5ne6 - Revision history

OCA at 12:50, 15 November 2023

OCA — Wed, 15 Nov 2023 12:50:35 GMT

←Older revision		Revision as of 12:50, 15 November 2023
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	<StructureSection load='5ne6' size='340' side='right'caption='[[5ne6]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='5ne6' size='340' side='right'caption='[[5ne6]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ne6]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Thema Thema~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NE6 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5NE6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ne6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima_MSB8 Thermotoga maritima MSB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NE6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5NE6 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~~></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]] 2Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>TM_1050, Tmari_1054 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~243274 THEMA])</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></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[http://en.wikipedia.org/wiki/Leucyl_aminopeptidase Leucyl aminopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.11.1 3.4.11.1]~~ </~~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=5ne6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ne6 OCA], [https://pdbe.org/5ne6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ne6 RCSB], [https://www.ebi.ac.uk/pdbsum/5ne6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ne6 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=5ne6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ne6 OCA], [~~http~~://pdbe.org/5ne6 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ne6 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ne6 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ne6 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q9X0E0_THEMA Q9X0E0_THEMA]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Leucyl aminopeptidase]]~~	+	[[Category: Thermotoga maritima MSB8]]
-	~~[[Category: Thema~~]]	+	[[Category: Bauvois C]]
-	[[Category: Bauvois, C]]	+	[[Category: Brandt N]]
-	[[Category: Brandt, N]]	+	[[Category: Dutoit R]]
-	[[Category: Dutoit, R]]	+
-	~~[[Category: Aminopeptidase]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Metal ion binding]]~~	+
-	~~[[Category: Peptidase m42]]~~	+
-	~~[[Category: Tetrahedral structure~~]]	+

OCA at 16:02, 29 January 2020

OCA — Wed, 29 Jan 2020 16:02:33 GMT

←Older revision		Revision as of 16:02, 29 January 2020
Line 1:		Line 1:

	==Crystal structure of dimeric TmPep1050 aminopeptidase==		==Crystal structure of dimeric TmPep1050 aminopeptidase==
-	<StructureSection load='5ne6' size='340' side='right' caption='[[5ne6]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='5ne6' size='340' side='right'caption='[[5ne6]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ne6]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NE6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NE6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ne6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thema Thema]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NE6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NE6 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></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></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TM_1050, Tmari_1054 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243274 THEMA])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Leucyl_aminopeptidase Leucyl aminopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.11.1 3.4.11.1] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Leucyl_aminopeptidase Leucyl aminopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.11.1 3.4.11.1] </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=5ne6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ne6 OCA], [http://pdbe.org/5ne6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ne6 RCSB], [http://www.ebi.ac.uk/pdbsum/5ne6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ne6 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=5ne6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ne6 OCA], [http://pdbe.org/5ne6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ne6 RCSB], [http://www.ebi.ac.uk/pdbsum/5ne6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ne6 ProSAT]</span></td></tr>
Line 10:		Line 11:
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
-	~~Several aminopeptidases of the~~ M42 ~~family have been described as~~ tetrahedral-shaped ~~dodecameric (TET) aminopeptidases~~. ~~A current hypothesis suggests that these enzymes are involved, along with~~ the ~~tricorn peptidase, in degrading peptides produced~~ by the ~~proteasome~~. ~~Yet~~ the ~~M42 family remains ill defined, as some members have been annotated as cellulases because~~ of ~~their homology with CelM~~, ~~formerly described as an endoglucanase~~ of ~~Clostridium thermocellum~~. ~~Here we describe~~ the ~~catalytic functions and substrate profiles CelM and~~ of TmPep1050~~, the latter having been annotated as an endoglucanase~~ of Thermotoga maritima~~. Both enzymes were shown to catalyze hydrolysis of nonpolar aliphatic L-amino acid-pNA substrates~~, the ~~L-leucine derivative appearing as the best substrate~~. ~~No significant endoglucanase activity was measured, either for TmPep1050 or CelM. Addition~~ of ~~cobalt ions enhanced~~ the ~~activity of both enzymes significantly, while both~~ the ~~chelating agent EDTA~~ and ~~bestatin~~, ~~a specific inhibitor of metalloaminopeptidases~~, ~~proved inhibitory~~. ~~Our results strongly suggest~~ that ~~one should avoid annotating members of~~ the ~~M42 aminopeptidase family as cellulases~~. ~~In an updated assessment~~ of the ~~distribution of M42 aminopeptidases, we found TET aminopeptidases to be distributed widely amongst archaea~~ and ~~bacteria. We additionally observed that several phyla lack both TET and tricorn. This suggests that other complexes may act downstream from the proteasome~~.	+	The M42 aminopeptidases are dinuclear aminopeptidases displaying a peculiar tetrahedral-shaped structure with twelve subunits. Their quaternary structure results from the self-assembly of six dimers controlled by their divalent metal ion cofactors. The oligomeric state transition remains debated despite the structural characterization of several archaeal M42 aminopeptidases. The main bottleneck is the lack of dimer structures, hindering the understanding of structural changes occurring during the oligomerization process. We present the first dimer structure of an M42 aminopeptidase, TmPep1050 of Thermotoga maritima, along with the dodecamer structure. The comparison of both structures allows to describe how the metal ion cofactors modulate the active site fold and, subsequently, affect the interaction interface between dimers. A mutational study shows that the M1 site strictly controls dodecamer formation. The dodecamer structure of TmPep1050 also reveals that a part of the dimerization domain delimits the catalytic pocket and could participate in substrate binding.

-	~~Functional characterization~~ of ~~two~~ M42 ~~aminopeptidases erroneously annotated as cellulases~~.,Dutoit R, Brandt N, ~~Legrain C~~, ~~Bauvois C PLoS One~~. ~~2012;7(11)~~:~~e50639~~. doi: 10.~~1371~~/~~journal.pone~~.~~0050639~~. ~~Epub 2012 Nov 30~~. PMID:~~23226342~~<ref>PMID:~~23226342~~</ref>	+	How metal cofactors drive dimer-dodecamer transition of the M42 aminopeptidase TmPep1050 of Thermotoga maritima.,Dutoit R, Van Gompel T, Brandt N, Van Elder D, Van Dyck J, Sobott F, Droogmans L J Biol Chem. 2019 Oct 14. pii: RA119.009281. doi: 10.1074/jbc.RA119.009281. PMID:31611236<ref>PMID:31611236</ref>

	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 5ne6" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ne6" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Glucanase 3D structures\|Glucanase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Leucyl aminopeptidase]]		[[Category: Leucyl aminopeptidase]]
		+	[[Category: Thema]]
	[[Category: Bauvois, C]]		[[Category: Bauvois, C]]
	[[Category: Brandt, N]]		[[Category: Brandt, N]]

OCA at 05:18, 16 May 2018

OCA — Wed, 16 May 2018 05:18:17 GMT

←Older revision		Revision as of 05:18, 16 May 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ne6 is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of dimeric TmPep1050 aminopeptidase==
		+	<StructureSection load='5ne6' size='340' side='right' caption='[[5ne6]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5ne6]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NE6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NE6 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></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Leucyl_aminopeptidase Leucyl aminopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.11.1 3.4.11.1] </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=5ne6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ne6 OCA], [http://pdbe.org/5ne6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ne6 RCSB], [http://www.ebi.ac.uk/pdbsum/5ne6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ne6 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Several aminopeptidases of the M42 family have been described as tetrahedral-shaped dodecameric (TET) aminopeptidases. A current hypothesis suggests that these enzymes are involved, along with the tricorn peptidase, in degrading peptides produced by the proteasome. Yet the M42 family remains ill defined, as some members have been annotated as cellulases because of their homology with CelM, formerly described as an endoglucanase of Clostridium thermocellum. Here we describe the catalytic functions and substrate profiles CelM and of TmPep1050, the latter having been annotated as an endoglucanase of Thermotoga maritima. Both enzymes were shown to catalyze hydrolysis of nonpolar aliphatic L-amino acid-pNA substrates, the L-leucine derivative appearing as the best substrate. No significant endoglucanase activity was measured, either for TmPep1050 or CelM. Addition of cobalt ions enhanced the activity of both enzymes significantly, while both the chelating agent EDTA and bestatin, a specific inhibitor of metalloaminopeptidases, proved inhibitory. Our results strongly suggest that one should avoid annotating members of the M42 aminopeptidase family as cellulases. In an updated assessment of the distribution of M42 aminopeptidases, we found TET aminopeptidases to be distributed widely amongst archaea and bacteria. We additionally observed that several phyla lack both TET and tricorn. This suggests that other complexes may act downstream from the proteasome.

-	~~Authors: Dutoit~~, R., Brandt, N., ~~Bauvois~~, C.	+	Functional characterization of two M42 aminopeptidases erroneously annotated as cellulases.,Dutoit R, Brandt N, Legrain C, Bauvois C PLoS One. 2012;7(11):e50639. doi: 10.1371/journal.pone.0050639. Epub 2012 Nov 30. PMID:23226342<ref>PMID:23226342</ref>

-	~~Description: Crystal structure~~ of ~~dimeric TmPep1050~~ aminopeptidase	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5ne6" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Leucyl aminopeptidase]]
		+	[[Category: Bauvois, C]]
	[[Category: Brandt, N]]		[[Category: Brandt, N]]
	[[Category: Dutoit, R]]		[[Category: Dutoit, R]]
-	[[Category: ~~Bauvois, C~~]]	+	[[Category: Aminopeptidase]]
		+	[[Category: Lyase]]
		+	[[Category: Metal ion binding]]
		+	[[Category: Peptidase m42]]
		+	[[Category: Tetrahedral structure]]

OCA at 09:56, 5 April 2017

OCA — Wed, 05 Apr 2017 09:56:55 GMT

←Older revision		Revision as of 09:56, 5 April 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5ne6 is ON HOLD	+	The entry 5ne6 is ON HOLD until Paper Publication

	Authors: Dutoit, R., Brandt, N., Bauvois, C.		Authors: Dutoit, R., Brandt, N., Bauvois, C.

OCA: Protected "5ne6" [edit=sysop:move=sysop]

OCA — Wed, 15 Mar 2017 17:29:15 GMT

Protected "5ne6" [edit=sysop:move=sysop]

←Older revision

Revision as of 17:29, 15 March 2017

OCA: New page: '''Unreleased structure''' The entry 5ne6 is ON HOLD Authors: Dutoit, R., Brandt, N., Bauvois, C. Description: Crystal structure of dimeric TmPep1050 aminopeptidase [[Category: Unrelea...

OCA — Wed, 15 Mar 2017 17:29:14 GMT

New page: '''Unreleased structure''' The entry 5ne6 is ON HOLD Authors: Dutoit, R., Brandt, N., Bauvois, C. Description: Crystal structure of dimeric TmPep1050 aminopeptidase [[Category: Unrelea...

New page

'''Unreleased structure'''

The entry 5ne6 is ON HOLD

Authors: Dutoit, R., Brandt, N., Bauvois, C.

Description: Crystal structure of dimeric TmPep1050 aminopeptidase
[[Category: Unreleased Structures]]
[[Category: Brandt, N]]
[[Category: Dutoit, R]]
[[Category: Bauvois, C]]