R463 in huGDH) on the pivot helix. The structure of the ADP-resistant, R463A mutant of human GDH is identical to native GDH with the exception of the truncated side chain on the pivot helix. Together, these results strongly suggest that ADP activates by facilitating the opening of the catalytic cleft. From alignment of GDH from various sources, it is likely that the antenna evolved in the protista prior to the formation of purine regulatory sites. This suggests that there was some selective advantage of the antenna itself and that animals evolved new functions for GDH through the addition of allosteric regulation.

-	~~Authors: Smith~~, T.J.	+	Structural studies on ADP activation of mammalian glutamate dehydrogenase and the evolution of regulation.,Banerjee S, Schmidt T, Fang J, Stanley CA, Smith TJ Biochemistry. 2003 Apr 1;42(12):3446-56. PMID:12653548<ref>PMID:12653548</ref>

-	~~Description~~: ~~Bovine glutamate dehydrogenase complexed with ADP~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Smith, T.J]]	+	<div class="pdbe-citations 6dhk" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Bos taurus]]
		+	[[Category: Glutamate dehydrogenase]]
		+	[[Category: Smith, T J]]
		+	[[Category: Adp]]
		+	[[Category: Dehydrogenase]]
		+	[[Category: Glutamate]]
		+	[[Category: Oxidoreductase]]

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

OCA — Wed, 30 May 2018 04:08:00 GMT

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

←Older revision

Revision as of 04:08, 30 May 2018

OCA: New page: '''Unreleased structure''' The entry 6dhk is ON HOLD Authors: Smith, T.J. Description: Bovine glutamate dehydrogenase complexed with ADP Category: Unreleased Structures [[Category:...

OCA — Wed, 30 May 2018 04:07:59 GMT

New page: '''Unreleased structure''' The entry 6dhk is ON HOLD Authors: Smith, T.J. Description: Bovine glutamate dehydrogenase complexed with ADP Category: Unreleased Structures [[Category:...

New page

'''Unreleased structure'''

The entry 6dhk is ON HOLD

Authors: Smith, T.J.

Description: Bovine glutamate dehydrogenase complexed with ADP
[[Category: Unreleased Structures]]
[[Category: Smith, T.J]]