6dhq - Revision history

OCA at 14:34, 13 March 2024

OCA — Wed, 13 Mar 2024 14:34:32 GMT

←Older revision		Revision as of 14:34, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='6dhq' size='340' side='right'caption='[[6dhq]], [[Resolution\|resolution]] 2.30Å' scene=''>		<StructureSection load='6dhq' size='340' side='right'caption='[[6dhq]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dhq]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3qmu 3qmu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DHQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6DHQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dhq]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3qmu 3qmu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DHQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DHQ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLU:GLUTAMIC+ACID'>GLU</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</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]] 2.3Å</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=GLU:GLUTAMIC+ACID'>GLU</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</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=6dhq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dhq OCA], [~~http~~://pdbe.org/6dhq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6dhq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6dhq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6dhq 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=6dhq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dhq OCA], [https://pdbe.org/6dhq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dhq RCSB], [https://www.ebi.ac.uk/pdbsum/6dhq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dhq 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 is found in all organisms and catalyses the oxidative deamination of l-glutamate to 2-oxoglutarate~~. ~~However, only animal GDH utilizes both NAD(H) or NADP(H) with comparable efficacy and exhibits a complex pattern of allosteric inhibition by a wide variety of small molecules~~. The major allosteric inhibitors are GTP and NADH and the two main allosteric activators are ADP and NAD(+). The structures presented here have refined and modified the previous structural model of allosteric regulation inferred from the original boGDH.NADH.GLU.GTP complex. The boGDH.NAD(+).alpha-KG complex structure clearly demonstrates that the second coenzyme-binding site lies directly under the "pivot helix" of the NAD(+) binding domain. In this complex, phosphates are observed to occupy the inhibitory GTP site and may be ~~responsible for the previously observed structural stabilization by polyanions. The boGDH.NADPH.GLU.GTP complex shows the location of the additional phosphate on the active site coenzyme molecule~~ and the GTP molecule bound to the GTP inhibitory site. As expected, since NADPH does not bind well to the second coenzyme site, no evidence of a bound molecule is observed at the second coenzyme site under the pivot helix. Therefore, these results suggest that the inhibitory GTP site is as previously identified. However, ADP, NAD(+), and NADH all bind under the pivot helix, but a second GTP molecule does not. Kinetic analysis of a hyperinsulinism/hyperammonemia mutant strongly suggests that ATP can inhibit the reaction by ~~binding to~~ the ~~GTP site. Finally, the fact that NADH, NAD(+), and ADP all bind to the same site requires a re-analysis~~ of the ~~previous models for NADH inhibition.~~	+
-		+
-	~~Structures of bovine~~ glutamate ~~dehydrogenase complexes elucidate the mechanism of purine regulation.,Smith TJ, Peterson PE, Schmidt T, Fang J, Stanley CA J Mol Biol. 2001 Mar 23;307~~(2)~~:707-20~~. ~~PMID:11254391~~<ref>PMID:~~11254391~~</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6dhq" 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: Bovine]]~~	+
-	~~[[Category: Dehydrogenase]]~~	+
-	~~[[Category: Glutamate]]~~	+
-	~~[[Category: Gtp]]~~	+
-	~~[[Category: Nadph]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 09:05, 11 November 2020

OCA — Wed, 11 Nov 2020 09:05:26 GMT

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

	==Bovine glutamate dehydrogenase complexed with NADPH, glutamate, and GTP==		==Bovine glutamate dehydrogenase complexed with NADPH, glutamate, and GTP==
-	<StructureSection load='6dhq' size='340' side='right' caption='[[6dhq]], [[Resolution\|resolution]] 2.30Å' scene=''>	+	<StructureSection load='6dhq' size='340' side='right'caption='[[6dhq]], [[Resolution\|resolution]] 2.30Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dhq]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3qmu 3qmu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DHQ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6DHQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dhq]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3qmu 3qmu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DHQ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6DHQ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLU:GLUTAMIC+ACID'>GLU</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLU:GLUTAMIC+ACID'>GLU</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</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=6dhq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dhq OCA], [http://pdbe.org/6dhq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dhq RCSB], [http://www.ebi.ac.uk/pdbsum/6dhq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dhq 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=6dhq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dhq OCA], [http://pdbe.org/6dhq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dhq RCSB], [http://www.ebi.ac.uk/pdbsum/6dhq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dhq 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 6dhq" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6dhq" 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: Bovine]]		[[Category: Bovine]]

OCA at 07:05, 25 July 2018

OCA — Wed, 25 Jul 2018 07:05:48 GMT

←Older revision		Revision as of 07:05, 25 July 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The~~ entry 6dhq is ~~ON HOLD~~	+	==Bovine glutamate dehydrogenase complexed with NADPH, glutamate, and GTP==
		+	<StructureSection load='6dhq' size='340' side='right' caption='[[6dhq]], [[Resolution\|resolution]] 2.30Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6dhq]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=3qmu 3qmu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DHQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DHQ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLU:GLUTAMIC+ACID'>GLU</scene>, <scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</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=6dhq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dhq OCA], [http://pdbe.org/6dhq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dhq RCSB], [http://www.ebi.ac.uk/pdbsum/6dhq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dhq ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Glutamate dehydrogenase is found in all organisms and catalyses the oxidative deamination of l-glutamate to 2-oxoglutarate. However, only animal GDH utilizes both NAD(H) or NADP(H) with comparable efficacy and exhibits a complex pattern of allosteric inhibition by a wide variety of small molecules. The major allosteric inhibitors are GTP and NADH and the two main allosteric activators are ADP and NAD(+). The structures presented here have refined and modified the previous structural model of allosteric regulation inferred from the original boGDH.NADH.GLU.GTP complex. The boGDH.NAD(+).alpha-KG complex structure clearly demonstrates that the second coenzyme-binding site lies directly under the "pivot helix" of the NAD(+) binding domain. In this complex, phosphates are observed to occupy the inhibitory GTP site and may be responsible for the previously observed structural stabilization by polyanions. The boGDH.NADPH.GLU.GTP complex shows the location of the additional phosphate on the active site coenzyme molecule and the GTP molecule bound to the GTP inhibitory site. As expected, since NADPH does not bind well to the second coenzyme site, no evidence of a bound molecule is observed at the second coenzyme site under the pivot helix. Therefore, these results suggest that the inhibitory GTP site is as previously identified. However, ADP, NAD(+), and NADH all bind under the pivot helix, but a second GTP molecule does not. Kinetic analysis of a hyperinsulinism/hyperammonemia mutant strongly suggests that ATP can inhibit the reaction by binding to the GTP site. Finally, the fact that NADH, NAD(+), and ADP all bind to the same site requires a re-analysis of the previous models for NADH inhibition.

-	~~Authors:~~ Smith, T.J.	+	Structures of bovine glutamate dehydrogenase complexes elucidate the mechanism of purine regulation.,Smith TJ, Peterson PE, Schmidt T, Fang J, Stanley CA J Mol Biol. 2001 Mar 23;307(2):707-20. PMID:11254391<ref>PMID:11254391</ref>

-	~~Description: Bovine glutamate dehydrogenase complexed with NADPH~~, ~~glutamate, and GTP~~	+	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 6dhq" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Bos taurus]]
		+	[[Category: Glutamate dehydrogenase]]
		+	[[Category: Smith, T J]]
		+	[[Category: Bovine]]
		+	[[Category: Dehydrogenase]]
		+	[[Category: Glutamate]]
		+	[[Category: Gtp]]
		+	[[Category: Nadph]]
		+	[[Category: Oxidoreductase]]

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

OCA — Wed, 30 May 2018 04:08:19 GMT

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

←Older revision

Revision as of 04:08, 30 May 2018

OCA: New page: '''Unreleased structure''' The entry 6dhq is ON HOLD Authors: Smith, T.J. Description: Bovine glutamate dehydrogenase complexed with NADPH, glutamate, and GTP [[Category: Unreleased St...

OCA — Wed, 30 May 2018 04:08:17 GMT

New page: '''Unreleased structure''' The entry 6dhq is ON HOLD Authors: Smith, T.J. Description: Bovine glutamate dehydrogenase complexed with NADPH, glutamate, and GTP [[Category: Unreleased St...

New page

'''Unreleased structure'''

The entry 6dhq is ON HOLD

Authors: Smith, T.J.

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