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4ytg

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Revision as of 07:24, 10 May 2023

Crystal structure of Porphyromonas gingivalis peptidylarginine deiminase (PPAD) mutant C351A in complex with dipeptide Met-Arg.

Structural highlights

4ytg is a 1 chain structure with sequence from Porphyromonas gingivalis W83. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.^[1]

Publication Abstract from PubMed

Citrullination is a post-translational modification of higher organisms that deiminates arginines in proteins and peptides. It occurs in physiological processes but also pathologies such as multiple sclerosis, fibrosis, Alzheimer's disease and rheumatoid arthritis (RA). The reaction is catalyzed by peptidylarginine deiminases (PADs), which are found in vertebrates but not in lower organisms. RA has been epidemiologically associated with periodontal disease, whose main infective agent is Porphyromonas gingivalis. Uniquely among microbes, P. gingivalis secretes a PAD, termed PPAD (Porphyromonas peptidylarginine deiminase), which is genetically unrelated to eukaryotic PADs. Here, we studied function of PPAD and its substrate-free, substrate-complex, and substrate-mimic-complex structures. It comprises a flat cylindrical catalytic domain with five-fold alpha/beta-propeller architecture and a C-terminal immunoglobulin-like domain. The PPAD active site is a funnel located on one of the cylinder bases. It accommodates arginines from peptide substrates after major rearrangement of a "Michaelis loop" that closes the cleft. The guanidinium and carboxylate groups of substrates are tightly bound, which explains activity of PPAD against arginines at C-termini but not within peptides. Catalysis is based on a cysteine-histidine-asparagine triad, which is shared with human PAD1-PAD4 and other guanidino-group modifying enzymes. We provide a working mechanism hypothesis based on 18 structure-derived point mutants.

Structure and mechanism of a bacterial host-protein citrullinating virulence factor, Porphyromonas gingivalis peptidylarginine deiminase.,Goulas T, Mizgalska D, Garcia-Ferrer I, Kantyka T, Guevara T, Szmigielski B, Sroka A, Millan C, Uson I, Veillard F, Potempa B, Mydel P, Sola M, Potempa J, Gomis-Ruth FX Sci Rep. 2015 Jul 1;5:11969. doi: 10.1038/srep11969. PMID:26132828^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ McGraw WT, Potempa J, Farley D, Travis J. Purification, characterization, and sequence analysis of a potential virulence factor from Porphyromonas gingivalis, peptidylarginine deiminase. Infect Immun. 1999 Jul;67(7):3248-56. PMID:10377098
↑ Goulas T, Mizgalska D, Garcia-Ferrer I, Kantyka T, Guevara T, Szmigielski B, Sroka A, Millan C, Uson I, Veillard F, Potempa B, Mydel P, Sola M, Potempa J, Gomis-Ruth FX. Structure and mechanism of a bacterial host-protein citrullinating virulence factor, Porphyromonas gingivalis peptidylarginine deiminase. Sci Rep. 2015 Jul 1;5:11969. doi: 10.1038/srep11969. PMID:26132828 doi:http://dx.doi.org/10.1038/srep11969

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4ytg"

@@ Line 1: / Line 1: @@
 ==Crystal structure of Porphyromonas gingivalis peptidylarginine deiminase (PPAD) mutant C351A in complex with dipeptide Met-Arg.==
-<StructureSection load='4ytg' size='340' side='right' caption='[[4ytg]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+<StructureSection load='4ytg' size='340' side='right'caption='[[4ytg]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4ytg]] is a 1 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=4YTG OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YTG FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4ytg]] is a 1 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=4YTG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YTG FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ARG:ARGININE'>ARG</scene>, <scene name='pdbligand=AZI:AZIDE+ION'>AZI</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CYS:CYSTEINE'>CYS</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MET:METHIONINE'>MET</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ARG:ARGININE'>ARG</scene>, <scene name='pdbligand=AZI:AZIDE+ION'>AZI</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CYS:CYSTEINE'>CYS</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MET:METHIONINE'>MET</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4yt9|4yt9]]</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=4ytg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ytg OCA], [https://pdbe.org/4ytg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ytg RCSB], [https://www.ebi.ac.uk/pdbsum/4ytg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ytg ProSAT]</span></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=4ytg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ytg OCA], [http://pdbe.org/4ytg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ytg RCSB], [http://www.ebi.ac.uk/pdbsum/4ytg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ytg 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>
+[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;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Porgi]]
+[[Category: Large Structures]]
-[[Category: Garcia-Ferrer, I]]
+[[Category: Porphyromonas gingivalis W83]]
-[[Category: Gomis-Ruth, F X]]
+[[Category: Garcia-Ferrer I]]
-[[Category: Goulas, T]]
+[[Category: Gomis-Ruth FX]]
-[[Category: Guevara, T]]
+[[Category: Goulas T]]
-[[Category: Kantyka, T]]
+[[Category: Guevara T]]
-[[Category: Millan, C]]
+[[Category: Kantyka T]]
-[[Category: Mizgalska, D]]
+[[Category: Millan C]]
-[[Category: Mydel, P]]
+[[Category: Mizgalska D]]
-[[Category: Potempa, B]]
+[[Category: Mydel P]]
-[[Category: Potempa, J]]
+[[Category: Potempa B]]
-[[Category: Sola, M]]
+[[Category: Potempa J]]
-[[Category: Sroka, A]]
+[[Category: Sola M]]
-[[Category: Szmigielski, B]]
+[[Category: Sroka A]]
-[[Category: Uson, I]]
+[[Category: Szmigielski B]]
-[[Category: Veillard, F]]
+[[Category: Uson I]]
-[[Category: Citrullination]]
+[[Category: Veillard F]]
-[[Category: Hydrolase]]
-[[Category: Peptidylarginine deiminase]]

4ytg

From Proteopedia

Revision as of 07:24, 10 May 2023

Crystal structure of Porphyromonas gingivalis peptidylarginine deiminase (PPAD) mutant C351A in complex with dipeptide Met-Arg.

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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