6fpc - Revision history

OCA at 12:30, 9 May 2024

2024-05-09T12:30:22Z

← Older revision		Revision as of 12:30, 9 May 2024
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	==Structure of the PRO-PRO endopeptidase (PPEP-2) from Paenibacillus alvei==		==Structure of the PRO-PRO endopeptidase (PPEP-2) from Paenibacillus alvei==
	<StructureSection load='6fpc' size='340' side='right' caption='[[6fpc]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='6fpc' size='340' side='right'caption='[[6fpc]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6fpc]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_6344 Atcc 6344~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6FPC OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6FPC FirstGlance]. <br>		<table><tr><td colspan='2'>[[6fpc]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Paenibacillus_alvei Paenibacillus alvei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6FPC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6FPC FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=CD:CADMIUM+ION'>CD</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]] 1.75Å</td></tr>
	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~PAV_1c07830 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=44250 ATCC 6344])</td~~></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<~~tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Pro-Pro_endopeptidase Pro-Pro endopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.89 3.4.24.89]~~ </~~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=6fpc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6fpc OCA], [https://pdbe.org/6fpc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6fpc RCSB], [https://www.ebi.ac.uk/pdbsum/6fpc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6fpc 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=6fpc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6fpc OCA], [~~http~~://pdbe.org/6fpc PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6fpc RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6fpc PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6fpc ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/PPEP2_PAEA2 PPEP2_PAEA2] Zinc-dependent endoprotease with a unique preference for proline residues surrounding the scissile bond, which cleaves in a PLP-\|-PVP motif. Cleaves the cell surface protein encoded by an adjacent gene, which contains two PPEP-2 cleaving sites and putative extracellular matrix-binding domains. Thereby, may have a role in the regulation of P.alvei adhesion. Is not able to cleave within the PVP-\|-PVQ motif, and only shows a very poor cleavage of the VNP-\|-PVP motif in vitro, which is the optimal substrate peptide for PPEP-1 from P.difficile.<ref>PMID:29794027</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Atcc 6344~~]]		[[Category: Large Structures]]
	[[Category: ~~Pro-Pro endopeptidase~~]]		[[Category: Paenibacillus alvei]]
	[[Category: Hensbergen~~, P J~~]]		[[Category: Hensbergen PJ]]
	[[Category: Klychnikov~~, O I~~]]		[[Category: Klychnikov OI]]
	[[Category: Strelkov~~, S V~~]]		[[Category: Strelkov SV]]
	[[Category: Weeks~~, S D]]~~		[[Category: Weeks SD]]
	~~[[Category: Endopeptidase]]~~
	~~[[Category: Hydrolase]]~~
	~~[[Category: Metalloprotease]]~~
	~~[[Category: Zinc~~]]

OCA at 06:22, 6 June 2018

2018-06-06T06:22:23Z

← Older revision		Revision as of 06:22, 6 June 2018
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	<StructureSection load='6fpc' size='340' side='right' caption='[[6fpc]], [[Resolution\|resolution]] 1.75Å' scene=''>		<StructureSection load='6fpc' size='340' side='right' caption='[[6fpc]], [[Resolution\|resolution]] 1.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6fpc]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6FPC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6FPC FirstGlance]. <br>		<table><tr><td colspan='2'>[[6fpc]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_6344 Atcc 6344]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6FPC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6FPC FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</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=CD:CADMIUM+ION'>CD</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">PAV_1c07830 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=44250 ATCC 6344])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pro-Pro_endopeptidase Pro-Pro endopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.89 3.4.24.89] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pro-Pro_endopeptidase Pro-Pro endopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.89 3.4.24.89] </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=6fpc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6fpc OCA], [http://pdbe.org/6fpc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6fpc RCSB], [http://www.ebi.ac.uk/pdbsum/6fpc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6fpc 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=6fpc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6fpc OCA], [http://pdbe.org/6fpc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6fpc RCSB], [http://www.ebi.ac.uk/pdbsum/6fpc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6fpc ProSAT]</span></td></tr>
	</table>		</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Pro-Pro endopeptidases (PPEPs) belong to a recently discovered family of proteases capable of hydrolyzing a Pro-Pro bond. The first member from the bacterial pathogen Clostridium difficile (PPEP-1) cleaves two C. difficile cell-surface proteins involved in adhesion, one of which is encoded by the gene adjacent to the ppep-1 gene. However, related PPEPs may exist in other bacteria and may shed light on substrate specificity in this enzyme family. Here we report on the homolog of PPEP-1 in Paenibacillus alvei, which we denoted PPEP-2. We found that PPEP-2 is a secreted metalloprotease, which likewise cleaved a cell-surface protein encoded by an adjacent gene. However, the cleavage motif of PPEP-2, PLP\|PVP, is distinct from that of PPEP-1 (VNP\|PVP). As a result, an optimal substrate peptide for PPEP-2 was not cleaved by PPEP-1 and vice versa To gain insight into the specificity mechanism of PPEP-2, we determined its crystal structure at 1.75 A resolution and further confirmed the structure in solution using small-angle X-ray scattering (SAXS). We show that a four-amino-acid loop, which is distinct in PPEP-1 and -2 (GGST in PPEP-1 and SERV in PPEP-2), plays a crucial role in substrate specificity. A PPEP-2 variant in which the four loop residues had been swapped for those from PPEP-1, displayed a shift in substrate specificity toward PPEP-1 substrates. Our results provide detailed insights into the PPEP-2 structure and the structural determinants of substrate specificity in this new family of PPEP proteases.

			Discovery of a new Pro-Pro endopeptidase, PPEP-2, provides mechanistic insights into the differences in substrate specificity within the PPEP family.,Klychnikov OI, Shamorkina TM, Weeks SD, van Leeuwen HC, Corver J, Drijfhout JW, van Veelen PA, Sluchanko NN, Strelkov SV, Hensbergen PJ J Biol Chem. 2018 May 23. pii: RA118.003244. doi: 10.1074/jbc.RA118.003244. PMID:29794027<ref>PMID:29794027</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 6fpc" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Atcc 6344]]
	[[Category: Pro-Pro endopeptidase]]		[[Category: Pro-Pro endopeptidase]]
	[[Category: Hensbergen, P J]]		[[Category: Hensbergen, P J]]

OCA at 05:39, 30 May 2018

2018-05-30T05:39:33Z

← Older revision		Revision as of 05:39, 30 May 2018
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	~~'''Unreleased structure'''~~

	~~The entry~~ 6fpc is ~~ON HOLD until Paper Publication~~		==Structure of the PRO-PRO endopeptidase (PPEP-2) from Paenibacillus alvei==
			<StructureSection load='6fpc' size='340' side='right' caption='[[6fpc]], [[Resolution\|resolution]] 1.75Å' scene=''>
	~~Authors~~: ~~Weeks~~, S.D., ~~Klychnikov~~, O.I., ~~Hensbergen~~, P.J.		== Structural highlights ==
			<table><tr><td colspan='2'>[[6fpc]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6FPC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6FPC FirstGlance]. <br>
	~~Description~~: ~~Structure of the PRO~~-~~PRO~~ endopeptidase ~~(PPEP-2) from Paenibacillus alvei~~		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	[[Category: ~~Unreleased Structures~~]]		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pro-Pro_endopeptidase Pro-Pro endopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.24.89 3.4.24.89] </span></td></tr>
	[[Category: Klychnikov, O.I]]		<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=6fpc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6fpc OCA], [http://pdbe.org/6fpc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6fpc RCSB], [http://www.ebi.ac.uk/pdbsum/6fpc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6fpc ProSAT]</span></td></tr>
	[[Category: Weeks, S.D]]		</table>
	[[Category: ~~Hensbergen, P.J~~]]		__TOC__
			</StructureSection>
			[[Category: Pro-Pro endopeptidase]]
			[[Category: Hensbergen, P J]]
			[[Category: Klychnikov, O I]]
			[[Category: Strelkov, S V]]
			[[Category: Weeks, S D]]
			[[Category: Endopeptidase]]
			[[Category: Hydrolase]]
			[[Category: Metalloprotease]]
			[[Category: Zinc]]

OCA at 06:06, 23 May 2018

2018-05-23T06:06:42Z

← Older revision		Revision as of 06:06, 23 May 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 6fpc is ON HOLD		The entry 6fpc is ON HOLD until Paper Publication

	Authors: Weeks, S.D., Klychnikov, O.I., Hensbergen, P.J.		Authors: Weeks, S.D., Klychnikov, O.I., Hensbergen, P.J.

OCA at 04:11, 16 May 2018

2018-05-16T04:11:04Z

← Older revision		Revision as of 04:11, 16 May 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 6fpc is ON HOLD ~~until Paper Publication~~		The entry 6fpc is ON HOLD

	Authors: Weeks, S.D., Klychnikov, O.I., Hensbergen, P.J.		Authors: Weeks, S.D., Klychnikov, O.I., Hensbergen, P.J.

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

2018-02-28T05:08:40Z

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

← Older revision	Revision as of 05:08, 28 February 2018
(No difference)

OCA: New page: '''Unreleased structure''' The entry 6fpc is ON HOLD until Paper Publication Authors: Weeks, S.D., Klychnikov, O.I., Hensbergen, P.J. Description: Structure of the PRO-PRO endopeptidas...

2018-02-28T05:08:38Z

New page: '''Unreleased structure''' The entry 6fpc is ON HOLD until Paper Publication Authors: Weeks, S.D., Klychnikov, O.I., Hensbergen, P.J. Description: Structure of the PRO-PRO endopeptidas...

New page

'''Unreleased structure'''

The entry 6fpc is ON HOLD until Paper Publication

Authors: Weeks, S.D., Klychnikov, O.I., Hensbergen, P.J.

Description: Structure of the PRO-PRO endopeptidase (PPEP-2) from Paenibacillus alvei
[[Category: Unreleased Structures]]
[[Category: Klychnikov, O.I]]
[[Category: Weeks, S.D]]
[[Category: Hensbergen, P.J]]