5d8n - Revision history

OCA at 08:44, 27 September 2023

OCA — Wed, 27 Sep 2023 08:44:11 GMT

←Older revision		Revision as of 08:44, 27 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5d8n]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Solanum_lycopersicum Solanum lycopersicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D8N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5D8N FirstGlance]. <br>		<table><tr><td colspan='2'>[[5d8n]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Solanum_lycopersicum Solanum lycopersicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D8N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5D8N FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.15Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=5d8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d8n OCA], [https://pdbe.org/5d8n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5d8n RCSB], [https://www.ebi.ac.uk/pdbsum/5d8n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5d8n 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=5d8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d8n OCA], [https://pdbe.org/5d8n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5d8n RCSB], [https://www.ebi.ac.uk/pdbsum/5d8n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5d8n ProSAT]</span></td></tr>
	</table>		</table>

OCA at 10:25, 21 June 2023

OCA — Wed, 21 Jun 2023 10:25:53 GMT

←Older revision		Revision as of 10:25, 21 June 2023
Line 3:		Line 3:
	<StructureSection load='5d8n' size='340' side='right'caption='[[5d8n]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='5d8n' size='340' side='right'caption='[[5d8n]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5d8n]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Lycopersicon_esculentum Lycopersicon esculentum~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D8N OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5D8N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5d8n]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Solanum_lycopersicum Solanum lycopersicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D8N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5D8N FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LAPA1, LAP, LAP2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4081 Lycopersicon esculentum])</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=5d8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d8n OCA], [https://pdbe.org/5d8n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5d8n RCSB], [https://www.ebi.ac.uk/pdbsum/5d8n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5d8n ProSAT]</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=5d8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d8n OCA], [~~http~~://pdbe.org/5d8n PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5d8n RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5d8n PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5d8n ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/AMPL1_SOLLC AMPL1_SOLLC]] Presumably involved in the processing and regular turnover of intracellular proteins.	+	[https://www.uniprot.org/uniprot/AMPL1_SOLLC AMPL1_SOLLC] Presumably involved in the processing and regular turnover of intracellular proteins.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 27:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lycopersicon esculentum~~]]	+	[[Category: Solanum lycopersicum]]
-	[[Category: DuPrez~~, K T~~]]	+	[[Category: DuPrez KT]]
-	[[Category: Fan, L]]	+	[[Category: Fan L]]
-	[[Category: Scranton~~, M A~~]]	+	[[Category: Scranton MA]]
-	[[Category: Walling~~, L L]]~~	+	[[Category: Walling LL]]
-	~~[[Category: Hydrolase~~]]	+

OCA at 07:30, 27 November 2019

OCA — Wed, 27 Nov 2019 07:30:13 GMT

←Older revision		Revision as of 07:30, 27 November 2019
Line 1:		Line 1:

	==Tomato leucine aminopeptidase mutant - K354E==		==Tomato leucine aminopeptidase mutant - K354E==
-	<StructureSection load='5d8n' size='340' side='right' caption='[[5d8n]], [[Resolution\|resolution]] 2.15Å' scene=''>	+	<StructureSection load='5d8n' size='340' side='right'caption='[[5d8n]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5d8n]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Lycopersicon_esculentum Lycopersicon esculentum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D8N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5D8N FirstGlance]. <br>		<table><tr><td colspan='2'>[[5d8n]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Lycopersicon_esculentum Lycopersicon esculentum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D8N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5D8N FirstGlance]. <br>
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5d8n" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5d8n" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Aminopeptidase 3D structures\|Aminopeptidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Lycopersicon esculentum]]		[[Category: Lycopersicon esculentum]]
	[[Category: DuPrez, K T]]		[[Category: DuPrez, K T]]

OCA at 06:18, 1 November 2017

OCA — Wed, 01 Nov 2017 06:18:02 GMT

←Older revision		Revision as of 06:18, 1 November 2017
Line 3:		Line 3:
	<StructureSection load='5d8n' size='340' side='right' caption='[[5d8n]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='5d8n' size='340' side='right' caption='[[5d8n]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5d8n]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D8N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5D8N FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5d8n]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Lycopersicon_esculentum Lycopersicon esculentum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D8N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5D8N FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=5d8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d8n OCA], [http://pdbe.org/5d8n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5d8n RCSB], [http://www.ebi.ac.uk/pdbsum/5d8n PDBsum]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">LAPA1, LAP, LAP2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4081 Lycopersicon esculentum])</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=5d8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d8n OCA], [http://pdbe.org/5d8n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5d8n RCSB], [http://www.ebi.ac.uk/pdbsum/5d8n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5d8n ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/AMPL1_SOLLC AMPL1_SOLLC]] Presumably involved in the processing and regular turnover of intracellular proteins.		[[http://www.uniprot.org/uniprot/AMPL1_SOLLC AMPL1_SOLLC]] Presumably involved in the processing and regular turnover of intracellular proteins.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Tomato plants express acidic leucine aminopeptidase (LAP-A) in response to various environmental stressors. LAP-A not only functions as a peptidase for diverse peptide substrates, but also displays chaperone activity. A K354E mutation has been shown to abolish the peptidase activity but to enhance the chaperone activity of LAP-A. To better understand this moonlighting function of LAP-A, the crystal structure of the K354E mutant was determined at 2.15 A resolution. The structure reveals that the K354E mutation destabilizes an active-site loop and causes significant rearrangement of active-site residues, leading to loss of the catalytic metal-ion coordination required for the peptidase activity. Although the mutant was crystallized in the same hexameric form as wild-type LAP-A, gel-filtration chromatography revealed an apparent shift from the hexamer to lower-order oligomers for the K354E mutant, showing a mixture of monomers to trimers in solution. In addition, surface-probing assays indicated that the K354E mutant has more accessible hydrophobic areas than wild-type LAP-A. Consistently, computational thermodynamic estimations of the interfaces between LAP-A monomers suggest that increased exposure of hydrophobic surfaces occurs upon hexamer breakdown. These results suggest that the K354E mutation disrupts the active-site loop, which also contributes to the hexameric assembly, and destabilizes the hexamers, resulting in much greater hydrophobic areas accessible for efficient chaperone activity than in the wild-type LAP-A.
		+
		+	Structural insights into chaperone-activity enhancement by a K354E mutation in tomato acidic leucine aminopeptidase.,DuPrez KT, Scranton MA, Walling LL, Fan L Acta Crystallogr D Struct Biol. 2016 May;72(Pt 5):694-702. doi:, 10.1107/S205979831600509X. Epub 2016 Apr 26. PMID:27139632<ref>PMID:27139632</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5d8n" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Lycopersicon esculentum]]
	[[Category: DuPrez, K T]]		[[Category: DuPrez, K T]]
	[[Category: Fan, L]]		[[Category: Fan, L]]

OCA at 17:05, 15 May 2016

OCA — Sun, 15 May 2016 17:05:26 GMT

←Older revision		Revision as of 17:05, 15 May 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5d8n ~~is ON HOLD until Paper Publication~~	+	==Tomato leucine aminopeptidase mutant - K354E==
-		+	<StructureSection load='5d8n' size='340' side='right' caption='[[5d8n]], [[Resolution\|resolution]] 2.15Å' scene=''>
-	~~Authors~~: ~~DuPrez, K~~.T., ~~Scranton~~, M.A., ~~Walling, L~~.L., ~~Fan~~, L.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5d8n]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D8N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5D8N FirstGlance]. <br>
-	~~Description: Tomato leucine aminopeptidase mutant -K354E~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<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=5d8n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d8n OCA], [http://pdbe.org/5d8n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5d8n RCSB], [http://www.ebi.ac.uk/pdbsum/5d8n PDBsum]</span></td></tr>
-	[[Category: ~~Duprez~~, K.T]]	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/AMPL1_SOLLC AMPL1_SOLLC]] Presumably involved in the processing and regular turnover of intracellular proteins.
		+	__TOC__
		+	</StructureSection>
		+	[[Category: DuPrez, K T]]
	[[Category: Fan, L]]		[[Category: Fan, L]]
-	[[Category: Walling, L.L]]	+	[[Category: Scranton, M A]]
-	[[Category: ~~Scranton, M.A~~]]	+	[[Category: Walling, L L]]
		+	[[Category: Hydrolase]]

OCA at 11:00, 16 December 2015

OCA — Wed, 16 Dec 2015 11:00:16 GMT

←Older revision		Revision as of 11:00, 16 December 2015
Line 7:		Line 7:
	Description: Tomato leucine aminopeptidase mutant -K354E		Description: Tomato leucine aminopeptidase mutant -K354E
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Duprez, K.T]]
	[[Category: Fan, L]]		[[Category: Fan, L]]
	[[Category: Walling, L.L]]		[[Category: Walling, L.L]]
	[[Category: Scranton, M.A]]		[[Category: Scranton, M.A]]
-	[[Category: Duprez, K.T]]

OCA at 09:55, 9 September 2015

OCA — Wed, 09 Sep 2015 09:55:57 GMT

←Older revision		Revision as of 09:55, 9 September 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5d8n is ON HOLD	+	The entry 5d8n is ON HOLD until Paper Publication

	Authors: DuPrez, K.T., Scranton, M.A., Walling, L.L., Fan, L.		Authors: DuPrez, K.T., Scranton, M.A., Walling, L.L., Fan, L.

OCA: Protected "5d8n" [edit=sysop:move=sysop]

OCA — Wed, 26 Aug 2015 12:34:00 GMT

Protected "5d8n" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:34, 26 August 2015

OCA: New page: '''Unreleased structure''' The entry 5d8n is ON HOLD Authors: DuPrez, K.T., Scranton, M.A., Walling, L.L., Fan, L. Description: Tomato leucine aminopeptidase mutant -K354E [[Category: ...

OCA — Wed, 26 Aug 2015 12:33:57 GMT

New page: '''Unreleased structure''' The entry 5d8n is ON HOLD Authors: DuPrez, K.T., Scranton, M.A., Walling, L.L., Fan, L. Description: Tomato leucine aminopeptidase mutant -K354E [[Category: ...

New page

'''Unreleased structure'''

The entry 5d8n is ON HOLD

Authors: DuPrez, K.T., Scranton, M.A., Walling, L.L., Fan, L.

Description: Tomato leucine aminopeptidase mutant -K354E
[[Category: Unreleased Structures]]
[[Category: Fan, L]]
[[Category: Walling, L.L]]
[[Category: Scranton, M.A]]
[[Category: Duprez, K.T]]