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Literature summary for 3.4.21.83 extracted from

  • Mikhailova, A.G.; Rakitina, T.V.; Timofeev, V.I.; Karlinsky, D.M.; Korzhenevskiy, D.A.; Agapova, Y.K.; Vlaskina, A.V.; Ovchinnikova, M.V.; Gorlenko, V.A.; Rumsh, L.D.
    Activity modulation of the oligopeptidase B from Serratia proteamaculans by site-directed mutagenesis of amino acid residues surrounding catalytic triad histidine (2017), Biochimie, 139, 125-136 .
    View publication on PubMed

Protein Variants

Protein Variants Comment Organism
D647A site-directed mutagenesis, the mutant shows altered substrate specificity compared to the wild-type enzyme Serratia proteamaculans
D647F site-directed mutagenesis, the mutant shows altered substrate specificity compared to the wild-type enzyme Serratia proteamaculans
D649A site-directed mutagenesis, the mutant shows altered substrate specificity compared to the wild-type enzyme Serratia proteamaculans
D649F site-directed mutagenesis, the mutant shows altered substrate specificity compared to the wild-type enzyme Serratia proteamaculans
E125A site-directed mutagenesis, the mutant shows altered substrate specificity compared to the wild-type enzyme Serratia proteamaculans
E125R site-directed mutagenesis, the mutant shows altered substrate specificity compared to the wild-type enzyme Serratia proteamaculans
E75A site-directed mutagenesis, the mutant shows altered substrate specificity compared to the wild-type enzyme Serratia proteamaculans
E75A/R658A site-directed mutagenesis, the mutant shows altered substrate specificity compared to the wild-type enzyme Serratia proteamaculans
E75F site-directed mutagenesis, the mutant shows altered substrate specificity compared to the wild-type enzyme Serratia proteamaculans
E96A site-directed mutagenesis, the mutant shows altered substrate specificity compared to the wild-type enzyme Serratia proteamaculans
E96A/E125A site-directed mutagenesis, the mutant shows altered substrate specificity compared to the wild-type enzyme Serratia proteamaculans
E96A/K660A site-directed mutagenesis, the mutant shows altered substrate specificity compared to the wild-type enzyme Serratia proteamaculans
E96F site-directed mutagenesis, the mutant shows altered substrate specificity compared to the wild-type enzyme Serratia proteamaculans
K655A site-directed mutagenesis, the mutant shows altered substrate specificity compared to the wild-type enzyme Serratia proteamaculans
K655R site-directed mutagenesis, the mutant shows altered substrate specificity compared to the wild-type enzyme Serratia proteamaculans
K660A site-directed mutagenesis, the mutant shows altered substrate specificity compared to the wild-type enzyme Serratia proteamaculans
K660F site-directed mutagenesis, the mutant shows altered substrate specificity compared to the wild-type enzyme Serratia proteamaculans
R658A site-directed mutagenesis, the mutant shows altered substrate specificity compared to the wild-type enzyme Serratia proteamaculans
R658A/K660A site-directed mutagenesis, the mutant shows altered substrate specificity compared to the wild-type enzyme Serratia proteamaculans
R658F site-directed mutagenesis, the mutant shows altered substrate specificity compared to the wild-type enzyme Serratia proteamaculans
S656F site-directed mutagenesis, the mutant shows altered substrate specificity compared to the wild-type enzyme Serratia proteamaculans
S656Ter site-directed mutagenesis, mutation S656Ter gives the truncated protein PSP1-655 Serratia proteamaculans

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
additional information
-
additional information Michaelis-Menten kinetics of wild-type and mutant enzymes, overview Serratia proteamaculans
0.0028
-
benzyloxycarbonyl-L-argininyl-L-arginyl-4-nitroanilide recombinant mutant E125A, pH 8.0, 25°C Serratia proteamaculans
0.00473
-
benzyloxycarbonyl-L-argininyl-L-arginyl-4-nitroanilide recombinant wild-type enzyme, pH 8.0, 25°C Serratia proteamaculans
0.00552
-
benzyloxycarbonyl-L-lysyl-L-arginyl-4-nitroanilide recombinant mutant D647A, pH 8.0, 25°C Serratia proteamaculans
0.00861
-
benzyloxycarbonyl-L-lysyl-L-arginyl-4-nitroanilide recombinant mutant D649A, pH 8.0, 25°C Serratia proteamaculans
0.00864
-
benzyloxycarbonyl-L-argininyl-L-arginyl-4-nitroanilide recombinant mutant D647A, pH 8.0, 25°C Serratia proteamaculans
0.00954
-
benzyloxycarbonyl-L-argininyl-L-arginyl-4-nitroanilide recombinant mutant K660A, pH 8.0, 25°C Serratia proteamaculans
0.0106
-
benzyloxycarbonyl-L-argininyl-L-arginyl-4-nitroanilide recombinant mutant D649A, pH 8.0, 25°C Serratia proteamaculans
0.01086
-
benzyloxycarbonyl-L-lysyl-L-arginyl-4-nitroanilide recombinant mutant K660A, pH 8.0, 25°C Serratia proteamaculans
0.0172
-
benzyloxycarbonyl-L-lysyl-L-arginyl-4-nitroanilide recombinant mutant E125A, pH 8.0, 25°C Serratia proteamaculans
0.0194
-
benzyloxycarbonyl-L-lysyl-L-arginyl-4-nitroanilide recombinant wild-type enzyme, pH 8.0, 25°C Serratia proteamaculans
0.0279
-
Nalpha-benzoyl-DL-argininyl-4-nitroanilide recombinant mutant D649A, pH 8.0, 25°C Serratia proteamaculans
0.0316
-
Nalpha-benzoyl-DL-argininyl-4-nitroanilide recombinant mutant D647A, pH 8.0, 25°C Serratia proteamaculans
0.0317
-
benzyloxycarbonyl-L-argininyl-L-arginyl-4-nitroanilide recombinant mutant K655A, pH 8.0, 25°C Serratia proteamaculans
0.046
-
Nalpha-benzoyl-DL-argininyl-4-nitroanilide recombinant mutant E125A, pH 8.0, 25°C Serratia proteamaculans
0.0708
-
Nalpha-benzoyl-DL-argininyl-4-nitroanilide recombinant mutant K660A, pH 8.0, 25°C Serratia proteamaculans
0.0836
-
Nalpha-benzoyl-DL-argininyl-4-nitroanilide recombinant wild-type enzyme, pH 8.0, 25°C Serratia proteamaculans
0.143
-
benzyloxycarbonyl-L-lysyl-L-arginyl-4-nitroanilide recombinant mutant K655A, pH 8.0, 25°C Serratia proteamaculans
0.51
-
Nalpha-benzoyl-DL-argininyl-4-nitroanilide recombinant mutant K655A, pH 8.0, 25°C Serratia proteamaculans

Organism

Organism UniProt Comment Textmining
Serratia proteamaculans B3VI58
-
-

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
benzyloxycarbonyl-L-argininyl-L-arginyl-4-nitroanilide + H2O
-
Serratia proteamaculans Nalpha-benzoyl-L-arginyl-L-arginine + 4-nitroaniline
-
?
benzyloxycarbonyl-L-lysyl-L-arginyl-4-nitroanilide + H2O
-
Serratia proteamaculans Nalpha-benzoyl-L-lysyl-L-arginine + 4-nitroaniline
-
?
Nalpha-benzoyl-DL-argininyl-4-nitroanilide + H2O
-
Serratia proteamaculans Nalpha-benzoyl-DL-arginine + 4-nitroaniline
-
?

Subunits

Subunits Comment Organism
More the enzyme has a two-domain structure of the enzyme including C-terminal peptidase catalytic domain and N-terminal seven-bladed beta-propeller domain Serratia proteamaculans

Synonyms

Synonyms Comment Organism
OpdB
-
Serratia proteamaculans

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
25
-
assay at Serratia proteamaculans

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
4.73
-
Nalpha-benzoyl-DL-argininyl-4-nitroanilide recombinant mutant K655A, pH 8.0, 25°C Serratia proteamaculans
6.27
-
Nalpha-benzoyl-DL-argininyl-4-nitroanilide recombinant mutant K660A, pH 8.0, 25°C Serratia proteamaculans
6.5
-
Nalpha-benzoyl-DL-argininyl-4-nitroanilide recombinant mutant D647A, pH 8.0, 25°C Serratia proteamaculans
11.31
-
benzyloxycarbonyl-L-argininyl-L-arginyl-4-nitroanilide recombinant mutant K655A, pH 8.0, 25°C Serratia proteamaculans
14.35
-
Nalpha-benzoyl-DL-argininyl-4-nitroanilide recombinant wild-type enzyme, pH 8.0, 25°C Serratia proteamaculans
16.8
-
Nalpha-benzoyl-DL-argininyl-4-nitroanilide recombinant mutant D649A, pH 8.0, 25°C Serratia proteamaculans
24.05
-
benzyloxycarbonyl-L-argininyl-L-arginyl-4-nitroanilide recombinant mutant K660A, pH 8.0, 25°C Serratia proteamaculans
25.23
-
benzyloxycarbonyl-L-lysyl-L-arginyl-4-nitroanilide recombinant mutant D647A, pH 8.0, 25°C Serratia proteamaculans
27.35
-
benzyloxycarbonyl-L-lysyl-L-arginyl-4-nitroanilide recombinant mutant K655A, pH 8.0, 25°C Serratia proteamaculans
29.97
-
benzyloxycarbonyl-L-lysyl-L-arginyl-4-nitroanilide recombinant mutant K660A, pH 8.0, 25°C Serratia proteamaculans
30.84
-
benzyloxycarbonyl-L-argininyl-L-arginyl-4-nitroanilide recombinant mutant D647A, pH 8.0, 25°C Serratia proteamaculans
32.36
-
benzyloxycarbonyl-L-argininyl-L-arginyl-4-nitroanilide recombinant mutant D649A, pH 8.0, 25°C Serratia proteamaculans
33.975
-
benzyloxycarbonyl-L-argininyl-L-arginyl-4-nitroanilide recombinant wild-type enzyme, pH 8.0, 25°C Serratia proteamaculans
45.37
-
benzyloxycarbonyl-L-argininyl-L-arginyl-4-nitroanilide recombinant mutant E125A, pH 8.0, 25°C Serratia proteamaculans
51.22
-
benzyloxycarbonyl-L-lysyl-L-arginyl-4-nitroanilide recombinant mutant D649A, pH 8.0, 25°C Serratia proteamaculans
52.34
-
benzyloxycarbonyl-L-lysyl-L-arginyl-4-nitroanilide recombinant wild-type enzyme, pH 8.0, 25°C Serratia proteamaculans
63.71
-
Nalpha-benzoyl-DL-argininyl-4-nitroanilide recombinant mutant E125A, pH 8.0, 25°C Serratia proteamaculans
85.55
-
benzyloxycarbonyl-L-lysyl-L-arginyl-4-nitroanilide recombinant mutant E125A, pH 8.0, 25°C Serratia proteamaculans

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
8
-
assay at Serratia proteamaculans

General Information

General Information Comment Organism
evolution oligopeptidase B is a trypsin-like peptidase belonging to the family of serine prolyl oligopeptidases with a two-domain structure of the enzyme including C-terminal peptidase catalytic domain and N-terminal seven-bladed beta-propeller domain Serratia proteamaculans
malfunction the removal of negatively charged Asp647 and Asp649 leads therefore to better binding of lysine at P2 substrate position and decreased binding of arginine at the same position Serratia proteamaculans
additional information comparative structure of the enzyme using the structures of both closed form of OpdB from Leishmania major (PDB ID 2XE4) and open form of OpdB from Trypanosoma brucei (PDB ID 4BP8) as templates, overview Serratia proteamaculans

kcat/KM [mM/s]

kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
9.28
-
Nalpha-benzoyl-DL-argininyl-4-nitroanilide recombinant mutant K655A, pH 8.0, 25°C Serratia proteamaculans
88.56
-
Nalpha-benzoyl-DL-argininyl-4-nitroanilide recombinant mutant K660A, pH 8.0, 25°C Serratia proteamaculans
171.65
-
Nalpha-benzoyl-DL-argininyl-4-nitroanilide recombinant wild-type enzyme, pH 8.0, 25°C Serratia proteamaculans
191.3
-
benzyloxycarbonyl-L-lysyl-L-arginyl-4-nitroanilide recombinant mutant K655A, pH 8.0, 25°C Serratia proteamaculans
205.7
-
Nalpha-benzoyl-DL-argininyl-4-nitroanilide recombinant mutant D647A, pH 8.0, 25°C Serratia proteamaculans
356.8
-
benzyloxycarbonyl-L-argininyl-L-arginyl-4-nitroanilide recombinant mutant K655A, pH 8.0, 25°C Serratia proteamaculans
602.15
-
Nalpha-benzoyl-DL-argininyl-4-nitroanilide recombinant mutant D649A, pH 8.0, 25°C Serratia proteamaculans
1385
-
Nalpha-benzoyl-DL-argininyl-4-nitroanilide recombinant mutant E125A, pH 8.0, 25°C Serratia proteamaculans
2521
-
benzyloxycarbonyl-L-argininyl-L-arginyl-4-nitroanilide recombinant mutant K660A, pH 8.0, 25°C Serratia proteamaculans
2697.9
-
benzyloxycarbonyl-L-lysyl-L-arginyl-4-nitroanilide recombinant wild-type enzyme, pH 8.0, 25°C Serratia proteamaculans
2759.7
-
benzyloxycarbonyl-L-lysyl-L-arginyl-4-nitroanilide recombinant mutant K660A, pH 8.0, 25°C Serratia proteamaculans
3052.8
-
benzyloxycarbonyl-L-argininyl-L-arginyl-4-nitroanilide recombinant mutant D649A, pH 8.0, 25°C Serratia proteamaculans
3569.4
-
benzyloxycarbonyl-L-argininyl-L-arginyl-4-nitroanilide recombinant mutant D647A, pH 8.0, 25°C Serratia proteamaculans
4588.8
-
benzyloxycarbonyl-L-lysyl-L-arginyl-4-nitroanilide recombinant mutant D647A, pH 8.0, 25°C Serratia proteamaculans
4973.8
-
benzyloxycarbonyl-L-lysyl-L-arginyl-4-nitroanilide recombinant mutant E125A, pH 8.0, 25°C Serratia proteamaculans
5948.9
-
benzyloxycarbonyl-L-lysyl-L-arginyl-4-nitroanilide recombinant mutant D649A, pH 8.0, 25°C Serratia proteamaculans
7182.9
-
benzyloxycarbonyl-L-argininyl-L-arginyl-4-nitroanilide recombinant wild-type enzyme, pH 8.0, 25°C Serratia proteamaculans
16203.6
-
benzyloxycarbonyl-L-argininyl-L-arginyl-4-nitroanilide recombinant mutant E125A, pH 8.0, 25°C Serratia proteamaculans