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Literature summary extracted from

  • Rodriguez, S.B.; Stitt, B.L.; Ash, D.E.
    Expression of peptidylarginine deiminase from Porphyromonas gingivalis in Escherichia coli: enzyme purification and characterization (2009), Arch. Biochem. Biophys., 488, 14-22.
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

EC Number Cloned (Comment) Organism
3.5.3.6 two recombinant forms of the Porphyromonas gingivalis PAD, a truncated form with a 43-amino acid N-terminal deletion and the full-length form of PAD, are expressed in Escherichia coli BL21 Star (DE3)pLysS cells Porphyromonas gingivalis

Inhibitors

EC Number Inhibitors Comment Organism Structure
3.5.3.6 Cd2+ 53% inhibition at 1 mM Cd2+ Porphyromonas gingivalis
3.5.3.6 Zn2+ at 1 mM Zn2+, the enzyme activity is inhibited by 26% Porphyromonas gingivalis

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
3.5.3.6 0.01 0.02 N-alpha-benzoyl-L-arginine in 50 mM CHES/HCl, pH 9.5 containing 10 mM dithiothreitol, at 37°C Porphyromonas gingivalis
3.5.3.6 0.021
-
 bradykinin-L-Arg in 50 mM CHES/HCl, pH 9.5 containing 10 mM dithiothreitol, at 37°C Porphyromonas gingivalis
3.5.3.6 0.033
-
 bradykinin antagonist-L-Arg in 50 mM CHES/HCl, pH 9.5 containing 10 mM dithiothreitol, at 37°C Porphyromonas gingivalis
3.5.3.6 0.07
-
 L-Pro-L-Arg-L-Phe in 50 mM CHES/HCl, pH 9.5 containing 10 mM dithiothreitol, at 37°C Porphyromonas gingivalis
3.5.3.6 0.089
-
 L-Pro-L-Phe-L-Arg in 50 mM CHES/HCl, pH 9.5 containing 10 mM dithiothreitol, at 37°C Porphyromonas gingivalis
3.5.3.6 1.2
-
 L-Arg in 50 mM CHES/HCl, pH 9.5 containing 10 mM dithiothreitol, at 37°C Porphyromonas gingivalis
3.5.3.6 1.5
-
 Nomega-hydroxy-L-arginine in 50 mM CHES/HCl, pH 9.5 containing 10 mM dithiothreitol, at 37°C Porphyromonas gingivalis
3.5.3.6 1.9
-
 D-Arg in 50 mM CHES/HCl, pH 9.5 containing 10 mM dithiothreitol, at 37°C Porphyromonas gingivalis
3.5.3.6 4.7
-
 homoarginine
-
 Porphyromonas gingivalis
3.5.3.6 6
-
 L-canavanine-L-Arg in 50 mM CHES/HCl, pH 9.5 containing 10 mM dithiothreitol, at 37°C Porphyromonas gingivalis
3.5.3.6 6.9
-
 L-Arginine hydroxamate in 50 mM CHES/HCl, pH 9.5 containing 10 mM dithiothreitol, at 37°C Porphyromonas gingivalis
3.5.3.6 18
-
 benzoyl-L-arginine ethyl ester in 50 mM CHES/HCl, pH 9.5 containing 10 mM dithiothreitol, at 37°C Porphyromonas gingivalis
3.5.3.6 31
-
 agmatine-L-Arg
-
 Porphyromonas gingivalis

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
3.5.3.6 additional information PAD is not a metalloenzyme Porphyromonas gingivalis

Molecular Weight [Da]

EC Number Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
3.5.3.6 51000
-
 purified recombinant truncated PAD (missing 43 N-terminal amino acid residues but including Xpress and poly-His tags), SDS-PAGE Porphyromonas gingivalis
3.5.3.6 53000
-
 active enzyme, gel filtration Porphyromonas gingivalis
3.5.3.6 60880
-
 truncated PAD with its poly-His and Xpress epitope tags, calculated from amino acid sequence Porphyromonas gingivalis
3.5.3.6 60890
-
 MALDI-TOF mass spectrometry Porphyromonas gingivalis

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
3.5.3.6 protein L-Arg + H2O Porphyromonas gingivalis
-
 protein L-citrulline + NH3
-
 ?
3.5.3.6 protein L-Arg + H2O Porphyromonas gingivalis BAA-308-5 (W83)
-
 protein L-citrulline + NH3
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
3.5.3.6 Porphyromonas gingivalis
-
-
-
3.5.3.6 Porphyromonas gingivalis BAA-308-5 (W83)
-
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
3.5.3.6 Ni+-NTA resin column chromatography, ultrafiltration, and gel filtration Porphyromonas gingivalis

Specific Activity [micromol/min/mg]

EC Number Specific Activity Minimum [µmol/min/mg] Specific Activity Maximum [µmol/min/mg] Comment Organism
3.5.3.6 0.000345
-
 crude extract, pH 9.5, at 37°C Porphyromonas gingivalis
3.5.3.6 0.175
-
 after purification, pH 9.5, at 37°C Porphyromonas gingivalis

Storage Stability

EC Number Storage Stability Organism
3.5.3.6 25°C or -80°C, in the presence of 0.5 mM 2-mercaptoethanol or 1 mM dithiothreitol and 0.1% (w/v) sodium azide in 50 mM potassium phosphate buffer (pH 7.8), 2 weeks, no appreciable loss of activity Porphyromonas gingivalis
3.5.3.6 4°C or -20°C, in the presence of 0.5 mM 2-mercaptoethanol or 1 mM dithiothreitol and 0.1% (w/v) sodium azide in 50 mM potassium phosphate buffer (pH 7.8), 2 weeks, aggregation of the protein occurs Porphyromonas gingivalis

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
3.5.3.6 agmatine-L-Arg + H2O 3.2% activity compared to L-Arg Porphyromonas gingivalis N5-carbamoyl-N2-[4-(carbamoylamino)butyl]-L-ornithine + NH3
-
 ?
3.5.3.6 benzoyl-L-arginine ethyl ester + H2O 8.1% activity compared to L-Arg Porphyromonas gingivalis benzoyl-L-citrulline ethyl ester + NH3
-
 ?
3.5.3.6 benzoyl-L-arginine ethyl ester + H2O 8.1% activity compared to L-Arg Porphyromonas gingivalis BAA-308-5 (W83) benzoyl-L-citrulline ethyl ester + NH3
-
 ?
3.5.3.6 bradykinin-L-Arg + H2O 18.8% activity compared to L-Arg Porphyromonas gingivalis bradykinin-L-citrulline + NH3
-
 ?
3.5.3.6 D-Arg + H2O 26.4% activity compared to L-Arg Porphyromonas gingivalis ?
-
 ?
3.5.3.6 homoarginine + H2O 50% activity compared to L-Arg Porphyromonas gingivalis (2S)-2-amino-6-[(aminocarbonyl)amino]hexanoic acid + NH3
-
 ?
3.5.3.6 KRPPGFSPL + H2O 3.1% activity compared to L-Arg Porphyromonas gingivalis L-lysyl-N5-carbamoyl-L-ornithyl-L-prolyl-L-prolylglycyl-L-phenylalanyl-L-seryl-L-prolyl-L-leucine + NH3
-
 ?
3.5.3.6 L-Arg + H2O 100% activity Porphyromonas gingivalis citrulline + NH3
-
 ?
3.5.3.6 L-Arg + H2O 100% activity Porphyromonas gingivalis BAA-308-5 (W83) citrulline + NH3
-
 ?
3.5.3.6 L-arginine hydroxamate + H2O 68.2% activity compared to L-Arg Porphyromonas gingivalis ?
-
 ?
3.5.3.6 L-canavanine-L-Arg + H2O 2.5% activity compared to L-Arg Porphyromonas gingivalis O-ureido-L-homoserine + NH3
-
 ?
3.5.3.6 L-Pro-L-Arg-L-Phe + H2O 3.4% activity compared to L-Arg Porphyromonas gingivalis ?
-
 ?
3.5.3.6 L-Pro-L-Phe-L-Arg + H2O 78.2% activity compared to L-Arg Porphyromonas gingivalis ?
-
 ?
3.5.3.6 additional information no activity with Nomega,Nomega-dimethyl-L-arginine Porphyromonas gingivalis ?
-
 ?
3.5.3.6 additional information no activity with Nomega,Nomega-dimethyl-L-arginine Porphyromonas gingivalis BAA-308-5 (W83) ?
-
 ?
3.5.3.6 N-alpha-benzoyl-L-arginine + H2O 54.5% activity compared to L-Arg Porphyromonas gingivalis N-alpha-benzoyl-L-citrulline + NH3
-
 ?
3.5.3.6 N-alpha-benzoyl-L-arginine + H2O 54.5% activity compared to L-Arg Porphyromonas gingivalis BAA-308-5 (W83) N-alpha-benzoyl-L-citrulline + NH3
-
 ?
3.5.3.6 Nomega-hydroxy-L-arginine + H2O 2.1% activity compared to L-Arg Porphyromonas gingivalis Nomega-hydroxy-L-citrulline + NH3
-
 ?
3.5.3.6 protein L-Arg + H2O
-
 Porphyromonas gingivalis protein L-citrulline + NH3
-
 ?
3.5.3.6 protein L-Arg + H2O
-
 Porphyromonas gingivalis BAA-308-5 (W83) protein L-citrulline + NH3
-
 ?

Synonyms

EC Number Synonyms Comment Organism
3.5.3.6 PAD
-
 Porphyromonas gingivalis
3.5.3.6 peptidylarginine deiminase
-
 Porphyromonas gingivalis

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
3.5.3.6 55
-
-
 Porphyromonas gingivalis

Temperature Stability [°C]

EC Number Temperature Stability Minimum [°C] Temperature Stability Maximum [°C] Comment Organism
3.5.3.6 4
-
 PAD is cold sensitive, it aggregates within 30 min at 4°C, but aggregated PAD displays variable activity for up to one week after re-suspension with storage buffer Porphyromonas gingivalis
3.5.3.6 100
-
 no product formation is observed in reaction mixtures containing the PAD sample that have been boiled Porphyromonas gingivalis

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
3.5.3.6 0.0046
-
 Nomega-hydroxy-L-arginine in 50 mM CHES/HCl, pH 9.5 containing 10 mM dithiothreitol, at 37°C Porphyromonas gingivalis
3.5.3.6 0.0052
-
 L-canavanine-L-Arg in 50 mM CHES/HCl, pH 9.5 containing 10 mM dithiothreitol, at 37°C Porphyromonas gingivalis
3.5.3.6 0.0068
-
 bradykinin antagonist-L-Arg in 50 mM CHES/HCl, pH 9.5 containing 10 mM dithiothreitol, at 37°C Porphyromonas gingivalis
3.5.3.6 0.007
-
 agmatine-L-Arg
-
 Porphyromonas gingivalis
3.5.3.6 0.0075
-
 L-Pro-L-Arg-L-Phe in 50 mM CHES/HCl, pH 9.5 containing 10 mM dithiothreitol, at 37°C Porphyromonas gingivalis
3.5.3.6 0.019
-
 benzoyl-L-arginine ethyl ester in 50 mM CHES/HCl, pH 9.5 containing 10 mM dithiothreitol, at 37°C Porphyromonas gingivalis
3.5.3.6 0.043
-
 bradykinin-L-Arg in 50 mM CHES/HCl, pH 9.5 containing 10 mM dithiothreitol, at 37°C Porphyromonas gingivalis
3.5.3.6 0.058
-
 D-Arg in 50 mM CHES/HCl, pH 9.5 containing 10 mM dithiothreitol, at 37°C Porphyromonas gingivalis
3.5.3.6 0.11
-
 homoarginine
-
 Porphyromonas gingivalis
3.5.3.6 0.12
-
 N-alpha-benzoyl-L-arginine in 50 mM CHES/HCl, pH 9.5 containing 10 mM dithiothreitol, at 37°C Porphyromonas gingivalis
3.5.3.6 0.15
-
 L-Arginine hydroxamate in 50 mM CHES/HCl, pH 9.5 containing 10 mM dithiothreitol, at 37°C Porphyromonas gingivalis
3.5.3.6 0.17
-
 L-Pro-L-Phe-L-Arg in 50 mM CHES/HCl, pH 9.5 containing 10 mM dithiothreitol, at 37°C Porphyromonas gingivalis
3.5.3.6 0.22
-
 L-Arg in 50 mM CHES/HCl, pH 9.5 containing 10 mM dithiothreitol, at 37°C Porphyromonas gingivalis

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
3.5.3.6 9.5
-
-
 Porphyromonas gingivalis

pH Range

EC Number pH Minimum pH Maximum Comment Organism
3.5.3.6 6 11 38.5% activity remaining at pH 6.0 and 3.4% activity remaining at pH 11.0 Porphyromonas gingivalis

pH Stability

EC Number pH Stability pH Stability Maximum Comment Organism
3.5.3.6 7 9.5 the enzyme at 13 mg/ml remains active at pH 7.0, 8.0 and 9.5 for several days at 25°C Porphyromonas gingivalis

Cofactor

EC Number Cofactor Comment Organism Structure
3.5.3.6 additional information PAD does not need a cofactor for catalysis and stability Porphyromonas gingivalis

kcat/KM [mM/s]

EC Number kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
3.5.3.6 0.00023
-
 agmatine-L-Arg
-
 Porphyromonas gingivalis
3.5.3.6 0.00093
-
 L-canavanine-L-Arg in 50 mM CHES/HCl, pH 9.5 containing 10 mM dithiothreitol, at 37°C Porphyromonas gingivalis
3.5.3.6 0.00099
-
 benzoyl-L-arginine ethyl ester in 50 mM CHES/HCl, pH 9.5 containing 10 mM dithiothreitol, at 37°C Porphyromonas gingivalis
3.5.3.6 0.003
-
 Nomega-hydroxy-L-arginine in 50 mM CHES/HCl, pH 9.5 containing 10 mM dithiothreitol, at 37°C Porphyromonas gingivalis
3.5.3.6 0.022
-
 L-Arginine hydroxamate in 50 mM CHES/HCl, pH 9.5 containing 10 mM dithiothreitol, at 37°C Porphyromonas gingivalis
3.5.3.6 0.024
-
 homoarginine
-
 Porphyromonas gingivalis
3.5.3.6 0.031
-
 D-Arg in 50 mM CHES/HCl, pH 9.5 containing 10 mM dithiothreitol, at 37°C Porphyromonas gingivalis
3.5.3.6 0.11
-
 L-Pro-L-Arg-L-Phe in 50 mM CHES/HCl, pH 9.5 containing 10 mM dithiothreitol, at 37°C Porphyromonas gingivalis
3.5.3.6 0.19
-
 L-Arg in 50 mM CHES/HCl, pH 9.5 containing 10 mM dithiothreitol, at 37°C Porphyromonas gingivalis
3.5.3.6 0.21
-
 bradykinin antagonist-L-Arg in 50 mM CHES/HCl, pH 9.5 containing 10 mM dithiothreitol, at 37°C Porphyromonas gingivalis
3.5.3.6 1.9
-
 L-Pro-L-Phe-L-Arg in 50 mM CHES/HCl, pH 9.5 containing 10 mM dithiothreitol, at 37°C Porphyromonas gingivalis
3.5.3.6 2.1
-
 bradykinin-L-Arg in 50 mM CHES/HCl, pH 9.5 containing 10 mM dithiothreitol, at 37°C Porphyromonas gingivalis
3.5.3.6 6 12 N-alpha-benzoyl-L-arginine in 50 mM CHES/HCl, pH 9.5 containing 10 mM dithiothreitol, at 37°C Porphyromonas gingivalis