Any feedback?
Please rate this page
(literature.php)
(0/150)

BRENDA support

Literature summary extracted from

  • Kumar, S.; Kanudia, P.; Karthikeyan, S.; Chakraborti, P.K.
    Identification of crucial amino acids of bacterial peptide deformylases affecting enzymatic activity in response to oxidative stress (2014), J. Bacteriol., 196, 90-99.
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

EC Number Cloned (Comment) Organism
3.5.1.88 gene def, subcloning in Escherichia coli strain DH5alpha, recombinant expression of His-tagged enzyme in Escherichia coli strain BL21(DE3) Mycobacterium tuberculosis
3.5.1.88 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

EC Number Protein Variants Comment Organism
3.5.1.88 C106S site-directed mutagenesis, inactive mutant Mycobacterium tuberculosis
3.5.1.88 C130M site-directed mutagenesis Salmonella enterica subsp. enterica serovar Typhimurium
3.5.1.88 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
3.5.1.88 C59S site-directed mutagenesis, unaltered IC50 value for H2O2 compared to the wild-type enzyme Mycobacterium tuberculosis
3.5.1.88 C68S site-directed mutagenesis, the mutant protein exhibits 32fold reduced IC50s for H2O2 compared to wild-type mPDF Mycobacterium tuberculosis
3.5.1.88 M145C site-directed mutagenesis, the mutant shows reduced enzyme activity and increased sensitivity to H2O2 compared to the wild-type enzyme Mycobacterium tuberculosis
3.5.1.88 M145S site-directed mutagenesis, the mutant shows higly reduced enzyme activity and increased sensitivity to H2O2 compared to the wild-type enzyme Mycobacterium tuberculosis
3.5.1.88 V63C site-directed mutagenesis Salmonella enterica subsp. enterica serovar Typhimurium

Inhibitors

EC Number Inhibitors Comment Organism Structure
3.5.1.88 Diethylenetriaminepentaacetic acid binding structure analysis, overview Mycobacterium tuberculosis
3.5.1.88 Diethylenetriaminepentaacetic acid binding structure analysis, overview Salmonella enterica subsp. enterica serovar Typhimurium
3.5.1.88 EDTA
-
 Mycobacterium tuberculosis
3.5.1.88 EDTA
-
 Salmonella enterica subsp. enterica serovar Typhimurium
3.5.1.88 H2O2 slight inhibition, binding structure analysis, overview Mycobacterium tuberculosis
3.5.1.88 H2O2 binding structure analysis, overview Salmonella enterica subsp. enterica serovar Typhimurium
3.5.1.88 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
3.5.1.88 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]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
3.5.1.88 2.9
-
 N-formyl-Met-Ala pH 7.0, 30°C, recombinant wild-type enzyme Mycobacterium tuberculosis
3.5.1.88 4.7
-
 N-formyl-Met-Ala pH 7.0, 30°C, recombinant enzyme mutant M145C Mycobacterium tuberculosis
3.5.1.88 7.7
-
 N-formyl-Met-Ala pH 7.0, 30°C, recombinant enzyme mutant C130M/V63C Salmonella enterica subsp. enterica serovar Typhimurium
3.5.1.88 480
-
 N-formyl-Met-Ala pH 7.0, 30°C, recombinant wild-type enzyme Salmonella enterica subsp. enterica serovar Typhimurium

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
3.5.1.88 Fe2+ iron-containing enzyme variant, the apo-enzyme is enzymatically inactive, conserved metal ion coordinating Cys106 of mPDF Mycobacterium tuberculosis
3.5.1.88 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)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
3.5.1.88 formyl-L-methionyl peptide + H2O Mycobacterium tuberculosis
-
 formate + methionyl peptide
-
 ?
3.5.1.88 formyl-L-methionyl peptide + H2O Salmonella enterica subsp. enterica serovar Typhimurium
-
 formate + methionyl peptide
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
3.5.1.88 Mycobacterium tuberculosis P9WIJ3 gene def
-
3.5.1.88 Salmonella enterica subsp. enterica serovar Typhimurium Q8ZLM7 gene def
-

Purification (Commentary)

EC Number Purification (Comment) Organism
3.5.1.88 recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and dialysis Salmonella enterica subsp. enterica serovar Typhimurium
3.5.1.88 recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickl affinity chromatography and dialysis Mycobacterium tuberculosis

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
3.5.1.88 formyl-L-methionyl peptide + H2O
-
 Mycobacterium tuberculosis formate + methionyl peptide
-
 ?
3.5.1.88 formyl-L-methionyl peptide + H2O
-
 Salmonella enterica subsp. enterica serovar Typhimurium formate + methionyl peptide
-
 ?
3.5.1.88 N-formyl-Met-Ala + H2O
-
 Mycobacterium tuberculosis formate + Met-Ala
-
 ?
3.5.1.88 N-formyl-Met-Ala + H2O
-
 Salmonella enterica subsp. enterica serovar Typhimurium formate + Met-Ala
-
 ?

Synonyms

EC Number Synonyms Comment Organism
3.5.1.88 mPDF
-
 Mycobacterium tuberculosis
3.5.1.88 PDF
-
 Mycobacterium tuberculosis
3.5.1.88 PDF
-
 Salmonella enterica subsp. enterica serovar Typhimurium
3.5.1.88 sPDF
-
 Salmonella enterica subsp. enterica serovar Typhimurium

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
3.5.1.88 30
-
 assay at Mycobacterium tuberculosis
3.5.1.88 30
-
 assay at Salmonella enterica subsp. enterica serovar Typhimurium

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
3.5.1.88 0.8
-
 N-formyl-Met-Ala pH 7.0, 30°C, recombinant enzyme mutant C130M/V63C Salmonella enterica subsp. enterica serovar Typhimurium
3.5.1.88 3.1
-
 N-formyl-Met-Ala pH 7.0, 30°C, recombinant enzyme mutant M145C Mycobacterium tuberculosis
3.5.1.88 4.1
-
 N-formyl-Met-Ala pH 7.0, 30°C, recombinant wild-type enzyme Salmonella enterica subsp. enterica serovar Typhimurium
3.5.1.88 8.8
-
 N-formyl-Met-Ala pH 7.0, 30°C, recombinant wild-type enzyme Mycobacterium tuberculosis

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
3.5.1.88 7
-
 assay at Mycobacterium tuberculosis
3.5.1.88 7
-
 assay at Salmonella enterica subsp. enterica serovar Typhimurium

IC50 Value

EC Number IC50 Value IC50 Value Maximum Comment Organism Inhibitor Structure
3.5.1.88 0.000045
-
 pH 7.0, 30°C, recombinant wild-type enzyme Salmonella enterica subsp. enterica serovar Typhimurium H2O2
3.5.1.88 0.000049
-
 pH 7.0, 30°C, recombinant enzyme mutant C130S Salmonella enterica subsp. enterica serovar Typhimurium H2O2
3.5.1.88 0.00015
-
 pH 7.0, 30°C, recombinant enzyme mutant V63C Salmonella enterica subsp. enterica serovar Typhimurium H2O2
3.5.1.88 0.00016
-
 pH 7.0, 30°C, recombinant enzyme mutant C130M Salmonella enterica subsp. enterica serovar Typhimurium H2O2
3.5.1.88 0.00144
-
 pH 7.0, 30°C, recombinant enzyme mutant C130M/V63C Salmonella enterica subsp. enterica serovar Typhimurium H2O2
3.5.1.88 0.06
-
 pH 7.0, 30°C, recombinant enzyme mutant M145C Mycobacterium tuberculosis H2O2
3.5.1.88 0.07
-
 pH 7.0, 30°C, recombinant enzyme mutant M145S Mycobacterium tuberculosis H2O2
3.5.1.88 0.5
-
 pH 7.0, 30°C, recombinant enzyme mutant C58S Mycobacterium tuberculosis H2O2
3.5.1.88 13.6
-
 pH 7.0, 30°C, recombinant enzyme mutant C59C Mycobacterium tuberculosis H2O2
3.5.1.88 16.1
-
 pH 7.0, 30°C, recombinant wild-type enzyme Mycobacterium tuberculosis H2O2

General Information

EC Number General Information Comment Organism
3.5.1.88 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
3.5.1.88 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]

EC Number kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
3.5.1.88 0.1
-
 N-formyl-Met-Ala pH 7.0, 30°C, recombinant enzyme mutant C130M/V63C Salmonella enterica subsp. enterica serovar Typhimurium
3.5.1.88 0.5
-
 N-formyl-Met-Ala pH 7.0, 30°C, recombinant wild-type enzyme Salmonella enterica subsp. enterica serovar Typhimurium
3.5.1.88 0.7
-
 N-formyl-Met-Ala pH 7.0, 30°C, recombinant enzyme mutant M145C Mycobacterium tuberculosis
3.5.1.88 3
-
 N-formyl-Met-Ala pH 7.0, 30°C, recombinant wild-type enzyme Mycobacterium tuberculosis