Any feedback?
Literature summary for 3.5.1.88 extracted from
- Identification of crucial amino acids of bacterial peptide deformylases affecting enzymatic activity in response to oxidative stress (2014), J. Bacteriol., 196, 90-99.
Cloned(Commentary)
| Cloned (Comment) | Organism |
|---|---|
| gene def, subcloning in Escherichia coli strain DH5alpha, recombinant expression of His-tagged enzyme in Escherichia coli strain BL21(DE3) | Mycobacterium tuberculosis |
| gene def, subcloning in Escherichia coli strain DH5alpha, recombinant expression of His-tagged enzyme in Escherichia coli strain BL21(DE3) | Salmonella enterica subsp. enterica serovar Typhimurium |
Protein Variants
| Protein Variants | Comment | Organism |
|---|---|---|
| C106S | site-directed mutagenesis, inactive mutant | Mycobacterium tuberculosis |
| C130M | site-directed mutagenesis | Salmonella enterica subsp. enterica serovar Typhimurium |
| C130M/V63C | site-directed mutagenesis, the mutant shows reduced enzyme activity and decreased sensitivity to H2O2 compared to the wild-type enzyme | Salmonella enterica subsp. enterica serovar Typhimurium |
| C59S | site-directed mutagenesis, unaltered IC50 value for H2O2 compared to the wild-type enzyme | Mycobacterium tuberculosis |
| C68S | site-directed mutagenesis, the mutant protein exhibits 32fold reduced IC50s for H2O2 compared to wild-type mPDF | Mycobacterium tuberculosis |
| M145C | site-directed mutagenesis, the mutant shows reduced enzyme activity and increased sensitivity to H2O2 compared to the wild-type enzyme | Mycobacterium tuberculosis |
| M145S | site-directed mutagenesis, the mutant shows higly reduced enzyme activity and increased sensitivity to H2O2 compared to the wild-type enzyme | Mycobacterium tuberculosis |
| V63C | site-directed mutagenesis | Salmonella enterica subsp. enterica serovar Typhimurium |
Inhibitors
| Inhibitors | Comment | Organism | Structure |
|---|---|---|---|
| Diethylenetriaminepentaacetic acid | binding structure analysis, overview | Mycobacterium tuberculosis |  |
| Diethylenetriaminepentaacetic acid | binding structure analysis, overview | Salmonella enterica subsp. enterica serovar Typhimurium | |
| EDTA | - |
Mycobacterium tuberculosis | |
| EDTA | - |
Salmonella enterica subsp. enterica serovar Typhimurium | |
| H2O2 | slight inhibition, binding structure analysis, overview | Mycobacterium tuberculosis | |
| H2O2 | binding structure analysis, overview | Salmonella enterica subsp. enterica serovar Typhimurium | |
| additional information | iron-containing PDFs are sensitive to treatment with oxidizing agents because of oxidation of Fe2+ to Fe3+ at the metal binding core | Mycobacterium tuberculosis | |
| additional information | iron-containing PDFs are sensitive to treatment with oxidizing agents because of oxidation of Fe2+ to Fe3+ at the metal binding core | Salmonella enterica subsp. enterica serovar Typhimurium |
KM Value [mM]
| KM Value [mM] | KM Value Maximum [mM] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 2.9 | - |
N-formyl-Met-Ala | pH 7.0, 30°C, recombinant wild-type enzyme | Mycobacterium tuberculosis | |
| 4.7 | - |
N-formyl-Met-Ala | pH 7.0, 30°C, recombinant enzyme mutant M145C | Mycobacterium tuberculosis | |
| 7.7 | - |
N-formyl-Met-Ala | pH 7.0, 30°C, recombinant enzyme mutant C130M/V63C | Salmonella enterica subsp. enterica serovar Typhimurium | |
| 480 | - |
N-formyl-Met-Ala | pH 7.0, 30°C, recombinant wild-type enzyme | Salmonella enterica subsp. enterica serovar Typhimurium | |
Metals/Ions
| Metals/Ions | Comment | Organism | Structure |
|---|---|---|---|
| Fe2+ | iron-containing enzyme variant, the apo-enzyme is enzymatically inactive, conserved metal ion coordinating Cys106 of mPDF | Mycobacterium tuberculosis | |
| Fe2+ | iron-containing enzyme variant, the apo-enzyme is enzymatically inactive, conserved metal ion coordinating Cys90 of sPDF, oxidation of Fe2+ to Fe3+ reduces the enzyme activity | Salmonella enterica subsp. enterica serovar Typhimurium | |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| formyl-L-methionyl peptide + H2O | Mycobacterium tuberculosis | - |
formate + methionyl peptide | - |
? | |
| formyl-L-methionyl peptide + H2O | Salmonella enterica subsp. enterica serovar Typhimurium | - |
formate + methionyl peptide | - |
? | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Mycobacterium tuberculosis | P9WIJ3 | gene def | - |
| Salmonella enterica subsp. enterica serovar Typhimurium | Q8ZLM7 | gene def | - |
Purification (Commentary)
| Purification (Comment) | Organism |
|---|---|
| recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and dialysis | Salmonella enterica subsp. enterica serovar Typhimurium |
| recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickl affinity chromatography and dialysis | Mycobacterium tuberculosis |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| formyl-L-methionyl peptide + H2O | - |
Mycobacterium tuberculosis | formate + methionyl peptide | - |
? | |
| formyl-L-methionyl peptide + H2O | - |
Salmonella enterica subsp. enterica serovar Typhimurium | formate + methionyl peptide | - |
? | |
| N-formyl-Met-Ala + H2O | - |
Mycobacterium tuberculosis | formate + Met-Ala | - |
? | |
| N-formyl-Met-Ala + H2O | - |
Salmonella enterica subsp. enterica serovar Typhimurium | formate + Met-Ala | - |
? | |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| mPDF | - |
Mycobacterium tuberculosis |
- |
Mycobacterium tuberculosis | |
- |
Salmonella enterica subsp. enterica serovar Typhimurium | |
| sPDF | - |
Salmonella enterica subsp. enterica serovar Typhimurium |
Temperature Optimum [°C]
| Temperature Optimum [°C] | Temperature Optimum Maximum [°C] | Comment | Organism |
|---|---|---|---|
| 30 | - |
assay at | Mycobacterium tuberculosis |
| 30 | - |
assay at | Salmonella enterica subsp. enterica serovar Typhimurium |
Turnover Number [1/s]
| Turnover Number Minimum [1/s] | Turnover Number Maximum [1/s] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 0.8 | - |
N-formyl-Met-Ala | pH 7.0, 30°C, recombinant enzyme mutant C130M/V63C | Salmonella enterica subsp. enterica serovar Typhimurium | |
| 3.1 | - |
N-formyl-Met-Ala | pH 7.0, 30°C, recombinant enzyme mutant M145C | Mycobacterium tuberculosis | |
| 4.1 | - |
N-formyl-Met-Ala | pH 7.0, 30°C, recombinant wild-type enzyme | Salmonella enterica subsp. enterica serovar Typhimurium | |
| 8.8 | - |
N-formyl-Met-Ala | pH 7.0, 30°C, recombinant wild-type enzyme | Mycobacterium tuberculosis | |
pH Optimum
| pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
|---|---|---|---|
| 7 | - |
assay at | Mycobacterium tuberculosis |
| 7 | - |
assay at | Salmonella enterica subsp. enterica serovar Typhimurium |
IC50 Value
| IC50 Value | IC50 Value Maximum | Comment | Organism | Inhibitor | Structure |
|---|---|---|---|---|---|
| 0.000045 | - |
pH 7.0, 30°C, recombinant wild-type enzyme | Salmonella enterica subsp. enterica serovar Typhimurium | H2O2 | |
| 0.000049 | - |
pH 7.0, 30°C, recombinant enzyme mutant C130S | Salmonella enterica subsp. enterica serovar Typhimurium | H2O2 | |
| 0.00015 | - |
pH 7.0, 30°C, recombinant enzyme mutant V63C | Salmonella enterica subsp. enterica serovar Typhimurium | H2O2 | |
| 0.00016 | - |
pH 7.0, 30°C, recombinant enzyme mutant C130M | Salmonella enterica subsp. enterica serovar Typhimurium | H2O2 | |
| 0.00144 | - |
pH 7.0, 30°C, recombinant enzyme mutant C130M/V63C | Salmonella enterica subsp. enterica serovar Typhimurium | H2O2 | |
| 0.06 | - |
pH 7.0, 30°C, recombinant enzyme mutant M145C | Mycobacterium tuberculosis | H2O2 | |
| 0.07 | - |
pH 7.0, 30°C, recombinant enzyme mutant M145S | Mycobacterium tuberculosis | H2O2 | |
| 0.5 | - |
pH 7.0, 30°C, recombinant enzyme mutant C58S | Mycobacterium tuberculosis | H2O2 | |
| 13.6 | - |
pH 7.0, 30°C, recombinant enzyme mutant C59C | Mycobacterium tuberculosis | H2O2 | |
| 16.1 | - |
pH 7.0, 30°C, recombinant wild-type enzyme | Mycobacterium tuberculosis | H2O2 | |
General Information
| General Information | Comment | Organism |
|---|---|---|
| physiological function | peptide deformylase is an essential bacterial metalloprotease involved in deformylation of N-formyl group from nascent polypeptide chains during protein synthesis | Mycobacterium tuberculosis |
| physiological function | peptide deformylase is an essential bacterial metalloprotease involved in deformylation of N-formyl group from nascent polypeptide chains during protein synthesis | Salmonella enterica subsp. enterica serovar Typhimurium |
kcat/KM [mM/s]
| kcat/KM Value [1/mMs-1] | kcat/KM Value Maximum [1/mMs-1] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 0.1 | - |
N-formyl-Met-Ala | pH 7.0, 30°C, recombinant enzyme mutant C130M/V63C | Salmonella enterica subsp. enterica serovar Typhimurium | |
| 0.5 | - |
N-formyl-Met-Ala | pH 7.0, 30°C, recombinant wild-type enzyme | Salmonella enterica subsp. enterica serovar Typhimurium | |
| 0.7 | - |
N-formyl-Met-Ala | pH 7.0, 30°C, recombinant enzyme mutant M145C | Mycobacterium tuberculosis | |
| 3 | - |
N-formyl-Met-Ala | pH 7.0, 30°C, recombinant wild-type enzyme | Mycobacterium tuberculosis | |
Use of this online version of BRENDA is free under the CC BY 4.0 license. See terms of use for full details.
Release 2023.1 (January 2023)
Legal
Curated at
Member of
