title: Structure and mechanism of a bacterial host-protein citrullinating virulence factor, Porphyromonas gingivalis peptidylarginine deiminase.
abstract: 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 α/β-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.
authors.affiliation: Proteolysis Lab; Department of Structural Biology ("María de Maeztu" Unit of Excellence); Molecular Biology Institute of Barcelona, CSIC; Barcelona Science Park, Helix Building; c/Baldiri Reixac, 15-21; E-08028 Barcelona Spain.
authors.forename: Theodoros
authors.initials: T
authors.lastname: Goulas
authors.affiliation: Laboratory of Microbiology; Faculty of Biochemistry, Biophysics and Biotechnology; Jagiellonian University; Gonostajowa 7; PL-30-387 Kraków Poland.
authors.forename: Danuta
authors.initials: D
authors.lastname: Mizgalska
authors.affiliation: Proteolysis Lab; Department of Structural Biology ("María de Maeztu" Unit of Excellence); Molecular Biology Institute of Barcelona, CSIC; Barcelona Science Park, Helix Building; c/Baldiri Reixac, 15-21; E-08028 Barcelona Spain.
authors.forename: Irene
authors.initials: I
authors.lastname: Garcia-Ferrer
authors.affiliation: 1] Laboratory of Microbiology; Faculty of Biochemistry, Biophysics and Biotechnology; Jagiellonian University; Gonostajowa 7; PL-30-387 Kraków Poland [2] Małopolska Center of Biotechnology, Jagiellonian University; Gonostajowa 7; PL-30-387 Kraków Poland.
authors.forename: Tomasz
authors.initials: T
authors.lastname: Kantyka
authors.affiliation: Proteolysis Lab; Department of Structural Biology ("María de Maeztu" Unit of Excellence); Molecular Biology Institute of Barcelona, CSIC; Barcelona Science Park, Helix Building; c/Baldiri Reixac, 15-21; E-08028 Barcelona Spain.
authors.forename: Tibisay
authors.initials: T
authors.lastname: Guevara
authors.affiliation: Laboratory of Microbiology; Faculty of Biochemistry, Biophysics and Biotechnology; Jagiellonian University; Gonostajowa 7; PL-30-387 Kraków Poland.
authors.forename: Borys
authors.initials: B
authors.lastname: Szmigielski
authors.affiliation: Laboratory of Microbiology; Faculty of Biochemistry, Biophysics and Biotechnology; Jagiellonian University; Gonostajowa 7; PL-30-387 Kraków Poland.
authors.forename: Aneta
authors.initials: A
authors.lastname: Sroka
authors.affiliation: Crystallographic Methods; Department of Structural Biology ("María de Maeztu" Unit of Excellence); Molecular Biology Institute of Barcelona, CSIC; Barcelona Science Park, Helix Building; c/Baldiri Reixac, 15-21; E-08028 Barcelona Spain.
authors.forename: Claudia
authors.initials: C
authors.lastname: Millán
authors.affiliation: 1] Crystallographic Methods; Department of Structural Biology ("María de Maeztu" Unit of Excellence); Molecular Biology Institute of Barcelona, CSIC; Barcelona Science Park, Helix Building; c/Baldiri Reixac, 15-21; E-08028 Barcelona Spain [2] Institució Catalana de Recerca i Estudis Avançats; Passeig Lluís Companys, 23; E-08003 Barcelona Spain.
authors.forename: Isabel
authors.initials: I
authors.lastname: Usón
authors.affiliation: Department of Oral Immunology and Infectious Diseases; University of Louisville School of Dentistry; Louisville, KY 40202 USA.
authors.forename: Florian
authors.initials: F
authors.lastname: Veillard
authors.affiliation: Department of Oral Immunology and Infectious Diseases; University of Louisville School of Dentistry; Louisville, KY 40202 USA.
authors.forename: Barbara
authors.initials: B
authors.lastname: Potempa
authors.affiliation: Broegelmann Research Laboratory; Department of Clinical Science; The Gade Institute; University of Bergen; N-5021 Bergen Norway.
authors.forename: Piotr
authors.initials: P
authors.lastname: Mydel
authors.affiliation: Structural MitoLab; Department of Structural Biology ("María de Maeztu" Unit of Excellence); Molecular Biology Institute of Barcelona, CSIC; Barcelona Science Park, Helix Building; c/Baldiri Reixac, 15-21; E-08028 Barcelona Spain.
authors.forename: Maria
authors.initials: M
authors.lastname: Solà
authors.affiliation: 1] Laboratory of Microbiology; Faculty of Biochemistry, Biophysics and Biotechnology; Jagiellonian University; Gonostajowa 7; PL-30-387 Kraków Poland [2] Department of Oral Immunology and Infectious Diseases; University of Louisville School of Dentistry; Louisville, KY 40202 USA.
authors.forename: Jan
authors.initials: J
authors.lastname: Potempa
authors.affiliation: Proteolysis Lab; Department of Structural Biology ("María de Maeztu" Unit of Excellence); Molecular Biology Institute of Barcelona, CSIC; Barcelona Science Park, Helix Building; c/Baldiri Reixac, 15-21; E-08028 Barcelona Spain.
authors.forename: F Xavier
authors.initials: FX
authors.lastname: Gomis-Rüth
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry*; D020134:Catalytic Domain; D002956:Citrulline / Q000737:chemistry; D018360:Crystallography, X-Ray; D006867:Hydrolases / Q000737:chemistry*; D008958:Models, Molecular; D016966:Porphyromonas gingivalis / Q000201:enzymology*; D011485:Protein Binding; D011499:Protein Processing, Post-Translational; D017433:Protein Structure, Secondary; D000076342:Protein-Arginine Deiminases; D040681:Structural Homology, Protein; D037521:Virulence Factors / Q000737:chemistry*
chemical_list: D001426:Bacterial Proteins; D037521:Virulence Factors; D002956:Citrulline; D006867:Hydrolases; D000076342:Protein-Arginine Deiminases