5AK8 image
Deposition Date 2015-03-02
Release Date 2015-07-22
Last Version Date 2024-05-08
Entry Detail
PDB ID:
5AK8
Keywords:
Title:
Structure of C351A mutant of Porphyromonas gingivalis peptidylarginine deiminase
Biological Source:
Source Organism:
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.48 Å
R-Value Free:
0.16
R-Value Work:
0.12
R-Value Observed:
0.12
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:PEPTIDYLARGININE DEIMINASE
Gene (Uniprot):PG_1424
Mutations:YES
Chain IDs:A
Chain Length:438
Number of Molecules:1
Biological Source:PORPHYROMONAS GINGIVALIS
Primary Citation
Crystal Structure of Porphyromonas Gingivalis Peptidylarginine Deiminase: Implications for Autoimmunity in Rheumatoid Arthritis.
Ann.Rheum.Dis. 75 1255 ? (2016)
PMID: 26209657 DOI: 10.1136/ANNRHEUMDIS-2015-207656

Abstact

BACKGROUND 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 PPAD(C351A) were crystallised and their 3D structures solved. Key residues identified from 3D structures were examined by mutations. Fibrinogen and α-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 α-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.

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Primary Citation of related structures