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Literature summary for 3.5.3.15 extracted from

  • Bereta, G.; Goulas, T.; Madej, M.; Bielecka, E.; Sola, M.; Potempa, J.; Xavier Gomis-Rueth, F.
    Structure, function, and inhibition of a genomic/clinical variant of Porphyromonas gingivalis peptidylarginine deiminase (2019), Protein Sci., 28, 478-486 .
    View publication on PubMedView publication on EuropePMC
Search for more literature for 3.5.3.15

Crystallization (Commentary)

Crystallization (Comment) Organism
in complex with inhibitor Cl-amidine, to 1.6 A resolution Porphyromonas gingivalis

Protein Variants

Protein Variants Comment Organism
additional information strain T2 shows three amino-acid substitutions directly preceding catalytic residue H236 (G231N/E232T/N235D) when compared with PPAD from the reference strain ATCC 33277. Mutations localize to a loop engaged in substrate/inhibitor binding. Mutation of these positions in the reference strain results in twofold higher cell-associated citrullinating activity. Similar to PPAD-T1, recombinant PPAD-T2 citrullinates arginines at the C-termini of general peptidic substrates but not within peptides Porphyromonas gingivalis

Inhibitors

Inhibitors Comment Organism Structure
Cl-amidine inhibitor binds covalently to the catalytic C351-Sgamma atom, mimicking a reaction intermediate Porphyromonas gingivalis

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
0.0054
-
 PPGFSPFR pH 7.5, 37°C Porphyromonas gingivalis
0.0074
-
 IHAREIFDSR pH 7.5, 37°C Porphyromonas gingivalis
0.038
-
 IHAREIFDSR pH 7.5, 37°C Porphyromonas gingivalis
0.045
-
 PPGFSPFR pH 7.5, 37°C Porphyromonas gingivalis

Organism

Organism UniProt Comment Textmining
Porphyromonas gingivalis
-
-
-
Porphyromonas gingivalis Q9RQJ2
-
-
Porphyromonas gingivalis ATCC 33277
-
-
-
Porphyromonas gingivalis T2 Q9RQJ2
-
-

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
IHAREIFDSR + H2O peptide derived from enolase Porphyromonas gingivalis IHAREIFDS-citrulline + NH3
-
 ?
IHAREIFDSR + H2O peptide derived from enolase Porphyromonas gingivalis ATCC 33277 IHAREIFDS-citrulline + NH3
-
 ?
IHAREIFDSR + H2O peptide derived from enolase Porphyromonas gingivalis T2 IHAREIFDS-citrulline + NH3
-
 ?
additional information no substrate: peptide GFSPFRSS Porphyromonas gingivalis ?
-
 ?
additional information no substrate: peptide GFSPFRSS Porphyromonas gingivalis ATCC 33277 ?
-
 ?
additional information no substrate: peptide GFSPFRSS Porphyromonas gingivalis T2 ?
-
 ?
PPGFSPFR + H2O peptide derived from bradykinin Porphyromonas gingivalis PPGFSPF-citrulline + NH3
-
 ?
PPGFSPFR + H2O peptide derived from bradykinin Porphyromonas gingivalis ATCC 33277 PPGFSPF-citrulline + NH3
-
 ?
PPGFSPFR + H2O peptide derived from bradykinin Porphyromonas gingivalis T2 PPGFSPF-citrulline + NH3
-
 ?

Temperature Stability [°C]

Temperature Stability Minimum [°C] Temperature Stability Maximum [°C] Comment Organism
67
-
 melting temperature Porphyromonas gingivalis
68
-
 melting temperature Porphyromonas gingivalis

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
2.88
-
 IHAREIFDSR pH 7.5, 37°C Porphyromonas gingivalis
3.03
-
 PPGFSPFR pH 7.5, 37°C Porphyromonas gingivalis
7
-
 IHAREIFDSR pH 7.5, 37°C Porphyromonas gingivalis
11.3
-
 PPGFSPFR pH 7.5, 37°C Porphyromonas gingivalis

kcat/KM [mM/s]

kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
0.184
-
 IHAREIFDSR pH 7.5, 37°C Porphyromonas gingivalis
0.255
-
 PPGFSPFR pH 7.5, 37°C Porphyromonas gingivalis
0.391
-
 IHAREIFDSR pH 7.5, 37°C Porphyromonas gingivalis
0.563
-
 PPGFSPFR pH 7.5, 37°C Porphyromonas gingivalis