6nw5 - Revision history

OCA at 11:51, 24 January 2024

OCA — Wed, 24 Jan 2024 11:51:42 GMT

←Older revision		Revision as of 11:51, 24 January 2024
Line 3:		Line 3:
	<StructureSection load='6nw5' size='340' side='right'caption='[[6nw5]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='6nw5' size='340' side='right'caption='[[6nw5]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6nw5]] is a 4 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=6NW5 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6NW5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6nw5]] is a 4 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=6NW5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6NW5 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=OH:HYDROXIDE+ION'>OH</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 1.7Å</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TM_1050, THEMA_09110, 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=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=OH:HYDROXIDE+ION'>OH</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=6nw5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nw5 OCA], [~~http~~://pdbe.org/6nw5 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6nw5 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6nw5 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6nw5 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=6nw5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nw5 OCA], [https://pdbe.org/6nw5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6nw5 RCSB], [https://www.ebi.ac.uk/pdbsum/6nw5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6nw5 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 17:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6nw5" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6nw5" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Aminopeptidase 3D structures\|Aminopeptidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 22:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Thema~~]]	+	[[Category: Thermotoga maritima MSB8]]
-	[[Category: Dutoit, R]]	+	[[Category: Dutoit R]]
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: M42 aminopeptidase]]~~	+
-	~~[[Category: Metal ion binding]]~~	+
-	~~[[Category: Mh clan]]~~	+
-	~~[[Category: Tet-aminopeptidase~~]]	+

OCA at 17:38, 20 November 2019

OCA — Wed, 20 Nov 2019 17:38:51 GMT

←Older revision		Revision as of 17:38, 20 November 2019
Line 3:		Line 3:
	<StructureSection load='6nw5' size='340' side='right'caption='[[6nw5]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='6nw5' size='340' side='right'caption='[[6nw5]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6nw5]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NW5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NW5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6nw5]] is a 4 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=6NW5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NW5 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=OH:HYDROXIDE+ION'>OH</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=OH:HYDROXIDE+ION'>OH</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TM_1050, THEMA_09110, Tmari_1054 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=243274 THEMA])</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=6nw5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nw5 OCA], [http://pdbe.org/6nw5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nw5 RCSB], [http://www.ebi.ac.uk/pdbsum/6nw5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nw5 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=6nw5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nw5 OCA], [http://pdbe.org/6nw5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nw5 RCSB], [http://www.ebi.ac.uk/pdbsum/6nw5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nw5 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	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.
		+
		+	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>
		+	</div>
		+	<div class="pdbe-citations 6nw5" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Thema]]
	[[Category: Dutoit, R]]		[[Category: Dutoit, R]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 06:54, 23 October 2019

OCA — Wed, 23 Oct 2019 06:54:49 GMT

←Older revision		Revision as of 06:54, 23 October 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6nw5 is ON HOLD~~	+	==Crystal structure of TmPep1050 aminopeptidase with its metal cofactors==
-		+	<StructureSection load='6nw5' size='340' side='right'caption='[[6nw5]], [[Resolution\|resolution]] 1.70Å' scene=''>
-	~~Authors: Dutoit, R.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6nw5]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6NW5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6NW5 FirstGlance]. <br>
-	~~Description:~~ Crystal structure of TmPep1050 aminopeptidase with its metal cofactors	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=OH:HYDROXIDE+ION'>OH</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=6nw5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6nw5 OCA], [http://pdbe.org/6nw5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6nw5 RCSB], [http://www.ebi.ac.uk/pdbsum/6nw5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6nw5 ProSAT]</span></td></tr>
		+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Dutoit, R]]		[[Category: Dutoit, R]]
		+	[[Category: Hydrolase]]
		+	[[Category: M42 aminopeptidase]]
		+	[[Category: Metal ion binding]]
		+	[[Category: Mh clan]]
		+	[[Category: Tet-aminopeptidase]]

OCA: Protected "6nw5" [edit=sysop:move=sysop]

OCA — Wed, 13 Feb 2019 07:51:23 GMT

Protected "6nw5" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:51, 13 February 2019

OCA: New page: '''Unreleased structure''' The entry 6nw5 is ON HOLD Authors: Dutoit, R. Description: Crystal structure of TmPep1050 aminopeptidase with its metal cofactors [[Category: Unreleased Stru...

OCA — Wed, 13 Feb 2019 07:51:22 GMT

New page: '''Unreleased structure''' The entry 6nw5 is ON HOLD Authors: Dutoit, R. Description: Crystal structure of TmPep1050 aminopeptidase with its metal cofactors [[Category: Unreleased Stru...

New page

'''Unreleased structure'''

The entry 6nw5 is ON HOLD

Authors: Dutoit, R.

Description: Crystal structure of TmPep1050 aminopeptidase with its metal cofactors
[[Category: Unreleased Structures]]
[[Category: Dutoit, R]]