6i0x - Revision history

OCA at 11:44, 24 January 2024

OCA — Wed, 24 Jan 2024 11:44:06 GMT

←Older revision		Revision as of 11:44, 24 January 2024
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	==Porphyromonas gingivalis peptidylarginine deminase (PPAD) mutant G231N/E232T/N235D in complex with Cl-amidine.==		==Porphyromonas gingivalis peptidylarginine deminase (PPAD) mutant G231N/E232T/N235D in complex with Cl-amidine.==
-	<StructureSection load='6i0x' size='340' side='right' caption='[[6i0x]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='6i0x' size='340' side='right'caption='[[6i0x]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6i0x]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Porgi Porgi~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I0X OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6I0X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6i0x]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Porphyromonas_gingivalis_W83 Porphyromonas gingivalis W83]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I0X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6I0X FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BFB:N-[(1S)-1-(AMINOCARBONYL)-4-(ETHANIMIDOYLAMINO)BUTYL]BENZAMIDE'>BFB</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PG_1424 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=242619 PORGI])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BFB:N-[(1S)-1-(AMINOCARBONYL)-4-(ETHANIMIDOYLAMINO)BUTYL]BENZAMIDE'>BFB</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=6i0x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i0x OCA], [~~http~~://pdbe.org/6i0x PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6i0x RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6i0x PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6i0x 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=6i0x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i0x OCA], [https://pdbe.org/6i0x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6i0x RCSB], [https://www.ebi.ac.uk/pdbsum/6i0x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6i0x ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PAD_PORGI PAD_PORGI]] Deiminates the guanidino group of C-terminal arginine residues on a variety of peptides, including the vasoregulatory peptide-hormone bradykinin, to yield ammonia and a citrulline residue. May promote the growth of the pathogen in the periodontal pocket by producing ammonia, ammonia having a protective effect during acidic cleaning cycles in the mouth.<ref>PMID:10377098</ref>	+	[https://www.uniprot.org/uniprot/PAD_PORGI PAD_PORGI] Deiminates the guanidino group of C-terminal arginine residues on a variety of peptides, including the vasoregulatory peptide-hormone bradykinin, to yield ammonia and a citrulline residue. May promote the growth of the pathogen in the periodontal pocket by producing ammonia, ammonia having a protective effect during acidic cleaning cycles in the mouth.<ref>PMID:10377098</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Porgi~~]]	+	[[Category: Large Structures]]
-	[[Category: Gomis-Ruth~~, F X~~]]	+	[[Category: Porphyromonas gingivalis W83]]
-	[[Category: Goulas, T]]	+	[[Category: Gomis-Ruth FX]]
-	[[Category: Potempa, J]]	+	[[Category: Goulas T]]
-	[[Category: Sola, M]]	+	[[Category: Potempa J]]
-	~~[[Category: Arginine demininase]]~~	+	[[Category: Sola M]]
-	~~[[Category: Citrullination]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Odontopathogenic virulence factor]]~~	+
-	~~[[Category: Periodontal disease]]~~	+
-	~~[[Category: Rheumatoid arthitis~~]]	+

OCA at 09:31, 30 January 2019

OCA — Wed, 30 Jan 2019 09:31:11 GMT

←Older revision		Revision as of 09:31, 30 January 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6i0x is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Porphyromonas gingivalis peptidylarginine deminase (PPAD) mutant G231N/E232T/N235D in complex with Cl-amidine.==
		+	<StructureSection load='6i0x' size='340' side='right' caption='[[6i0x]], [[Resolution\|resolution]] 1.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6i0x]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Porgi Porgi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I0X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6I0X FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BFB:N-[(1S)-1-(AMINOCARBONYL)-4-(ETHANIMIDOYLAMINO)BUTYL]BENZAMIDE'>BFB</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PG_1424 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=242619 PORGI])</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=6i0x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i0x OCA], [http://pdbe.org/6i0x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6i0x RCSB], [http://www.ebi.ac.uk/pdbsum/6i0x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6i0x ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PAD_PORGI PAD_PORGI]] Deiminates the guanidino group of C-terminal arginine residues on a variety of peptides, including the vasoregulatory peptide-hormone bradykinin, to yield ammonia and a citrulline residue. May promote the growth of the pathogen in the periodontal pocket by producing ammonia, ammonia having a protective effect during acidic cleaning cycles in the mouth.<ref>PMID:10377098</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Citrullination is an essential post-translational modification in which the guanidinium group of protein and peptide arginines is deiminated by peptidylarginine deiminases (PADs). When deregulated, excessive citrullination leads to inflammation as in severe periodontal disease (PD) and rheumatoid arthritis (RA). Porphyromonas gingivalis is the major periodontopathogenic causative agent of PD and also an etiological agent of RA. It secretes a PAD, termed Porphyromonas PAD (PPAD), which is a virulence factor that causes aberrant citrullination. Analysis of P. gingivalis genomes of laboratory strains and clinical isolates unveiled a PPAD variant (PPAD-T2), which showed three amino-acid substitutions directly preceding catalytic residue H(236) (G(231) N/E(232) T/N(235) D) when compared with PPAD from the reference strain (PPAD-T1). Mutation of these positions in the reference strain resulted in twofold higher cell-associated citrullinating activity. Similarly to PPAD-T1, recombinant PPAD-T2 citrullinated arginines at the C-termini of general peptidic substrates but not within peptides. Catalytically, PPAD-T2 showed weaker substrate binding but higher turnover rates than PPAD-T1. In contrast, no differences were found in thermal stability. The 1.6A-resolution X-ray crystal structure of PPAD-T2 in complex with the general human PAD inhibitor, Cl-amidine, revealed that the inhibitor moiety is tightly bound and that mutations localize to a loop engaged in substrate/inhibitor binding. In particular, mutation G(231) N caused a slight structural rearrangement, which probably originated the higher substrate turnover observed. The present data compare two natural PPAD variants and will set the pace for the design of specific inhibitors against P. gingivalis-caused PD. This article is protected by copyright. All rights reserved.

-	~~Authors~~:	+	Structure, function and inhibition of a genomic/clinical variant of Porphyromonas gingivalis peptidylarginine deiminase.,Bereta G, Goulas T, Madej M, Bielecka E, Sola M, Potempa J, Gomis-Ruth FX Protein Sci. 2019 Jan 14. doi: 10.1002/pro.3571. PMID:30638292<ref>PMID:30638292</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 6i0x" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Porgi]]
		+	[[Category: Gomis-Ruth, F X]]
		+	[[Category: Goulas, T]]
		+	[[Category: Potempa, J]]
		+	[[Category: Sola, M]]
		+	[[Category: Arginine demininase]]
		+	[[Category: Citrullination]]
		+	[[Category: Hydrolase]]
		+	[[Category: Odontopathogenic virulence factor]]
		+	[[Category: Periodontal disease]]
		+	[[Category: Rheumatoid arthitis]]

OCA: Protected "6i0x" [edit=sysop:move=sysop]

OCA — Wed, 07 Nov 2018 10:34:56 GMT

Protected "6i0x" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:34, 7 November 2018

OCA: New page: '''Unreleased structure''' The entry 6i0x is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 07 Nov 2018 10:34:54 GMT

New page: '''Unreleased structure''' The entry 6i0x is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6i0x is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]