5ne9 - Revision history

OCA at 12:50, 15 November 2023

OCA — Wed, 15 Nov 2023 12:50:55 GMT

←Older revision		Revision as of 12:50, 15 November 2023
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	<StructureSection load='5ne9' size='340' side='right'caption='[[5ne9]], [[Resolution\|resolution]] 2.37Å' scene=''>		<StructureSection load='5ne9' size='340' side='right'caption='[[5ne9]], [[Resolution\|resolution]] 2.37Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ne9]] 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=5NE9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5NE9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ne9]] 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=5NE9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5NE9 FirstGlance]. <br>
-	</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>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.374Å</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=5ne9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ne9 OCA], [https://pdbe.org/5ne9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ne9 RCSB], [https://www.ebi.ac.uk/pdbsum/5ne9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ne9 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=5ne9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ne9 OCA], [~~http~~://pdbe.org/5ne9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ne9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ne9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ne9 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 ==
-	~~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 form functionally active complexes made of 12 subunits. Their assembly process appears to be regulated by their metal ion cofactors triggering a dimer-dodecamer transition. Upon metal ion binding, several structural modifications occur in the active site and at the interaction interface, shaping dimers to promote the self-assembly. To observe such modifications, stable oligomers must be isolated prior to structural study. Reported here is a method that allows the purification of stable dodecamers and dimers of TmPep1050, an M42 aminopeptidase of T. maritima, and their structure determination by X-ray crystallography. Dimers were prepared from dodecamers by removing metal ions with a chelating agent. Without their cofactor, dodecamers became less stable and were fully dissociated upon heating. The oligomeric structures were solved by the straightforward molecular replacement approach. To illustrate the methodology, the structure of a TmPep1050 variant, totally impaired in metal ion binding, is presented showing no further breakdown of dimers to monomers.

-	~~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>	+	X-Ray Crystallography to Study the Oligomeric State Transition of the Thermotoga maritima M42 Aminopeptidase TmPep1050.,Dutoit R, Brandt N, Van Elder D, Droogmans L J Vis Exp. 2020 May 13;(159). doi: 10.3791/61288. PMID:32478746<ref>PMID:32478746</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>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Leucyl aminopeptidase]]~~	+	[[Category: Thermotoga maritima MSB8]]
-	~~[[Category: Thema~~]]	+	[[Category: Dutoit R]]
-	[[Category: Dutoit, R]]	+
-	~~[[Category: Leucylaminopeptidase]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: M42 family]]~~	+
-	~~[[Category: Tetrahedral structure~~]]	+

OCA at 12:23, 25 December 2019

OCA — Wed, 25 Dec 2019 12:23:44 GMT

←Older revision		Revision as of 12:23, 25 December 2019
Line 1:		Line 1:

	==Crystal structure of H60A H307A mutant of Thermotoga maritima TmPEP1050 aminopeptidase==		==Crystal structure of H60A H307A mutant of Thermotoga maritima TmPEP1050 aminopeptidase==
-	<StructureSection load='5ne9' size='340' side='right' caption='[[5ne9]], [[Resolution\|resolution]] 2.37Å' scene=''>	+	<StructureSection load='5ne9' size='340' side='right'caption='[[5ne9]], [[Resolution\|resolution]] 2.37Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ne9]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NE9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NE9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ne9]] 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=5NE9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NE9 FirstGlance]. <br>
-	</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>	+	</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='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=5ne9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ne9 OCA], [http://pdbe.org/5ne9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ne9 RCSB], [http://www.ebi.ac.uk/pdbsum/5ne9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ne9 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=5ne9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ne9 OCA], [http://pdbe.org/5ne9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ne9 RCSB], [http://www.ebi.ac.uk/pdbsum/5ne9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ne9 ProSAT]</span></td></tr>
	</table>		</table>
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	</div>		</div>
	<div class="pdbe-citations 5ne9" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ne9" 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: Dutoit, R]]		[[Category: Dutoit, R]]
	[[Category: Leucylaminopeptidase]]		[[Category: Leucylaminopeptidase]]

OCA at 05:18, 16 May 2018

OCA — Wed, 16 May 2018 05:18:33 GMT

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

-	~~The entry~~ 5ne9 is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of H60A H307A mutant of Thermotoga maritima TmPEP1050 aminopeptidase==
		+	<StructureSection load='5ne9' size='340' side='right' caption='[[5ne9]], [[Resolution\|resolution]] 2.37Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5ne9]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5NE9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5NE9 FirstGlance]. <br>
		+	</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=5ne9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ne9 OCA], [http://pdbe.org/5ne9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ne9 RCSB], [http://www.ebi.ac.uk/pdbsum/5ne9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ne9 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.	+	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 ~~H60A H307A mutant~~ of ~~Thermotoga maritima TmPEP1050 aminopeptidase~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5ne9" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Leucyl aminopeptidase]]
	[[Category: Dutoit, R]]		[[Category: Dutoit, R]]
		+	[[Category: Leucylaminopeptidase]]
		+	[[Category: Lyase]]
		+	[[Category: M42 family]]
		+	[[Category: Tetrahedral structure]]

OCA at 09:57, 5 April 2017

OCA — Wed, 05 Apr 2017 09:57:03 GMT

←Older revision		Revision as of 09:57, 5 April 2017
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5ne9 is ON HOLD	+	The entry 5ne9 is ON HOLD until Paper Publication

	Authors: Dutoit, R.		Authors: Dutoit, R.

OCA: Protected "5ne9" [edit=sysop:move=sysop]

OCA — Wed, 15 Mar 2017 17:29:27 GMT

Protected "5ne9" [edit=sysop:move=sysop]

←Older revision

Revision as of 17:29, 15 March 2017

OCA: New page: '''Unreleased structure''' The entry 5ne9 is ON HOLD Authors: Dutoit, R. Description: Crystal structure of H60A H307A mutant of Thermotoga maritima TmPEP1050 aminopeptidase [[Category:...

OCA — Wed, 15 Mar 2017 17:29:26 GMT

New page: '''Unreleased structure''' The entry 5ne9 is ON HOLD Authors: Dutoit, R. Description: Crystal structure of H60A H307A mutant of Thermotoga maritima TmPEP1050 aminopeptidase [[Category:...

New page

'''Unreleased structure'''

The entry 5ne9 is ON HOLD

Authors: Dutoit, R.

Description: Crystal structure of H60A H307A mutant of Thermotoga maritima TmPEP1050 aminopeptidase
[[Category: Unreleased Structures]]
[[Category: Dutoit, R]]