6r7u - Revision history

OCA at 12:16, 24 January 2024

OCA — Wed, 24 Jan 2024 12:16:52 GMT

←Older revision		Revision as of 12:16, 24 January 2024
Line 3:		Line 3:
	<StructureSection load='6r7u' size='340' side='right'caption='[[6r7u]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='6r7u' size='340' side='right'caption='[[6r7u]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6r7u]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R7U OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6R7U FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6r7u]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Tannerella_forsythia Tannerella forsythia]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R7U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6R7U FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BO3:BORIC+ACID'>BO3</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=~~GOL~~:~~GLYCEROL~~'>~~GOL~~</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]] 1.6Å</td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=~~CSX~~:~~S-OXY+CYSTEINE~~'>~~CSX~~</scene>, <scene name='pdbligand=~~MSE~~:~~SELENOMETHIONINE~~'>~~MSE~~</scene></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BO3:BORIC+ACID'>BO3</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CSX:S-OXY+CYSTEINE'>CSX</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=6r7u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r7u OCA], [~~http~~://pdbe.org/6r7u PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6r7u RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6r7u PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6r7u 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=6r7u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r7u OCA], [https://pdbe.org/6r7u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6r7u RCSB], [https://www.ebi.ac.uk/pdbsum/6r7u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6r7u ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/G8ULV1_TANFA G8ULV1_TANFA]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Gomis-Ruth, F X]]
-	[[Category: Guevara, T]]
-	[[Category: Ksiazek, M]]
-	[[Category: Potempa, J]]
-	[[Category: Rodriguez-Banqueri, A]]
-	[[Category: Hydrolase]]
-	[[Category: Metallopeptidase zymogen]]
-	[[Category: Metzincin]]
-	[[Category: Pappalysin family]]
-	[[Category: Peridontal disease]]
-	[[Category: Periodontopathogen]]
	[[Category: Tannerella forsythia]]		[[Category: Tannerella forsythia]]
		+	[[Category: Gomis-Ruth FX]]
		+	[[Category: Guevara T]]
		+	[[Category: Ksiazek M]]
		+	[[Category: Potempa J]]
		+	[[Category: Rodriguez-Banqueri A]]

OCA at 08:06, 5 February 2020

OCA — Wed, 05 Feb 2020 08:06:54 GMT

←Older revision		Revision as of 08:06, 5 February 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6r7u is ~~ON HOLD until Paper~~ Publication	+	==Selenomethionine variant of Tannerella forsythia promirolysin mutant E225A==
		+	<StructureSection load='6r7u' size='340' side='right'caption='[[6r7u]], [[Resolution\|resolution]] 1.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6r7u]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R7U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6R7U FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BO3:BORIC+ACID'>BO3</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CSX:S-OXY+CYSTEINE'>CSX</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=6r7u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r7u OCA], [http://pdbe.org/6r7u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6r7u RCSB], [http://www.ebi.ac.uk/pdbsum/6r7u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6r7u ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Tannerella forsythia is an oral dysbiotic periodontopathogen involved in severe human periodontal disease. As part of its virulence factor armamentarium, at the site of colonization it secretes mirolysin, a metallopeptidase of the unicellular pappalysin family, as a zymogen that is proteolytically auto-activated extracellularly at the Ser54-Arg55 bond. Crystal structures of the catalytically impaired promirolysin point mutant E225A at 1.4 and 1.6 A revealed that latency is exerted by an N-terminal 34-residue pro-segment that shields the front surface of the 274-residue catalytic domain, thus preventing substrate access. The catalytic domain conforms to the metzincin clan of metallopeptidases and contains a double calcium site, which acts as a calcium switch for activity. The pro-segment traverses the active-site cleft in the opposite direction to the substrate, which precludes its cleavage. It is anchored to the mature enzyme through residue Arg21, which intrudes into the specificity pocket in cleft sub-site S1'. Moreover, residue Cys23 within a conserved cysteine-glycine motif blocks the catalytic zinc ion by a cysteine-switch mechanism, first described for mammalian matrix metallopeptidases. In addition, a 1.5 A structure was obtained for a complex of mature mirolysin and a tetradecapeptide, which filled the cleft from sub-site S1' to S6'. A citrate molecule in S1 completed a product-complex mimic that unveiled the mechanism of substrate binding and cleavage by mirolysin, the catalytic domain of which was already preformed in the zymogen. These results, including a preference for cleavage before basic residues, are likely to be valid for other unicellular pappalysins derived from archaea, bacteria, cyanobacteria, algae and fungi, including archetypal ulilysin from Methanosarcina acetivorans. They may further apply, at least in part, to the multi-domain orthologues of higher organisms.

-	~~Authors~~:	+	Structure-based mechanism of cysteine-switch latency and of catalysis by pappalysin-family metallopeptidases.,Guevara T, Rodriguez-Banqueri A, Ksiazek M, Potempa J, Gomis-Ruth FX IUCrJ. 2020 Jan 1;7(Pt 1):18-29. doi: 10.1107/S2052252519013848. eCollection 2020, Jan 1. PMID:31949901<ref>PMID:31949901</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6r7u" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Gomis-Ruth, F X]]
		+	[[Category: Guevara, T]]
		+	[[Category: Ksiazek, M]]
		+	[[Category: Potempa, J]]
		+	[[Category: Rodriguez-Banqueri, A]]
		+	[[Category: Hydrolase]]
		+	[[Category: Metallopeptidase zymogen]]
		+	[[Category: Metzincin]]
		+	[[Category: Pappalysin family]]
		+	[[Category: Peridontal disease]]
		+	[[Category: Periodontopathogen]]
		+	[[Category: Tannerella forsythia]]

OCA: Protected "6r7u" [edit=sysop:move=sysop]

OCA — Wed, 10 Apr 2019 05:40:47 GMT

Protected "6r7u" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:40, 10 April 2019

OCA: New page: '''Unreleased structure''' The entry 6r7u is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 10 Apr 2019 05:40:46 GMT

New page: '''Unreleased structure''' The entry 6r7u is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6r7u is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]