3r6v - Revision history

OCA at 12:12, 14 March 2024

OCA — Thu, 14 Mar 2024 12:12:56 GMT

←Older revision		Revision as of 12:12, 14 March 2024
Line 3:		Line 3:
	<StructureSection load='3r6v' size='340' side='right'caption='[[3r6v]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='3r6v' size='340' side='right'caption='[[3r6v]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3r6v]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_sp.~~_ym55~~-1 Bacillus sp. ~~ym55~~-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R6V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3R6V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3r6v]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_sp._YM55-1 Bacillus sp. YM55-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R6V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3R6V FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ASP:ASPARTIC+ACID'>ASP</scene>~~, ~~<scene name='pdbligand=CA:CALCIUM+ION'>CA</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]] 2.6Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>~~[[~~Related_structure~~\|~~Related:~~]]~~</b></td><td class="sblockDat"><div style='overflow: auto~~; ~~max-height: 3em;'>[[3r6q\|3r6q]], [[3r6y\|3r6y]]</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ASP:ASPARTIC+ACID'>ASP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>aspB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~96471 Bacillus sp. YM55-1])</td~~><~~/tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/Aspartate_ammonia-lyase Aspartate ammonia-lyase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.1 4.3.1.1]~~ </~~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=3r6v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r6v OCA], [https://pdbe.org/3r6v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3r6v RCSB], [https://www.ebi.ac.uk/pdbsum/3r6v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3r6v 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=3r6v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r6v OCA], [https://pdbe.org/3r6v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3r6v RCSB], [https://www.ebi.ac.uk/pdbsum/3r6v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3r6v ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/Q9LCC6_9BACI Q9LCC6_9BACI]
-	Aspartate ammonia lyases (or aspartases) catalyze the reversible deamination of l-aspartate into fumarate and ammonia. The lack of crystal structures of complexes with substrate, product, or substrate analogues so far precluded determination of their precise mechanism of catalysis. Here, we report crystal structures of AspB, the aspartase from Bacillus sp. YM55-1, in an unliganded state and in complex with l-aspartate at 2.4 and 2.6 A resolution, respectively. AspB forces the bound substrate to adopt a high-energy, enediolate-like conformation that is stabilized, in part, by an extensive network of hydrogen bonds between residues Thr101, Ser140, Thr141, and Ser319 and the substrate's beta-carboxylate group. Furthermore, substrate binding induces a large conformational change in the SS loop (residues G(317)SSIMPGKVN(326)) from an open conformation to one that closes over the active site. In the closed conformation, the strictly conserved SS loop residue Ser318 is at a suitable position to act as a catalytic base, abstracting the Cbeta proton of the substrate in the first step of the reaction mechanism. The catalytic importance of Ser318 was confirmed by site-directed mutagenesis. Site-directed mutagenesis of SS loop residues, combined with structural and kinetic analysis of a stable proteolytic AspB fragment, further suggests an important role for the small C-terminal domain of AspB in controlling the conformation of the SS loop and, hence, in regulating catalytic activity. Our results provide evidence supporting the notion that members of the aspartase/fumarase superfamily use a common catalytic mechanism involving general base-catalyzed formation of a stabilized enediolate intermediate.	+
-		+
-	~~Structural basis for the catalytic mechanism of aspartate ammonia lyase.,Fibriansah G, Veetil VP, Poelarends GJ, Thunnissen AM Biochemistry. 2011 Jul 12;50(27)~~:~~6053-62. Epub 2011 Jun 20. PMID:21661762<ref>PMID:21661762<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®~~/~~PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 3r6v" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	~~[[Category: Aspartate ammonia-lyase]]~~	+	[[Category: Bacillus sp. YM55-1]]
-	[[Category: Bacillus sp. ~~ym55~~-1]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Fibriansah, G]]	+	[[Category: Fibriansah G]]
-	[[Category: Poelarends~~, G J]]~~	+	[[Category: Poelarends GJ]]
-	~~[[Category: Thunnissen, A M.W H~~]]	+	[[Category: Puthan Veetil V]]
-	[[Category: Veetil, V ~~Puthan~~]]	+	[[Category: Thunnissen A-MWH]]
-	[[Category: ~~Aspartase]]~~	+
-	~~[[Category: Aspartate ammonia lyase]]~~	+
-	~~[[Category: Lyase~~]]	+

OCA at 05:51, 15 June 2022

OCA — Wed, 15 Jun 2022 05:51:36 GMT

←Older revision		Revision as of 05:51, 15 June 2022
Line 1:		Line 1:

	==Crystal structure of aspartase from Bacillus sp. YM55-1 with bound L-aspartate==		==Crystal structure of aspartase from Bacillus sp. YM55-1 with bound L-aspartate==
-	<StructureSection load='3r6v' size='340' side='right' caption='[[3r6v]], [[Resolution\|resolution]] 2.60Å' scene=''>	+	<StructureSection load='3r6v' size='340' side='right'caption='[[3r6v]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3r6v]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Bacillus_sp._ym55-1 Bacillus sp. ym55-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R6V OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3R6V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3r6v]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_sp._ym55-1 Bacillus sp. ym55-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R6V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3R6V FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ASP:ASPARTIC+ACID'>ASP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ASP:ASPARTIC+ACID'>ASP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3r6q\|3r6q]], [[3r6y\|3r6y]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3r6q\|3r6q]], [[3r6y\|3r6y]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aspB ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=96471 Bacillus sp. YM55-1])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aspB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=96471 Bacillus sp. YM55-1])</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Aspartate_ammonia-lyase Aspartate ammonia-lyase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.1 4.3.1.1] </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_ammonia-lyase Aspartate ammonia-lyase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.1 4.3.1.1] </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=3r6v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r6v OCA], [~~http~~://pdbe.org/3r6v PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3r6v RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3r6v PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3r6v 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=3r6v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r6v OCA], [https://pdbe.org/3r6v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3r6v RCSB], [https://www.ebi.ac.uk/pdbsum/3r6v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3r6v ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 25:		Line 25:
	[[Category: Aspartate ammonia-lyase]]		[[Category: Aspartate ammonia-lyase]]
	[[Category: Bacillus sp. ym55-1]]		[[Category: Bacillus sp. ym55-1]]
		+	[[Category: Large Structures]]
	[[Category: Fibriansah, G]]		[[Category: Fibriansah, G]]
	[[Category: Poelarends, G J]]		[[Category: Poelarends, G J]]

OCA at 15:57, 11 August 2016

OCA — Thu, 11 Aug 2016 15:57:07 GMT

←Older revision		Revision as of 15:57, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of aspartase from Bacillus sp. YM55-1 with bound L-aspartate==		==Crystal structure of aspartase from Bacillus sp. YM55-1 with bound L-aspartate==
	<StructureSection load='3r6v' size='340' side='right' caption='[[3r6v]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='3r6v' size='340' side='right' caption='[[3r6v]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3r6v]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_sp. Bacillus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R6V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3R6V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3r6v]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_sp._ym55-1 Bacillus sp. ym55-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R6V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3R6V FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ASP:ASPARTIC+ACID'>ASP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ASP:ASPARTIC+ACID'>ASP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3r6q\|3r6q]], [[3r6y\|3r6y]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3r6q\|3r6q]], [[3r6y\|3r6y]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aspB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~1409~~ Bacillus sp.])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aspB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=96471 Bacillus sp. YM55-1])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aspartate_ammonia-lyase Aspartate ammonia-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.1 4.3.1.1] </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_ammonia-lyase Aspartate ammonia-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.1 4.3.1.1] </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=3r6v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r6v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3r6v RCSB], [http://www.ebi.ac.uk/pdbsum/3r6v 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=3r6v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r6v OCA], [http://pdbe.org/3r6v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3r6v RCSB], [http://www.ebi.ac.uk/pdbsum/3r6v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3r6v ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 17:		Line 18:
	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 3r6v" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
Line 22:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Aspartate ammonia-lyase]]		[[Category: Aspartate ammonia-lyase]]
-	[[Category: Bacillus sp]]	+	[[Category: Bacillus sp. ym55-1]]
	[[Category: Fibriansah, G]]		[[Category: Fibriansah, G]]
	[[Category: Poelarends, G J]]		[[Category: Poelarends, G J]]

OCA at 09:11, 4 January 2015

OCA — Sun, 04 Jan 2015 09:11:40 GMT

←Older revision		Revision as of 09:11, 4 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3r6v]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_sp. Bacillus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R6V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3R6V FirstGlance]. <br>		<table><tr><td colspan='2'>[[3r6v]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_sp. Bacillus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R6V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3R6V FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ASP:ASPARTIC+ACID'>ASP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ASP:ASPARTIC+ACID'>ASP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3r6q\|3r6q]], [[3r6y\|3r6y]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3r6q\|3r6q]], [[3r6y\|3r6y]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aspB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1409 Bacillus sp.])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aspB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1409 Bacillus sp.])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aspartate_ammonia-lyase Aspartate ammonia-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.1 4.3.1.1] </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_ammonia-lyase Aspartate ammonia-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.1 4.3.1.1] </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=3r6v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r6v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3r6v RCSB], [http://www.ebi.ac.uk/pdbsum/3r6v 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=3r6v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r6v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3r6v RCSB], [http://www.ebi.ac.uk/pdbsum/3r6v PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 15:		Line 15:
	Structural basis for the catalytic mechanism of aspartate ammonia lyase.,Fibriansah G, Veetil VP, Poelarends GJ, Thunnissen AM Biochemistry. 2011 Jul 12;50(27):6053-62. Epub 2011 Jun 20. PMID:21661762<ref>PMID:21661762</ref>		Structural basis for the catalytic mechanism of aspartate ammonia lyase.,Fibriansah G, Veetil VP, Poelarends GJ, Thunnissen AM Biochemistry. 2011 Jul 12;50(27):6053-62. Epub 2011 Jun 20. PMID:21661762<ref>PMID:21661762</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, 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>
	== References ==		== References ==
Line 22:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Aspartate ammonia-lyase]]		[[Category: Aspartate ammonia-lyase]]
-	[[Category: Bacillus sp.]]	+	[[Category: Bacillus sp]]
-	[[Category: Fibriansah, G.]]	+	[[Category: Fibriansah, G]]
-	[[Category: Poelarends, G J.]]	+	[[Category: Poelarends, G J]]
-	[[Category: Thunnissen, A M.W H.]]	+	[[Category: Thunnissen, A M.W H]]
-	[[Category: Veetil, V Puthan.]]	+	[[Category: Veetil, V Puthan]]
	[[Category: Aspartase]]		[[Category: Aspartase]]
	[[Category: Aspartate ammonia lyase]]		[[Category: Aspartate ammonia lyase]]
	[[Category: Lyase]]		[[Category: Lyase]]

OCA at 04:42, 5 June 2014

OCA — Thu, 05 Jun 2014 04:42:18 GMT

←Older revision		Revision as of 04:42, 5 June 2014
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-	[[~~Image:~~3r6v.~~png~~\|~~left~~\|~~200px~~]]	+	==Crystal structure of aspartase from Bacillus sp. YM55-1 with bound L-aspartate==
		+	<StructureSection load='3r6v' size='340' side='right' caption='[[3r6v]], [[Resolution\|resolution]] 2.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3r6v]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_sp. Bacillus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R6V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3R6V FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ASP:ASPARTIC+ACID'>ASP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3r6q\|3r6q]], [[3r6y\|3r6y]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">aspB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1409 Bacillus sp.])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Aspartate_ammonia-lyase Aspartate ammonia-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.1 4.3.1.1] </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=3r6v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r6v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3r6v RCSB], [http://www.ebi.ac.uk/pdbsum/3r6v PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Aspartate ammonia lyases (or aspartases) catalyze the reversible deamination of l-aspartate into fumarate and ammonia. The lack of crystal structures of complexes with substrate, product, or substrate analogues so far precluded determination of their precise mechanism of catalysis. Here, we report crystal structures of AspB, the aspartase from Bacillus sp. YM55-1, in an unliganded state and in complex with l-aspartate at 2.4 and 2.6 A resolution, respectively. AspB forces the bound substrate to adopt a high-energy, enediolate-like conformation that is stabilized, in part, by an extensive network of hydrogen bonds between residues Thr101, Ser140, Thr141, and Ser319 and the substrate's beta-carboxylate group. Furthermore, substrate binding induces a large conformational change in the SS loop (residues G(317)SSIMPGKVN(326)) from an open conformation to one that closes over the active site. In the closed conformation, the strictly conserved SS loop residue Ser318 is at a suitable position to act as a catalytic base, abstracting the Cbeta proton of the substrate in the first step of the reaction mechanism. The catalytic importance of Ser318 was confirmed by site-directed mutagenesis. Site-directed mutagenesis of SS loop residues, combined with structural and kinetic analysis of a stable proteolytic AspB fragment, further suggests an important role for the small C-terminal domain of AspB in controlling the conformation of the SS loop and, hence, in regulating catalytic activity. Our results provide evidence supporting the notion that members of the aspartase/fumarase superfamily use a common catalytic mechanism involving general base-catalyzed formation of a stabilized enediolate intermediate.

-	~~<!--~~	+	Structural basis for the catalytic mechanism of aspartate ammonia lyase.,Fibriansah G, Veetil VP, Poelarends GJ, Thunnissen AM Biochemistry. 2011 Jul 12;50(27):6053-62. Epub 2011 Jun 20. PMID:21661762<ref>PMID:21661762</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_3r6v"~~, ~~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_3r6v\| PDB=3r6v \| SCENE= }}~~	+

-	~~===Crystal structure~~ of ~~aspartase from Bacillus sp. YM55-1 with bound L-aspartate===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_21661762}}, adds~~ the ~~Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 21661762 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_21661762}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3r6v]] is a 8 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Bacillus_sp. Bacillus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R6V OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:021661762<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Aspartate ammonia-lyase]]		[[Category: Aspartate ammonia-lyase]]
	[[Category: Bacillus sp.]]		[[Category: Bacillus sp.]]

OCA at 04:51, 10 August 2011

OCA — Wed, 10 Aug 2011 04:51:48 GMT

←Older revision		Revision as of 04:51, 10 August 2011
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-	[[Image:3r6v.~~jpg~~\|left\|200px]]	+	[[Image:3r6v.png\|left\|200px]]

	<!--		<!--

OCA at 07:29, 13 July 2011

OCA — Wed, 13 Jul 2011 07:29:29 GMT

←Older revision		Revision as of 07:29, 13 July 2011
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-	~~'''Unreleased structure'''~~	+	[[Image:3r6v.jpg\|left\|200px]]

-	The ~~entry 3r6v~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3r6v", 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_3r6v\| PDB=3r6v \| SCENE= }}

-	~~Authors: Fibriansah, G., Puthan Veetil, V., Poelarends, G.J., Thunnissen, A~~.-~~M.W.H.~~	+	===Crystal structure of aspartase from Bacillus sp. YM55-1 with bound L-aspartate===

-	~~Description~~: ~~Crystal~~ structure ~~of aspartase~~ from Bacillus sp. ~~YM55~~-~~1 with bound L~~-~~aspartate~~	+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_21661762}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 21661762 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_21661762}}
		+
		+	==About this Structure==
		+	[[3r6v]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_sp. Bacillus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R6V OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:021661762</ref><references group="xtra"/>
		+	[[Category: Aspartate ammonia-lyase]]
		+	[[Category: Bacillus sp.]]
		+	[[Category: Fibriansah, G.]]
		+	[[Category: Poelarends, G J.]]
		+	[[Category: Thunnissen, A M.W H.]]
		+	[[Category: Veetil, V Puthan.]]
		+	[[Category: Aspartase]]
		+	[[Category: Aspartate ammonia lyase]]
		+	[[Category: Lyase]]

OCA at 08:39, 6 April 2011

OCA — Wed, 06 Apr 2011 08:39:28 GMT

←Older revision		Revision as of 08:39, 6 April 2011
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	The entry 3r6v is ON HOLD		The entry 3r6v is ON HOLD

-	Authors: Fibriansah, G., Puthan Veetil, V., Poelarends, G.J., Thunnissen, A-M.W.H.	+	Authors: Fibriansah, G., Puthan Veetil, V., Poelarends, G.J., Thunnissen, A.-M.W.H.

	Description: Crystal structure of aspartase from Bacillus sp. YM55-1 with bound L-aspartate		Description: Crystal structure of aspartase from Bacillus sp. YM55-1 with bound L-aspartate

OCA: Protected "3r6v" [edit=sysop:move=sysop]

OCA — Wed, 30 Mar 2011 07:50:10 GMT

Protected "3r6v" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:50, 30 March 2011

OCA: New page: '''Unreleased structure''' The entry 3r6v is ON HOLD Authors: Fibriansah, G., Puthan Veetil, V., Poelarends, G.J., Thunnissen, A-M.W.H. Description: Crystal structure of aspartase from...

OCA — Wed, 30 Mar 2011 07:50:09 GMT

New page: '''Unreleased structure''' The entry 3r6v is ON HOLD Authors: Fibriansah, G., Puthan Veetil, V., Poelarends, G.J., Thunnissen, A-M.W.H. Description: Crystal structure of aspartase from...

New page

'''Unreleased structure'''

The entry 3r6v is ON HOLD

Authors: Fibriansah, G., Puthan Veetil, V., Poelarends, G.J., Thunnissen, A-M.W.H.

Description: Crystal structure of aspartase from Bacillus sp. YM55-1 with bound L-aspartate