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Literature summary for 3.5.1.88 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
Search for more literature for 3.5.1.88

Cloned(Commentary)

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

Protein Variants

Protein Variants Comment Organism
G151A the mutant shows wild type activity Mycobacterium tuberculosis
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
G49C the mutant retains nearly 36.1% activity compared to the wild type enzyme Mycobacterium tuberculosis
G49P the mutant is almost completely inactive Mycobacterium tuberculosis
L107E the mutant retains less than 10% activity compared to the wild type enzyme Mycobacterium tuberculosis

Inhibitors

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

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
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
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
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
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

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

Molecular Weight [Da]

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

Organism

Organism UniProt Comment Textmining
Mycobacterium tuberculosis
-
-
-
Mycobacterium tuberculosis H37Rv
-
-
-

Oxidation Stability

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

Purification (Commentary)

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

Renatured (Commentary)

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

Substrates and Products (Substrate)

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

Subunits

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

Synonyms

Synonyms Comment Organism
PDF
-
 Mycobacterium tuberculosis

Temperature Optimum [°C]

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

Temperature Stability [°C]

Temperature Stability Minimum [°C] Temperature Stability Maximum [°C] Comment Organism
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]

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

pH Optimum Minimum pH Optimum Maximum Comment Organism
7.4
-
-
 Mycobacterium tuberculosis

IC50 Value

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

kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
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
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
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
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