3.4.21.83: Oligopeptidase B
This is an abbreviated version!
For detailed information about Oligopeptidase B, go to the full flat file.
Word Map on EC 3.4.21.83
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3.4.21.83
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gingivalis
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prolyl
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leupeptin
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chymotrypsin-like
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antipain
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porphyromonas
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aprotinin
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chloromethyl
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chymostatin
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tlck
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tryptase
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2-macroglobulin
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benzamidine
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acrosin
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phenylmethanesulfonyl
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proteamaculans
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bapna
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drug development
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medicine
- 3.4.21.83
- gingivalis
-
prolyl
- leupeptin
-
chymotrypsin-like
- antipain
- porphyromonas
- aprotinin
-
chloromethyl
- chymostatin
- tlck
- tryptase
-
2-macroglobulin
- benzamidine
- acrosin
-
phenylmethanesulfonyl
- proteamaculans
-
bapna
- drug development
- medicine
Reaction
Hydrolysis of -Arg-/-, -Lys-/- bonds in oligopeptides, even when P1' residue is proline =
Synonyms
La_OpB, oligopeptidase B, oligopeptidase B-like, oligopeptidase B2, OP-Tb, OPB, OPB2, OPBTc, Opd B, OpdB, Protease II, Proteinase, Escherichia coli alkaline, II, PSP, Spro_3467, Tb-OP, Tc 120, Tc-OP, trypsin-like protease
ECTree
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Inhibitors
Inhibitors on EC 3.4.21.83 - Oligopeptidase B
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(2R)-2-amino-N-[4-(dimethylaminomethyl)phenyl]propanamide
ZINC 37042497, shows the lowest estimated binding energy by AutoDock program. The selected docking pose is also located close to the catalytic site and interacts through hydrogen bonds with Glu539, Ser614, Arg704, Glu659, and Phe641 residues. As the compound is protonated, it also makes ionic interactions with Glu539 and Glu659. Besides, it also performs hydrophobic contacts with Tyr537, Phe641, Leu655, and Ala615; ZINC 37042497, the compound shows hydrogen bonds with Arg655 and Glu612 residues, and it also forms an ionic interaction with Glu612 and hydrophobic contacts with Leu608, Tyr490, Ala569, and Val656
(3R)-3-amino-N-[3-(1H-tetrazol-5-yl)phenyl]butanamide
ZINC 37608688, located close to the catalytic site. It interacts through hydrogen bonds with Glu612, Pro607, Arg655 and Tyr490, and hydrophobic interactions with His688 and Arg655; ZINC 37608688, the compound forms hydrogen bonds with Tyr537, Pro654, Glu659 and Arg704. Moreover, compound 3 participates on hydrophobic interactions with Ala615, Phe641, Leu653, and Val705
1-(5-hydroxy-pyridine-3-carbonyl)-pyrrolidine-2-carboxylic acid
ZINC 19735155; ZINC 19735155, interacts with the binding site through hydrogen bonds with Ser568 and Glu612, Pi-stacking with Tyr490, and salt bridges with Glu612 and Arg567
4-(2-aminoethyl)benzenesulfonylfluoride
non-peptide irreversible serine-peptidase inhibitor
benzoyl-Arg-4-nitroanilide
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enzyme is inhibited by high concentrations of substrate
bovine basic pancreatic trypsin inhibitor
substrate Nalpha-benzoyl-DL-Arg-4-nitroanilide, competitive
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diisopropylfluorophosphate
non-peptide irreversible serine-peptidase inhibitor
m-phenanthroline
substrates Nalpha-benzoyl-DL-Arg-4-nitroanilide, acetyl-Leu-Leu-Arg-4-nitroanilide, anticompetitive
methanol
incubation in 20% (v/v) methanol (10-20 h, 4°C) results in partial decomposition of the high molecular weight PSP-GroEL complex with precipitation of denatured chaperonin and a small (no more than 10%) loss of PSP activity
N-ethyl-2-oxo-benzimidazole-5-sulphonamide
ZINC 63887176; ZINC 63887176, interacting through hydrogen bond with Glu659 and Pi-Pi stacking interaction with Tyr537
NaCl
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loss of almost 50 and 70% of its activity in the presence of 0.2 and 1.0 M NaCl, respectively. Presence of NaCl does not disrupt the dimeric structure
NEM
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Cys256 is the reactive cysteine residue that mediates OpdB inhibition. Cys256 adducts occlude the P1 substrate-binding site, preventing substrate binding
o-phenanthroline
substrates Nalpha-benzoyl-DL-Arg-4-nitroanilide, acetyl-Leu-Leu-Arg-4-nitroanilide, anticompetitive
p-chloromercuribenzoate
non-peptide irreversible serine-peptidase inhibitor
peptidyl phosphonate alpha-aminoalkyl diphenyl ester
irreversible peptidyl inhibitors
protamines
protamines, basic 30-32 residue peptides that are rich in Arg residues, are potent inhibitors of OpdB
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tert-butoxycarbonyl-L-Val-L-Leu-L-Lys-7-amido-4-methylcoumarin
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in the case of added dithiothreitol, reduced glutathione, or oxidized glutathione, a high concentration of the substrate tert-butoxycarbonyl-L-Val-L-Leu-L-Lys-7-amido-4-methylcoumarin inhibits the enzyme activity. By contrast, addition of 1 M NaCl to either dithiothreitol, reduced glutathione, or oxidized glutathione or 1 M NaCl alone prevents substrate inhibition
trans-4-guanidinomethylcyclohexanecarboxylic acid 4-tert-butylphenyl ester
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IC50: about 0.01 mM. Oligopeptidase B is much more sensitive than oligopeptidase B
ZnCl2
substrate Nalpha-benzoyl-DL-Arg-4-nitroanilide, noncompetitive
3,4-dichloroisocoumarin
non-peptide irreversible serine-peptidase inhibitor
irreversible inhibition
4-(2-aminoethyl)benzenesulfonyl fluoride
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OpdB activity toward tert-butoxycarbonyl-L-Val-L-Leu-L-Lys-7-amido-4-methylcoumarin hydrolysis is inhibited completely by 4 mM pefbloc SC
antipain
antipain-OPBcomplex shows hydrogen bonds with Ser568, Glu612, Glu660, and His688 residues. Besides, it can perform hydrogen bond or ionic interaction with Arg655 residue. Antipain also interacts through hydrogen bonds with Tyr537, Glu659 and Arg704; molecular docking
antipain
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OpdB activity toward tert-butoxycarbonyl-L-Val-L-Leu-L-Lys-7-amido-4-methylcoumarin hydrolysis is inhibited completely by 0.3 mM antipain
leupeptin
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OpdB activity toward tert-butoxycarbonyl-L-Val-L-Leu-L-Lys-7-amido-4-methylcoumarin hydrolysis is inhibited completely by 0.05 mM leupeptin
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1,10-phenanthroline; EDTA; not: chelating agents; PMSF; several natural trypsin inhibitors; sulfhydryl agents
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additional information
no inhibition by N-ethylmaleimide and iodoacetic acid. This is consistent with the absence of a cysteine residue at position 256 which is replaced by His
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additional information
virtual inhibitor screening, molecular docking using the three-dimensional structure model of OPB; virtual inhibitor screening, molecular docking using the three-dimensional structure model of OPB2
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additional information
virtual inhibitor screening, molecular docking using the three-dimensional structure model of OPB; virtual inhibitor screening, molecular docking using the three-dimensional structure model of OPB2
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additional information
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virtual inhibitor screening, molecular docking using the three-dimensional structure model of OPB; virtual inhibitor screening, molecular docking using the three-dimensional structure model of OPB2
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additional information
no inhibition of wild-type enzyme with iodoacetamide, iodoacetate, N-ethylmaleimide, EDTA, EGTA, bestatin,amastatin, arphamenine A, elastinal, dynorphin A or dynorphin B
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additional information
treatment of enzyme PSP with immobilized trypsin leads to production of a stable truncated enzyme form (PSP-Tr with about 75 kDa) which lacks 22 C-terminal amino acid residues and completely loses enzymatic activity, presumably because of changes in the nearest environment of His652 of the catalytic triad
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additional information
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treatment of enzyme PSP with immobilized trypsin leads to production of a stable truncated enzyme form (PSP-Tr with about 75 kDa) which lacks 22 C-terminal amino acid residues and completely loses enzymatic activity, presumably because of changes in the nearest environment of His652 of the catalytic triad
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additional information
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OpdB is not inhibited by E-64 (0.03 mM), pepstain (0.04 mM), EDTA (1 mM), chimostatin (0.2 mM), and phosphoramidon (0.4 mM)
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additional information
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reducing reagent such as dithiothreitol has no effect on the inactivation of wild type and mutant OPBs by heat and urea treatment
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