6r7w - Revision history

OCA at 12:16, 24 January 2024

OCA — Wed, 24 Jan 2024 12:16:54 GMT

←Older revision		Revision as of 12:16, 24 January 2024
Line 3:		Line 3:
	<StructureSection load='6r7w' size='340' side='right'caption='[[6r7w]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='6r7w' size='340' side='right'caption='[[6r7w]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6r7w]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_43037 Atcc 43037~~] and [~~http~~://en.wikipedia.org/wiki/~~Bacteroides_forsythus Bacteroides forsythus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R7W OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6R7W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6r7w]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Tannerella_forsythia Tannerella forsythia] and [https://en.wikipedia.org/wiki/Tannerella_forsythia_92A2 Tannerella forsythia 92A2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R7W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6R7W FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=EOH:ETHANOL'>EOH</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]] 1.5Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6r7u\|6r7u]], [[6r7v\|6r7v]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=EOH:ETHANOL'>EOH</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">BFO_2662 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=203275 Bacteroides forsythus])</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=6r7w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r7w OCA], [https://pdbe.org/6r7w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6r7w RCSB], [https://www.ebi.ac.uk/pdbsum/6r7w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6r7w 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=6r7w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r7w OCA], [~~http~~://pdbe.org/6r7w PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6r7w RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6r7w PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6r7w 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 ==
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 43037]]
-	[[Category: Bacteroides forsythus]]
	[[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: Periodontal disease]]
-	[[Category: Periodontopathogen]]
	[[Category: Tannerella forsythia]]		[[Category: Tannerella forsythia]]
		+	[[Category: Tannerella forsythia 92A2]]
		+	[[Category: Gomis-Ruth FX]]
		+	[[Category: Guevara T]]
		+	[[Category: Ksiazek M]]
		+	[[Category: Potempa J]]
		+	[[Category: Rodriguez-Banqueri A]]

OCA at 16:17, 29 January 2020

OCA — Wed, 29 Jan 2020 16:17:56 GMT

←Older revision		Revision as of 16:17, 29 January 2020
Line 3:		Line 3:
	<StructureSection load='6r7w' size='340' side='right'caption='[[6r7w]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='6r7w' size='340' side='right'caption='[[6r7w]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6r7w]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R7W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6R7W FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6r7w]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43037 Atcc 43037] and [http://en.wikipedia.org/wiki/Bacteroides_forsythus Bacteroides forsythus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R7W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6R7W FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=EOH:ETHANOL'>EOH</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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=EOH:ETHANOL'>EOH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6r7u\|6r7u]], [[6r7v\|6r7v]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6r7u\|6r7u]], [[6r7v\|6r7v]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BFO_2662 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=203275 Bacteroides forsythus])</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=6r7w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r7w OCA], [http://pdbe.org/6r7w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6r7w RCSB], [http://www.ebi.ac.uk/pdbsum/6r7w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6r7w 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=6r7w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r7w OCA], [http://pdbe.org/6r7w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6r7w RCSB], [http://www.ebi.ac.uk/pdbsum/6r7w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6r7w ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
-	Tannerella forsythia is a periodontal ~~pathogen expressing six secretory proteolytic enzymes with a unique multidomain structure referred to as KLIKK proteases~~. ~~Two~~ of ~~these proteases~~, ~~karilysin and~~ mirolysin, ~~were previously shown to protect~~ the ~~bacterium against complement-mediated bactericidal activity. The latter metalloprotease~~, ~~however, was not characterized at the protein level. Therefore, we purified recombinant mirolysin and subjected it to detailed biochemical characterization. Mirolysin was obtained~~ as a ~~66 kDa~~ zymogen~~, which autoproteolytically processed itself into a 31 kDa active form via truncations~~ at ~~both~~ the N- and ~~C-termini~~. ~~Further autodegradation was prevented by calcium. Substrate specificity was determined~~ by the ~~S1' subsite~~ of the ~~substrate~~-~~binding pocket~~, ~~which shows strong preference for Arg and Lys at~~ the ~~carbonyl side~~ of a ~~scissile peptide bond (P1' residue)~~. The ~~protease cleaved an array of host proteins~~, ~~including human fibronectin~~, ~~fibrinogen~~, ~~complement proteins C3~~, C4, and C5, ~~and~~ the ~~antimicrobial peptide, LL~~-37. ~~Degradation of LL~~-~~37 abolished not only~~ the ~~bactericidal activity~~ of ~~the peptide~~, ~~but also its ability to bind lipopolysaccharide (LPS), thus quenching~~ the ~~endotoxin proinflammatory activity~~. ~~Taken together, these~~ results ~~indicate that~~, ~~through~~ cleavage ~~of LL-37 and complement proteins~~, ~~mirolysin might~~ be ~~involved~~ in ~~evasion of~~ the ~~host immune response~~.	+	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.

-	~~Mirolysin, a LysargiNase from Tannerella forsythia, proteolytically inactivates the human cathelicidin, LL~~-37.,~~Koneru L~~, ~~Ksiazek M, Waligorska I, Straczek~~ A, ~~Lukasik~~ M~~, Madej M, Thogersen IB, Enghild JJ~~, Potempa J ~~Biol Chem~~. ~~2017 Mar~~;~~398~~(3):~~395~~-~~409~~. doi: 10.~~1515~~/~~hsz-2016-0267~~. PMID:~~27997347~~<ref>PMID:~~27997347~~</ref>	+	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>

	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>
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 43037]]
		+	[[Category: Bacteroides forsythus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Gomis-Ruth, F X]]		[[Category: Gomis-Ruth, F X]]

OCA at 11:12, 13 November 2019

OCA — Wed, 13 Nov 2019 11:12:03 GMT

←Older revision		Revision as of 11:12, 13 November 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6r7w is ~~ON HOLD~~	+	==Tannerella forsythia mature mirolysin in complex with a cleaved peptide.==
		+	<StructureSection load='6r7w' size='340' side='right'caption='[[6r7w]], [[Resolution\|resolution]] 1.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6r7w]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6R7W OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6R7W FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=EOH:ETHANOL'>EOH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6r7u\|6r7u]], [[6r7v\|6r7v]]</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=6r7w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6r7w OCA], [http://pdbe.org/6r7w PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6r7w RCSB], [http://www.ebi.ac.uk/pdbsum/6r7w PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6r7w ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Tannerella forsythia is a periodontal pathogen expressing six secretory proteolytic enzymes with a unique multidomain structure referred to as KLIKK proteases. Two of these proteases, karilysin and mirolysin, were previously shown to protect the bacterium against complement-mediated bactericidal activity. The latter metalloprotease, however, was not characterized at the protein level. Therefore, we purified recombinant mirolysin and subjected it to detailed biochemical characterization. Mirolysin was obtained as a 66 kDa zymogen, which autoproteolytically processed itself into a 31 kDa active form via truncations at both the N- and C-termini. Further autodegradation was prevented by calcium. Substrate specificity was determined by the S1' subsite of the substrate-binding pocket, which shows strong preference for Arg and Lys at the carbonyl side of a scissile peptide bond (P1' residue). The protease cleaved an array of host proteins, including human fibronectin, fibrinogen, complement proteins C3, C4, and C5, and the antimicrobial peptide, LL-37. Degradation of LL-37 abolished not only the bactericidal activity of the peptide, but also its ability to bind lipopolysaccharide (LPS), thus quenching the endotoxin proinflammatory activity. Taken together, these results indicate that, through cleavage of LL-37 and complement proteins, mirolysin might be involved in evasion of the host immune response.

-	~~Authors: Rodriguez-Banqueri~~, A., ~~Guevara~~, T., Ksiazek, M., ~~Potempa~~, J.~~, Gomis~~-~~Ruth, F~~.X.	+	Mirolysin, a LysargiNase from Tannerella forsythia, proteolytically inactivates the human cathelicidin, LL-37.,Koneru L, Ksiazek M, Waligorska I, Straczek A, Lukasik M, Madej M, Thogersen IB, Enghild JJ, Potempa J Biol Chem. 2017 Mar;398(3):395-409. doi: 10.1515/hsz-2016-0267. PMID:27997347<ref>PMID:27997347</ref>

-	~~Description: Tannerella forsythia mature mirolysin in complex with~~ a ~~cleaved peptide~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6r7w" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Gomis-Ruth, F X]]
	[[Category: Guevara, T]]		[[Category: Guevara, T]]
-	[[Category: Potempa, J]]
	[[Category: Ksiazek, M]]		[[Category: Ksiazek, M]]
-	[[Category: ~~Gomis-Ruth~~, ~~F.X~~]]	+	[[Category: Potempa, J]]
	[[Category: Rodriguez-Banqueri, A]]		[[Category: Rodriguez-Banqueri, A]]
		+	[[Category: Hydrolase]]
		+	[[Category: Metallopeptidase zymogen]]
		+	[[Category: Metzincin]]
		+	[[Category: Pappalysin family]]
		+	[[Category: Periodontal disease]]
		+	[[Category: Periodontopathogen]]
		+	[[Category: Tannerella forsythia]]

OCA: Protected "6r7w" [edit=sysop:move=sysop]

OCA — Wed, 10 Apr 2019 05:40:53 GMT

Protected "6r7w" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:40, 10 April 2019

OCA: New page: '''Unreleased structure''' The entry 6r7w is ON HOLD Authors: Rodriguez-Banqueri, A., Guevara, T., Ksiazek, M., Potempa, J., Gomis-Ruth, F.X. Description: Tannerella forsythia mature m...

OCA — Wed, 10 Apr 2019 05:40:52 GMT

New page: '''Unreleased structure''' The entry 6r7w is ON HOLD Authors: Rodriguez-Banqueri, A., Guevara, T., Ksiazek, M., Potempa, J., Gomis-Ruth, F.X. Description: Tannerella forsythia mature m...

New page

'''Unreleased structure'''

The entry 6r7w is ON HOLD

Authors: Rodriguez-Banqueri, A., Guevara, T., Ksiazek, M., Potempa, J., Gomis-Ruth, F.X.

Description: Tannerella forsythia mature mirolysin in complex with a cleaved peptide.
[[Category: Unreleased Structures]]
[[Category: Guevara, T]]
[[Category: Potempa, J]]
[[Category: Ksiazek, M]]
[[Category: Gomis-Ruth, F.X]]
[[Category: Rodriguez-Banqueri, A]]