2dc1 - Revision history

OCA at 13:47, 13 March 2024

OCA — Wed, 13 Mar 2024 13:47:13 GMT

←Older revision		Revision as of 13:47, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='2dc1' size='340' side='right'caption='[[2dc1]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='2dc1' size='340' side='right'caption='[[2dc1]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2dc1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Arcfl Arcfl~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DC1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DC1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2dc1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DC1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DC1 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CIT:CITRIC+ACID'>CIT</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]] 1.9Å</td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks~~'>~~[https:~~/~~/en.wikipedia.org/wiki/Aspartate_dehydrogenase Aspartate dehydrogenase]~~, ~~with EC number [https~~:~~//www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=1.4.1.21 1.4.1.21]~~ </~~span~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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=2dc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dc1 OCA], [https://pdbe.org/2dc1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dc1 RCSB], [https://www.ebi.ac.uk/pdbsum/2dc1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dc1 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=2dc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dc1 OCA], [https://pdbe.org/2dc1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dc1 RCSB], [https://www.ebi.ac.uk/pdbsum/2dc1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dc1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/ASPD_ARCFU ASPD_ARCFU]] Specifically catalyzes the NAD or NADP-dependent dehydrogenation of L-aspartate to iminoaspartate (By similarity).	+	[https://www.uniprot.org/uniprot/ASPD_ARCFU ASPD_ARCFU] Specifically catalyzes the NAD or NADP-dependent dehydrogenation of L-aspartate to iminoaspartate (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 20:		Line 20:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2dc1 ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2dc1 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The crystal structure of the highly thermostable L-aspartate dehydrogenase (L-aspDH; EC 1.4.1.21) from the hyperthermophilic archaeon Archaeoglobus fulgidus was determined in the presence of NAD and a substrate analog, citrate. The dimeric structure of A. fulgidus L-aspDH was refined at a resolution of 1.9 A with a crystallographic R-factor of 21.7% (R(free) = 22.6%). The structure indicates that each subunit consists of two domains separated by a deep cleft containing an active site. Structural comparison of the A. fulgidus L-aspDH/NAD/citrate ternary complex and the Thermotoga maritima L-aspDH/NAD binary complex showed that A. fulgidus L-aspDH assumes a closed conformation and that a large movement of the two loops takes place during substrate binding. Like T. maritima L-aspDH, the A. fulgidus enzyme is highly thermostable. But whereas a large number of inter- and intrasubunit ion pairs are responsible for the stability of A. fulgidus L-aspDH, a large number of inter- and intrasubunit aromatic pairs stabilize the T. maritima enzyme. Thus stabilization of these two L-aspDHs appears to be achieved in different ways. This is the first detailed description of substrate and coenzyme binding to L-aspDH and of the molecular basis of the high thermostability of a hyperthermophilic L-aspDH.
-
-	Crystal structure of archaeal highly thermostable L-aspartate dehydrogenase/NAD/citrate ternary complex.,Yoneda K, Sakuraba H, Tsuge H, Katunuma N, Ohshima T FEBS J. 2007 Aug;274(16):4315-25. Epub 2007 Jul 25. PMID:17651440<ref>PMID:17651440</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2dc1" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Arcfl]]~~	+	[[Category: Archaeoglobus fulgidus]]
-	~~[[Category: Aspartate dehydrogenase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ohshima, T]]	+	[[Category: Ohshima T]]
-	[[Category: Sakuraba, H]]	+	[[Category: Sakuraba H]]
-	[[Category: Tsuge, H]]	+	[[Category: Tsuge H]]
-	[[Category: Yoneda, K]]	+	[[Category: Yoneda K]]
-	~~[[Category: L-aspartate dehydrogenase]]~~	+
-	~~[[Category: Nad]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 10:29, 8 December 2021

OCA — Wed, 08 Dec 2021 10:29:32 GMT

←Older revision		Revision as of 10:29, 8 December 2021
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	<StructureSection load='2dc1' size='340' side='right'caption='[[2dc1]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='2dc1' size='340' side='right'caption='[[2dc1]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2dc1]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Arcfl Arcfl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DC1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2DC1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2dc1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Arcfl Arcfl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DC1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DC1 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Aspartate_dehydrogenase Aspartate dehydrogenase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.1.21 1.4.1.21] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Aspartate_dehydrogenase Aspartate dehydrogenase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.1.21 1.4.1.21] </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=2dc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dc1 OCA], [~~http~~://pdbe.org/2dc1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2dc1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2dc1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2dc1 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=2dc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dc1 OCA], [https://pdbe.org/2dc1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dc1 RCSB], [https://www.ebi.ac.uk/pdbsum/2dc1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dc1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/ASPD_ARCFU ASPD_ARCFU]] Specifically catalyzes the NAD or NADP-dependent dehydrogenation of L-aspartate to iminoaspartate (By similarity).	+	[[https://www.uniprot.org/uniprot/ASPD_ARCFU ASPD_ARCFU]] Specifically catalyzes the NAD or NADP-dependent dehydrogenation of L-aspartate to iminoaspartate (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 07:46, 4 March 2020

OCA — Wed, 04 Mar 2020 07:46:39 GMT

←Older revision		Revision as of 07:46, 4 March 2020
Line 1:		Line 1:

	==Crystal Structure Of L-Aspartate Dehydrogenase From Hyperthermophilic Archaeon Archaeoglobus fulgidus==		==Crystal Structure Of L-Aspartate Dehydrogenase From Hyperthermophilic Archaeon Archaeoglobus fulgidus==
-	<StructureSection load='2dc1' size='340' side='right' caption='[[2dc1]], [[Resolution\|resolution]] 1.90Å' scene=''>	+	<StructureSection load='2dc1' size='340' side='right'caption='[[2dc1]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dc1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arcfl Arcfl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DC1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DC1 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dc1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arcfl Arcfl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DC1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DC1 FirstGlance]. <br>
Line 35:		Line 35:
	[[Category: Arcfl]]		[[Category: Arcfl]]
	[[Category: Aspartate dehydrogenase]]		[[Category: Aspartate dehydrogenase]]
		+	[[Category: Large Structures]]
	[[Category: Ohshima, T]]		[[Category: Ohshima, T]]
	[[Category: Sakuraba, H]]		[[Category: Sakuraba, H]]

OCA at 06:32, 30 May 2018

OCA — Wed, 30 May 2018 06:32:58 GMT

←Older revision		Revision as of 06:32, 30 May 2018
Line 1:		Line 1:
		+
	==Crystal Structure Of L-Aspartate Dehydrogenase From Hyperthermophilic Archaeon Archaeoglobus fulgidus==		==Crystal Structure Of L-Aspartate Dehydrogenase From Hyperthermophilic Archaeon Archaeoglobus fulgidus==
	<StructureSection load='2dc1' size='340' side='right' caption='[[2dc1]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='2dc1' size='340' side='right' caption='[[2dc1]], [[Resolution\|resolution]] 1.90Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aspartate_dehydrogenase Aspartate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.1.21 1.4.1.21] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aspartate_dehydrogenase Aspartate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.1.21 1.4.1.21] </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=2dc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dc1 OCA], [http://pdbe.org/2dc1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dc1 RCSB], [http://www.ebi.ac.uk/pdbsum/2dc1 PDBsum]</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=2dc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dc1 OCA], [http://pdbe.org/2dc1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dc1 RCSB], [http://www.ebi.ac.uk/pdbsum/2dc1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2dc1 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 13:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dc/2dc1_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dc/2dc1_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 18:35, 8 February 2016

OCA — Mon, 08 Feb 2016 18:35:25 GMT

←Older revision		Revision as of 18:35, 8 February 2016
Line 17:		Line 17:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2dc1 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 14:18, 10 September 2015

OCA — Thu, 10 Sep 2015 14:18:00 GMT

←Older revision		Revision as of 14:18, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2dc1' size='340' side='right' caption='[[2dc1]], [[Resolution\|resolution]] 1.90Å' scene=''>		<StructureSection load='2dc1' size='340' side='right' caption='[[2dc1]], [[Resolution\|resolution]] 1.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2dc1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Archaeoglobus_fulgidus Archaeoglobus fulgidus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DC1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DC1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2dc1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Arcfl Arcfl]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DC1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DC1 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aspartate_dehydrogenase Aspartate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.1.21 1.4.1.21] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aspartate_dehydrogenase Aspartate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.1.21 1.4.1.21] </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=2dc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dc1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dc1 RCSB], [http://www.ebi.ac.uk/pdbsum/2dc1 PDBsum]</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=2dc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dc1 OCA], [http://pdbe.org/2dc1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dc1 RCSB], [http://www.ebi.ac.uk/pdbsum/2dc1 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 27:		Line 27:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 2dc1" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Archaeoglobus fulgidus~~]]	+	[[Category: Arcfl]]
	[[Category: Aspartate dehydrogenase]]		[[Category: Aspartate dehydrogenase]]
	[[Category: Ohshima, T]]		[[Category: Ohshima, T]]

OCA at 01:20, 25 December 2014

OCA — Thu, 25 Dec 2014 01:20:55 GMT

←Older revision		Revision as of 01:20, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dc1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DC1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DC1 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dc1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DC1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DC1 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aspartate_dehydrogenase Aspartate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.1.21 1.4.1.21] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aspartate_dehydrogenase Aspartate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.1.21 1.4.1.21] </span></td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2dc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dc1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dc1 RCSB], [http://www.ebi.ac.uk/pdbsum/2dc1 PDBsum]</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=2dc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dc1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dc1 RCSB], [http://www.ebi.ac.uk/pdbsum/2dc1 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ASPD_ARCFU ASPD_ARCFU]] Specifically catalyzes the NAD or NADP-dependent dehydrogenation of L-aspartate to iminoaspartate (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 33:
	[[Category: Archaeoglobus fulgidus]]		[[Category: Archaeoglobus fulgidus]]
	[[Category: Aspartate dehydrogenase]]		[[Category: Aspartate dehydrogenase]]
-	[[Category: Ohshima, T.]]	+	[[Category: Ohshima, T]]
-	[[Category: Sakuraba, H.]]	+	[[Category: Sakuraba, H]]
-	[[Category: Tsuge, H.]]	+	[[Category: Tsuge, H]]
-	[[Category: Yoneda, K.]]	+	[[Category: Yoneda, K]]
	[[Category: L-aspartate dehydrogenase]]		[[Category: L-aspartate dehydrogenase]]
	[[Category: Nad]]		[[Category: Nad]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 01:06, 30 September 2014

OCA — Tue, 30 Sep 2014 01:06:17 GMT

←Older revision		Revision as of 01:06, 30 September 2014
Line 1:		Line 1:
-	[[~~Image~~:2dc1.~~png\|left~~\|200px]]	+	==Crystal Structure Of L-Aspartate Dehydrogenase From Hyperthermophilic Archaeon Archaeoglobus fulgidus==
		+	<StructureSection load='2dc1' size='340' side='right' caption='[[2dc1]], [[Resolution\|resolution]] 1.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2dc1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DC1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DC1 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene><br>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aspartate_dehydrogenase Aspartate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.1.21 1.4.1.21] </span></td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2dc1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dc1 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dc1 RCSB], [http://www.ebi.ac.uk/pdbsum/2dc1 PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dc/2dc1_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The crystal structure of the highly thermostable L-aspartate dehydrogenase (L-aspDH; EC 1.4.1.21) from the hyperthermophilic archaeon Archaeoglobus fulgidus was determined in the presence of NAD and a substrate analog, citrate. The dimeric structure of A. fulgidus L-aspDH was refined at a resolution of 1.9 A with a crystallographic R-factor of 21.7% (R(free) = 22.6%). The structure indicates that each subunit consists of two domains separated by a deep cleft containing an active site. Structural comparison of the A. fulgidus L-aspDH/NAD/citrate ternary complex and the Thermotoga maritima L-aspDH/NAD binary complex showed that A. fulgidus L-aspDH assumes a closed conformation and that a large movement of the two loops takes place during substrate binding. Like T. maritima L-aspDH, the A. fulgidus enzyme is highly thermostable. But whereas a large number of inter- and intrasubunit ion pairs are responsible for the stability of A. fulgidus L-aspDH, a large number of inter- and intrasubunit aromatic pairs stabilize the T. maritima enzyme. Thus stabilization of these two L-aspDHs appears to be achieved in different ways. This is the first detailed description of substrate and coenzyme binding to L-aspDH and of the molecular basis of the high thermostability of a hyperthermophilic L-aspDH.

-	~~{{STRUCTURE_2dc1\| PDB=2dc1 \| SCENE= }}~~	+	Crystal structure of archaeal highly thermostable L-aspartate dehydrogenase/NAD/citrate ternary complex.,Yoneda K, Sakuraba H, Tsuge H, Katunuma N, Ohshima T FEBS J. 2007 Aug;274(16):4315-25. Epub 2007 Jul 25. PMID:17651440<ref>PMID:17651440</ref>

-	~~===Crystal Structure Of L-Aspartate Dehydrogenase~~ From ~~Hyperthermophilic Archaeon Archaeoglobus fulgidus===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17651440}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2dc1]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2DC1 OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:017651440<~~/~~ref~~><~~ref group="xtra">PMID:016407195</ref><references group="xtra"~~/>	+
	[[Category: Archaeoglobus fulgidus]]		[[Category: Archaeoglobus fulgidus]]
	[[Category: Aspartate dehydrogenase]]		[[Category: Aspartate dehydrogenase]]

OCA: Protected "2dc1" [edit=sysop:move=sysop]

OCA — Sun, 06 Jan 2013 10:22:50 GMT

Protected "2dc1" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:22, 6 January 2013

OCA at 10:22, 6 January 2013

OCA — Sun, 06 Jan 2013 10:22:48 GMT

←Older revision		Revision as of 10:22, 6 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2dc1.png\|left\|200px]]		[[Image:2dc1.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2dc1", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_2dc1\| PDB=2dc1 \| SCENE= }}		{{STRUCTURE_2dc1\| PDB=2dc1 \| SCENE= }}

	===Crystal Structure Of L-Aspartate Dehydrogenase From Hyperthermophilic Archaeon Archaeoglobus fulgidus===		===Crystal Structure Of L-Aspartate Dehydrogenase From Hyperthermophilic Archaeon Archaeoglobus fulgidus===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17651440}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 17651440 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_17651440}}		{{ABSTRACT_PUBMED_17651440}}

	==About this Structure==		==About this Structure==
-	~~2DC1~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DC1 OCA].	+	[[2dc1]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DC1 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17651440~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017651440</ref><ref group="xtra">PMID:016407195</ref><references group="xtra"/>
	[[Category: Archaeoglobus fulgidus]]		[[Category: Archaeoglobus fulgidus]]
	[[Category: Aspartate dehydrogenase]]		[[Category: Aspartate dehydrogenase]]
Line 33:		Line 21:
	[[Category: Nad]]		[[Category: Nad]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 01:44:20 2009''