6ysa - Revision history

OCA at 10:53, 15 November 2023

OCA — Wed, 15 Nov 2023 10:53:54 GMT

←Older revision		Revision as of 10:53, 15 November 2023
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	<StructureSection load='6ysa' size='340' side='right'caption='[[6ysa]], [[Resolution\|resolution]] 2.01Å' scene=''>		<StructureSection load='6ysa' size='340' side='right'caption='[[6ysa]], [[Resolution\|resolution]] 2.01Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ysa]] is a 12 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Arath Arath~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YSA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6YSA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ysa]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YSA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YSA 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=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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]] 2.01Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~SNN~~:~~L-3-AMINOSUCCINIMIDE~~'>~~SNN~~</scene><~~/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=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=SNN:L-3-AMINOSUCCINIMIDE'>SNN</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">bVPE~~, ~~At1g62710, F23N19.7 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])~~<~~/td></tr>~~	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6ysa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ysa OCA], [https://pdbe.org/6ysa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ysa RCSB], [https://www.ebi.ac.uk/pdbsum/6ysa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ysa ProSAT]</span></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Legumain Legumain], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.22.34 3.4.22.34]~~ </~~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=6ysa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ysa OCA], [~~http~~://pdbe.org/6ysa PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6ysa RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6ysa PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6ysa ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/VPEB_ARATH VPEB_ARATH]] Asparagine-specific endopeptidase involved in the processing of vacuolar seed protein precursors into the mature forms (By similarity). Probably involved in post-translational proteolysis of seed storage proteins in the protein storage vacuole of developing seeds (PubMed:12417707, PubMed:14688293).[UniProtKB:P49043]<ref>PMID:12417707</ref> <ref>PMID:14688293</ref>	+	[https://www.uniprot.org/uniprot/VPEB_ARATH VPEB_ARATH] Asparagine-specific endopeptidase involved in the processing of vacuolar seed protein precursors into the mature forms (By similarity). Probably involved in post-translational proteolysis of seed storage proteins in the protein storage vacuole of developing seeds (PubMed:12417707, PubMed:14688293).[UniProtKB:P49043]<ref>PMID:12417707</ref> <ref>PMID:14688293</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Arath~~]]	+	[[Category: Arabidopsis thaliana]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Legumain]]~~	+	[[Category: Brandstetter H]]
-	[[Category: Brandstetter, H]]	+	[[Category: Dall E]]
-	[[Category: Dall, E]]	+	[[Category: Zauner FB]]
-	[[Category: Zauner~~, F B]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: Proenzyme]]~~	+
-	~~[[Category: Protease]]~~	+
-	~~[[Category: Vacuolar processing enzyme]]~~	+
-	~~[[Category: Vpe~~]]	+

OCA at 10:09, 12 August 2020

OCA — Wed, 12 Aug 2020 10:09:12 GMT

←Older revision		Revision as of 10:09, 12 August 2020
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	==Crystal structure of Arabidopsis thaliana legumain isoform beta in zymogen state==		==Crystal structure of Arabidopsis thaliana legumain isoform beta in zymogen state==
-	<StructureSection load='6ysa' size='340' side='right'caption='[[6ysa]]' scene=''>	+	<StructureSection load='6ysa' size='340' side='right'caption='[[6ysa]], [[Resolution\|resolution]] 2.01Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YSA OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6YSA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ysa]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YSA OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6YSA FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6ysa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ysa OCA], [http://pdbe.org/6ysa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ysa RCSB], [http://www.ebi.ac.uk/pdbsum/6ysa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ysa ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=SNN:L-3-AMINOSUCCINIMIDE'>SNN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">bVPE, At1g62710, F23N19.7 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Legumain Legumain], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.22.34 3.4.22.34] </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=6ysa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ysa OCA], [http://pdbe.org/6ysa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ysa RCSB], [http://www.ebi.ac.uk/pdbsum/6ysa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ysa ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/VPEB_ARATH VPEB_ARATH]] Asparagine-specific endopeptidase involved in the processing of vacuolar seed protein precursors into the mature forms (By similarity). Probably involved in post-translational proteolysis of seed storage proteins in the protein storage vacuole of developing seeds (PubMed:12417707, PubMed:14688293).[UniProtKB:P49043]<ref>PMID:12417707</ref> <ref>PMID:14688293</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The vacuolar cysteine protease legumain plays important functions in seed maturation and plant programmed cell death. Because of their dual protease and ligase activity, plant legumains have become of particular biotechnological interest e.g. for the synthesis of cyclic peptides for drug design or for protein engineering. However, the molecular mechanisms behind their dual protease and ligase activities are still poorly understood, limiting their applications. Here we present the crystal structure of Arabidopsis thaliana legumain isoform beta (AtLEGbeta) in its zymogen state. Combining structural and biochemical experiments, we show for the first time that plant legumains encode distinct, isoform-specific activation mechanisms. While the autocatalytic activation of isoform gamma (AtLEGgamma) is controlled by the latency-conferring dimer state, the activation of the monomeric AtLEGbeta is concentration independent. Additionally, in AtLEGbeta the plant-characteristic two-chain intermediate state is stabilized by hydrophobic rather than ionic interactions as in AtLEGgamma, resulting in significantly different pH-stability profiles. The crystal structure of AtLEGbeta reveiled unrestricted non-prime substrate binding pockets, consistent with the broad substrate specificity as determined by degradomic assays. Further to its protease activity, we show that AtLEGbeta exhibits a true peptide ligase activity. While cleavage-dependent transpeptidase activity has been reported for other plant legumains, AtLEGbeta is the first example of a plant legumain capable of linking free termini. The discovery of these isoform specific differences will allow to identify and rationally design efficient ligases with application in biotechnology and drug development.
		+
		+	Structural and functional studies of Arabidopsis thaliana legumain beta reveal isoform specific mechanisms of activation and substrate recognition.,Dall E, Zauner FB, Soh WT, Demir F, Dahms SO, Cabrele C, Huesgen PF, Brandstetter H J Biol Chem. 2020 Jul 21. pii: RA120.014478. doi: 10.1074/jbc.RA120.014478. PMID:32719006<ref>PMID:32719006</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6ysa" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Arath]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Brandstetter H]]	+	[[Category: Legumain]]
-	[[Category: Dall E]]	+	[[Category: Brandstetter, H]]
-	[[Category: Zauner FB]]	+	[[Category: Dall, E]]
		+	[[Category: Zauner, F B]]
		+	[[Category: Hydrolase]]
		+	[[Category: Ligase]]
		+	[[Category: Proenzyme]]
		+	[[Category: Protease]]
		+	[[Category: Vacuolar processing enzyme]]
		+	[[Category: Vpe]]

OCA at 11:11, 29 July 2020

OCA — Wed, 29 Jul 2020 11:11:45 GMT

←Older revision		Revision as of 11:11, 29 July 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6ysa is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of Arabidopsis thaliana legumain isoform beta in zymogen state==
-		+	<StructureSection load='6ysa' size='340' side='right'caption='[[6ysa]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YSA OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6YSA FirstGlance]. <br>
-	~~Description~~:	+	</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=6ysa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ysa OCA], [http://pdbe.org/6ysa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ysa RCSB], [http://www.ebi.ac.uk/pdbsum/6ysa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ysa ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Brandstetter H]]
		+	[[Category: Dall E]]
		+	[[Category: Zauner FB]]

OCA at 04:38, 6 May 2020

OCA — Wed, 06 May 2020 04:38:10 GMT

←Older revision		Revision as of 04:38, 6 May 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6ysa is ON HOLD	+	The entry 6ysa is ON HOLD until Paper Publication

	Authors:		Authors:

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

OCA — Wed, 29 Apr 2020 05:29:06 GMT

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

←Older revision

Revision as of 05:29, 29 April 2020

OCA: New page: '''Unreleased structure''' The entry 6ysa is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 29 Apr 2020 05:29:05 GMT

New page: '''Unreleased structure''' The entry 6ysa is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6ysa is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]