5ak7: Difference between revisions
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==Structure of wt Porphyromonas gingivalis peptidylarginine deiminase== | ==Structure of wt Porphyromonas gingivalis peptidylarginine deiminase== | ||
<StructureSection load='5ak7' size='340' side='right' caption='[[5ak7]], [[Resolution|resolution]] 1.46Å' scene=''> | <StructureSection load='5ak7' size='340' side='right'caption='[[5ak7]], [[Resolution|resolution]] 1.46Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[5ak7]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AK7 OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[5ak7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Porphyromonas_gingivalis Porphyromonas gingivalis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5AK7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5AK7 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ALA:ALANINE'>ALA</scene>, <scene name='pdbligand=ARG:ARGININE'>ARG</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene> | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.46Å</td></tr> | ||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ALA:ALANINE'>ALA</scene>, <scene name='pdbligand=ARG:ARGININE'>ARG</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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'>[ | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5ak7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ak7 OCA], [https://pdbe.org/5ak7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ak7 RCSB], [https://www.ebi.ac.uk/pdbsum/5ak7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ak7 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [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 == | ||
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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> | ||
</div> | </div> | ||
<div class="pdbe-citations 5ak7" style="background-color:#fffaf0;"></div> | |||
== References == | == References == | ||
<references/> | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Burgess-Brown | [[Category: Large Structures]] | ||
[[Category: Kiyani | [[Category: Porphyromonas gingivalis]] | ||
[[Category: Kopec | [[Category: Burgess-Brown N]] | ||
[[Category: Montgomery | [[Category: Kiyani W]] | ||
[[Category: Nowak | [[Category: Kopec J]] | ||
[[Category: Shrestha | [[Category: Montgomery A]] | ||
[[Category: Venables | [[Category: Nowak R]] | ||
[[Category: Yue | [[Category: Shrestha L]] | ||
[[Category: Venables PJ]] | |||
[[Category: Yue WW]] | |||
Latest revision as of 14:41, 9 May 2024
Structure of wt Porphyromonas gingivalis peptidylarginine deiminaseStructure of wt Porphyromonas gingivalis peptidylarginine deiminase
Structural highlights
FunctionPAD_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 PubMedBACKGROUND: Periodontitis (PD) is a known risk factor for rheumatoid arthritis (RA) and there is increasing evidence that the link between the two diseases is due to citrullination by the unique bacterial peptidylarginine deiminase (PAD) enzyme expressed by periodontal pathogen Pophyromonas gingivalis (PPAD). However, the precise mechanism by which PPAD could generate potentially immunogenic peptides has remained controversial due to lack of information about the structural and catalytic mechanisms of the enzyme. OBJECTIVES: By solving the 3D structure of PPAD we aim to characterise activity and elucidate potential mechanisms involved in breach of tolerance to citrullinated proteins in RA. METHODS: PPAD and a catalytically inactive mutant PPADC351A were crystallised and their 3D structures solved. Key residues identified from 3D structures were examined by mutations. Fibrinogen and alpha-enolase were incubated with PPAD and P. gingivalis arginine gingipain (RgpB) and citrullinated peptides formed were sequenced and quantified by mass spectrometry. RESULTS: Here, we solve the crystal structure of a truncated, highly active form of PPAD. We confirm catalysis is mediated by the following residues: Asp130, His236, Asp238, Asn297 and Cys351 and show Arg152 and Arg154 may determine the substrate specificity of PPAD for C-terminal arginines. We demonstrate the formation of 37 C-terminally citrullinated peptides from fibrinogen and 11 from alpha-enolase following incubation with tPPAD and RgpB. CONCLUSIONS: PPAD displays an unequivocal specificity for C-terminal arginine residues and readily citrullinates peptides from key RA autoantigens. The formation of these novel citrullinated peptides may be involved in breach of tolerance to citrullinated proteins in RA. Crystal structure of Porphyromonas gingivalis peptidylarginine deiminase: implications for autoimmunity in rheumatoid arthritis.,Montgomery AB, Kopec J, Shrestha L, Thezenas ML, Burgess-Brown NA, Fischer R, Yue WW, Venables PJ Ann Rheum Dis. 2015 Jul 24. pii: annrheumdis-2015-207656. doi:, 10.1136/annrheumdis-2015-207656. PMID:26209657[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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