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Literature summary extracted from

  • Narayanan, S.S.; Sokkar, P.; Ramachandran, M.; Nampoothiri, K.M.
    Glycine in the conserved motif III modulates the thermostability and oxidative stress resistance of peptide deformylase in Mycobacterium tuberculosis (2011), FEMS Microbiol. Lett., 320, 40-47.
    View publication on PubMed

Cloned(Commentary)

EC Number Cloned (Comment) Organism
3.5.1.88 expressed in Escherichia coli BL21(DE3) cells Mycobacterium tuberculosis

Protein Variants

EC Number Protein Variants Comment Organism
3.5.1.88 G151A the mutant shows wild type activity Mycobacterium tuberculosis
3.5.1.88 G151D the mutant shows 1.5 times the activity of the wild type enzyme against N-formyl-Met-Ala-Ser and deformylates N-formyl-Met-Leu-Phe with higher efficiency than the wild type enzyme. The mutation increases deformylase thermostability (2fold higher activity at 50°C compared with wild type activity at 30°C) and completely loses its activity upon incubating with 200 mM H2O2 Mycobacterium tuberculosis
3.5.1.88 G49C the mutant retains nearly 36.1% activity compared to the wild type enzyme Mycobacterium tuberculosis
3.5.1.88 G49P the mutant is almost completely inactive Mycobacterium tuberculosis
3.5.1.88 L107E the mutant retains less than 10% activity compared to the wild type enzyme Mycobacterium tuberculosis

Inhibitors

EC Number Inhibitors Comment Organism Structure
3.5.1.88 actinonin complete inhibition at 0.005 mM Mycobacterium tuberculosis

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
3.5.1.88 2.5
-
 N-formyl-Met-Ala-Ser mutant enzyme G151D, in 20 mM phosphate buffer, pH 7.4, temperature not specified in the publication Mycobacterium tuberculosis
3.5.1.88 4.3
-
 N-formyl-Met-Ala-Ser wild type enzyme, in 20 mM phosphate buffer, pH 7.4, temperature not specified in the publication Mycobacterium tuberculosis
3.5.1.88 4.4
-
 N-formyl-Met-Ala-Ser mutant enzyme G151A, in 20 mM phosphate buffer, pH 7.4, temperature not specified in the publication Mycobacterium tuberculosis
3.5.1.88 7.8
-
 N-formyl-Met-Ala-Ser mutant enzyme G49C, in 20 mM phosphate buffer, pH 7.4, temperature not specified in the publication Mycobacterium tuberculosis

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
3.5.1.88 Iron iron-containing enzyme Mycobacterium tuberculosis

Molecular Weight [Da]

EC Number Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
3.5.1.88 22500
-
 x * 22500, calculated from amino acid sequence Mycobacterium tuberculosis
3.5.1.88 29000
-
 x * 29000, SDS-PAGE Mycobacterium tuberculosis

Organism

EC Number Organism UniProt Comment Textmining
3.5.1.88 Mycobacterium tuberculosis
-
-
-
3.5.1.88 Mycobacterium tuberculosis H37Rv
-
-
-

Oxidation Stability

EC Number Oxidation Stability Organism
3.5.1.88 the presence of 500 mM H2O2 for 30 min does not affect the deformylase wild type activity Mycobacterium tuberculosis

Purification (Commentary)

EC Number Purification (Comment) Organism
3.5.1.88 Ni-NTA column chromatography, gel filtration Mycobacterium tuberculosis

Renatured (Commentary)

EC Number Renatured (Comment) Organism
3.5.1.88 refolding by dialysing against 20 mM phosphate buffer, pH 7.4 Mycobacterium tuberculosis

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
3.5.1.88 N-formyl-L-methionine + H2O worst substrate Mycobacterium tuberculosis formate + L-methionine
-
 ?
3.5.1.88 N-formyl-L-methionine + H2O worst substrate Mycobacterium tuberculosis H37Rv formate + L-methionine
-
 ?
3.5.1.88 N-formyl-Met-Ala-Ser + H2O best substrate Mycobacterium tuberculosis formate + Met-Ala-Ser
-
 ?
3.5.1.88 N-formyl-Met-Ala-Ser + H2O best substrate Mycobacterium tuberculosis H37Rv formate + Met-Ala-Ser
-
 ?
3.5.1.88 N-formyl-Met-Leu-Phe + H2O
-
 Mycobacterium tuberculosis formate + Met-Leu-Phe
-
 ?
3.5.1.88 N-formyl-Met-Leu-Phe + H2O
-
 Mycobacterium tuberculosis H37Rv formate + Met-Leu-Phe
-
 ?

Subunits

EC Number Subunits Comment Organism
3.5.1.88 ? x * 29000, SDS-PAGE Mycobacterium tuberculosis
3.5.1.88 ? x * 22500, calculated from amino acid sequence Mycobacterium tuberculosis

Synonyms

EC Number Synonyms Comment Organism
3.5.1.88 PDF
-
 Mycobacterium tuberculosis

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
3.5.1.88 20 30
-
 Mycobacterium tuberculosis

Temperature Stability [°C]

EC Number Temperature Stability Minimum [°C] Temperature Stability Maximum [°C] Comment Organism
3.5.1.88 30 50 the wild type enzyme is stable at 30°C with a half-life close to 4.5 h. At 40°C the half-life is reduced to 90 min and at 50°C to 40 min Mycobacterium tuberculosis

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
3.5.1.88 2
-
 N-formyl-Met-Ala-Ser mutant enzyme G49C, in 20 mM phosphate buffer, pH 7.4, temperature not specified in the publication Mycobacterium tuberculosis
3.5.1.88 3.5
-
 N-formyl-Met-Ala-Ser mutant enzyme G151A, in 20 mM phosphate buffer, pH 7.4, temperature not specified in the publication Mycobacterium tuberculosis
3.5.1.88 3.6
-
 N-formyl-Met-Ala-Ser wild type enzyme, in 20 mM phosphate buffer, pH 7.4, temperature not specified in the publication Mycobacterium tuberculosis
3.5.1.88 4.5
-
 N-formyl-Met-Ala-Ser mutant enzyme G151D, in 20 mM phosphate buffer, pH 7.4, temperature not specified in the publication Mycobacterium tuberculosis

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
3.5.1.88 7.4
-
-
 Mycobacterium tuberculosis

IC50 Value

EC Number IC50 Value IC50 Value Maximum Comment Organism Inhibitor Structure
3.5.1.88 0.00012
-
 wild type enzyme, in 20 mM phosphate buffer, pH 7.4, temperature not specified in the publication Mycobacterium tuberculosis actinonin
3.5.1.88 0.0008
-
 mutant enzyme G151D, in 20 mM phosphate buffer, pH 7.4, temperature not specified in the publication Mycobacterium tuberculosis actinonin

kcat/KM [mM/s]

EC Number kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
3.5.1.88 0.26
-
 N-formyl-Met-Ala-Ser mutant enzyme G49C, in 20 mM phosphate buffer, pH 7.4, temperature not specified in the publication Mycobacterium tuberculosis
3.5.1.88 0.795
-
 N-formyl-Met-Ala-Ser mutant enzyme G151A, in 20 mM phosphate buffer, pH 7.4, temperature not specified in the publication Mycobacterium tuberculosis
3.5.1.88 0.842
-
 N-formyl-Met-Ala-Ser wild type enzyme, in 20 mM phosphate buffer, pH 7.4, temperature not specified in the publication Mycobacterium tuberculosis
3.5.1.88 1.786
-
 N-formyl-Met-Ala-Ser mutant enzyme G151D, in 20 mM phosphate buffer, pH 7.4, temperature not specified in the publication Mycobacterium tuberculosis