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Literature summary extracted from

  • Eichinger, A.; Beisel, H.G.; Jacob, U.; Huber, R.; Medrano, F.J.; Banbula, A.; Potempa, J.; Travis, J.; Bode, W.
    Crystal structure of gingipain R: an Arg-specific bacterial cysteine proteinase with caspase-like fold (1999), EMBO J., 18, 5453-5462.
    View publication on PubMedView publication on EuropePMC

Application

EC Number Application Comment Organism
3.4.22.37 pharmacology enzyme structure is an excellent template for the rational design of drugs with a potential to cure and prevent periodontitis Porphyromonas gingivalis

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
3.4.22.37 purified RgpB free or in complex with fast acting, irreversible inhibitor D-Phe-Phe-Arg-chloromethylketone, activated by incubation for 30 min in 0.1 M HEPES, pH 8.0, 10 mM L-cysteine, 2.5 mM CaCl2, at 37°C, alkylation of the active site cysteine by addition of inhibitor, crystallization of dialysed sample by vapour diffusion method, 8 mg/ml protein in 3 mM MOPS, pH 7.2 0.02% NaN3, plus equal volume of reservoir solution: 3.4 M 1,6-hexandiol, 0.2 M MgCl2, 0.1 M Tris-HCl, pH 8.5, at 21°C, several weeks, X-ray diffraction structure determination at 1.5-2.16 A resolution and analysis, structure modeling Porphyromonas gingivalis

Inhibitors

EC Number Inhibitors Comment Organism Structure
3.4.22.37 D-Phe-Phe-Arg-chloromethylketone fast acting, irreversible alkylating inhibitor Porphyromonas gingivalis

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
3.4.22.37 protein + H2O Porphyromonas gingivalis
-
 peptides
-
 ?
3.4.22.37 protein + H2O Porphyromonas gingivalis HG66
-
 peptides
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
3.4.22.37 Porphyromonas gingivalis
-
 gingipain R2, i.e. RgpB, isozyme II
-
3.4.22.37 Porphyromonas gingivalis HG66
-
 gingipain R2, i.e. RgpB, isozyme II
-

Reaction

EC Number Reaction Comment Organism Reaction ID
3.4.22.37 hydrolysis of proteins and small molecule substrates, with a preference for Arg in P1 Cys244-His211 catalytic diad and a nearby Glu arranged around the S1 specificity pocket, which carries an Asp residue to enforce preference for Arg-P1 residues, mechanism and binding mode at the active site Porphyromonas gingivalis
a

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
3.4.22.37 protein + H2O
-
 Porphyromonas gingivalis peptides
-
 ?
3.4.22.37 protein + H2O
-
 Porphyromonas gingivalis HG66 peptides
-
 ?

Synonyms

EC Number Synonyms Comment Organism
3.4.22.37 Arg-specific cysteine protease
-
 Porphyromonas gingivalis
3.4.22.37 HRgpA
-
 Porphyromonas gingivalis
3.4.22.37 RgB
-
 Porphyromonas gingivalis

pI Value

EC Number Organism Comment pI Value Maximum pI Value
3.4.22.37 Porphyromonas gingivalis RgpB isozyme II, isoelectric focusing
-
 5.1