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Literature summary extracted from

  • Serero, A.; Giglione, C.; Meinnel, T.
    Distinctive features of the two classes of eukaryotic peptide deformylases (2001), J. Mol. Biol., 314, 695-708.
    View publication on PubMed

Inhibitors

EC Number Inhibitors Comment Organism Structure
3.5.1.88 actinonin
-
Arabidopsis thaliana
3.5.1.88 actinonin
-
Escherichia coli
3.5.1.88 imino[(5-methoxy-5-oxo-4-[2-(sulfanylmethyl)hexanoyl]aminopentyl)amino]methaneamine
-
Arabidopsis thaliana
3.5.1.88 imino[(5-methoxy-5-oxo-4-[2-(sulfanylmethyl)hexanoyl]aminopentyl)amino]methaneamine
-
Escherichia coli
3.5.1.88 methyl-1-(sulfanylmethyl)hexanoate
-
Arabidopsis thaliana
3.5.1.88 methyl-1-(sulfanylmethyl)hexanoate
-
Escherichia coli
3.5.1.88 Phe-Arg-beta-naphthylamide
-
Arabidopsis thaliana
3.5.1.88 thiorphan
-
Arabidopsis thaliana

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
3.5.1.88 additional information
-
additional information
-
Arabidopsis thaliana
3.5.1.88 0.23
-
N-Formyl-Met-Leu-Phe enzyme form PDF1A Arabidopsis thaliana
3.5.1.88 0.25
-
N-formyl-Met-Ala-Ser enzyme form PDF1A Arabidopsis thaliana
3.5.1.88 0.27
-
N-formyl-Met-Ala-Ser enzyme form PDF1A Solanum lycopersicum
3.5.1.88 0.42
-
N-formyl-Arg(NH2) enzyme form PDF1A Arabidopsis thaliana
3.5.1.88 0.42
-
N-formyl-Ser(NH2) enzyme form PDF1A Arabidopsis thaliana
3.5.1.88 0.5
-
N-formyl-L-Arg-amide enzyme form Ni-PDF1B Arabidopsis thaliana
3.5.1.88 0.6
-
N-formyl-Nle-Ala-Ser enzyme form PDF1A Arabidopsis thaliana
3.5.1.88 0.74
-
N-formyl-Asp(NH2) enzyme form PDF1A Arabidopsis thaliana
3.5.1.88 0.79
-
N-formyl-Leu(NH2) enzyme form PDF1A Arabidopsis thaliana
3.5.1.88 1
-
N-formyl-Asp(NH2) enzyme form Ni-PDF1B Arabidopsis thaliana
3.5.1.88 1
-
N-formyl-Ser(NH2) enzyme form Ni-PDF1B Arabidopsis thaliana
3.5.1.88 2
-
N-formyl-Met-Ser-Asn-Glu enzyme form Ni-PDF1B Arabidopsis thaliana
3.5.1.88 2.9
-
N-formyl-Gly(NH2) enzyme form PDF1A Arabidopsis thaliana
3.5.1.88 3
-
N-formyl-Phe-Ala-Ser enzyme form PDF1A Arabidopsis thaliana
3.5.1.88 4.1
-
N-formyl-Met-Ser-Asn-Glu enzyme form PDF1A Arabidopsis thaliana
3.5.1.88 4.3
-
N-formyl-Gly(NH2) enzyme form Ni-PDF1B Arabidopsis thaliana
3.5.1.88 5.6
-
N-formyl-Met-Ala-Ser enzyme form Ni-PDF1B Arabidopsis thaliana
3.5.1.88 8
-
N-formyl-Met-Leu-Glu enzyme form PDF1A Arabidopsis thaliana
3.5.1.88 8.2
-
N-formyl-Met-Ala-Ser enzyme form PDF1B Arabidopsis thaliana
3.5.1.88 9.4
-
N-formyl-Nva-Ala-Ser enzyme form PDF1A Arabidopsis thaliana
3.5.1.88 11
-
N-formyl-Nle-Ala-Ser enzyme form Ni-PDF1B Arabidopsis thaliana
3.5.1.88 12
-
N-formyl-Met-Leu-Glu enzyme form Ni-PDF1B Arabidopsis thaliana

Localization

EC Number Localization Comment Organism GeneOntology No. Textmining
3.5.1.88 chloroplast
-
Arabidopsis thaliana 9507
-

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
3.5.1.88 Fe
-
Escherichia coli
3.5.1.88 Fe PDF1B is an iron enzyme Arabidopsis thaliana
3.5.1.88 Zn PDF1A is a zinc enzyme, contains 0.8 mol of Zn per mol of enzyme Arabidopsis thaliana
3.5.1.88 Zn PDF1A is a zinc enzyme, contains 0.8 mol of Zn per mol of enzyme Solanum lycopersicum

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
3.5.1.88 N-formyl-L-methionine-polypeptide + H2O Escherichia coli
-
formate + L-methionine-polypeptide
-
?
3.5.1.88 N-formyl-L-methionine-polypeptide + H2O Arabidopsis thaliana deformylase is likely to play an essential role in the chloroplast formate + L-methionine-polypeptide
-
?

Organism

EC Number Organism UniProt Comment Textmining
3.5.1.88 Arabidopsis thaliana
-
two classes of PDF: PDF1A and PDF1B
-
3.5.1.88 Escherichia coli
-
-
-
3.5.1.88 Solanum lycopersicum
-
two classes of PDF: PDF1A and PDF1B
-

Purification (Commentary)

EC Number Purification (Comment) Organism
3.5.1.88 two classes of PDF: PDF1A and PDF1B Arabidopsis thaliana
3.5.1.88 two classes of PDF: PDF1A and PDF1B Solanum lycopersicum

Source Tissue

EC Number Source Tissue Comment Organism Textmining
3.5.1.88 seedling
-
Arabidopsis thaliana
-

Storage Stability

EC Number Storage Stability Organism
3.5.1.88 -20°C, PDF1A is stable for at least 6 months Arabidopsis thaliana
3.5.1.88 -20°C, PDF1A is stable for at least 6 months Solanum lycopersicum

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
3.5.1.88 N-formyl-Asp(NH2) + H2O
-
Arabidopsis thaliana ?
-
?
3.5.1.88 N-formyl-Gly(NH2) + H2O
-
Arabidopsis thaliana ?
-
?
3.5.1.88 N-formyl-L-Arg(NH2) + H2O
-
Arabidopsis thaliana ?
-
?
3.5.1.88 N-formyl-L-Arg-amide + H2O
-
Arabidopsis thaliana ?
-
?
3.5.1.88 N-formyl-L-methionine-polypeptide + H2O
-
Escherichia coli formate + L-methionine-polypeptide
-
?
3.5.1.88 N-formyl-L-methionine-polypeptide + H2O deformylase is likely to play an essential role in the chloroplast Arabidopsis thaliana formate + L-methionine-polypeptide
-
?
3.5.1.88 N-formyl-Leu(NH2) + H2O
-
Arabidopsis thaliana ?
-
?
3.5.1.88 N-formyl-Met-Ala + H2O
-
Escherichia coli formate + Met-Ala
-
?
3.5.1.88 N-formyl-Met-Ala + H2O
-
Arabidopsis thaliana formate + Met-Ala
-
?
3.5.1.88 N-formyl-Met-Ala(OCH3) + H2O
-
Escherichia coli formate + Met-Ala(OCH3)
-
?
3.5.1.88 N-formyl-Met-Ala(OCH3) + H2O
-
Arabidopsis thaliana formate + Met-Ala(OCH3)
-
?
3.5.1.88 N-formyl-Met-Ala-Ser + H2O
-
Escherichia coli formate + Met-Ala-Ser
-
?
3.5.1.88 N-formyl-Met-Ala-Ser + H2O
-
Arabidopsis thaliana formate + Met-Ala-Ser
-
?
3.5.1.88 N-formyl-Met-Ala-Ser + H2O
-
Solanum lycopersicum formate + Met-Ala-Ser
-
?
3.5.1.88 N-formyl-Met-Leu-Glu + H2O
-
Escherichia coli formate + Met-Leu-Glu
-
?
3.5.1.88 N-formyl-Met-Leu-Glu + H2O
-
Arabidopsis thaliana formate + Met-Leu-Glu
-
?
3.5.1.88 N-formyl-Met-Leu-p-nitroanilide + H2O
-
Escherichia coli formate + Met-Leu-p-nitroanilide
-
?
3.5.1.88 N-formyl-Met-Leu-p-nitroanilide + H2O
-
Arabidopsis thaliana formate + Met-Leu-p-nitroanilide
-
?
3.5.1.88 N-formyl-Met-Leu-Phe + H2O
-
Escherichia coli formate + Met-Leu-Phe
-
?
3.5.1.88 N-formyl-Met-Leu-Phe + H2O
-
Arabidopsis thaliana formate + Met-Leu-Phe
-
?
3.5.1.88 N-formyl-Met-Ser-Asn-Glu + H2O
-
Escherichia coli formate + Met-Ser-Asn-Glu
-
?
3.5.1.88 N-formyl-Met-Ser-Asn-Glu + H2O
-
Arabidopsis thaliana formate + Met-Ser-Asn-Glu
-
?
3.5.1.88 N-formyl-Nle-Ala(NH2) + H2O
-
Escherichia coli formate + Nle-Ala(NH2)
-
?
3.5.1.88 N-formyl-Nle-Ala(NH2) + H2O
-
Arabidopsis thaliana formate + Nle-Ala(NH2)
-
?
3.5.1.88 N-formyl-Nle-Ala-Ser + H2O
-
Escherichia coli formate + Nle-Ala-Ser
-
?
3.5.1.88 N-formyl-Nle-Ala-Ser + H2O
-
Arabidopsis thaliana formate + Nle-Ala-Ser
-
?
3.5.1.88 N-formyl-Nle-Arg(NH2) + H2O
-
Escherichia coli formate + Nle-Arg(NH2)
-
?
3.5.1.88 N-formyl-Nle-Arg(NH2) + H2O
-
Arabidopsis thaliana formate + Nle-Arg(NH2)
-
?
3.5.1.88 N-formyl-Nle-Asp(NH2) + H2O
-
Escherichia coli formate + Nle-Asp(NH2)
-
?
3.5.1.88 N-formyl-Nle-Asp(NH2) + H2O
-
Arabidopsis thaliana formate + Nle-Asp(NH2)
-
?
3.5.1.88 N-formyl-Nle-Gly(NH2) + H2O
-
Escherichia coli formate + Nle-Gly(NH2)
-
?
3.5.1.88 N-formyl-Nle-Gly(NH2) + H2O
-
Arabidopsis thaliana formate + Nle-Gly(NH2)
-
?
3.5.1.88 N-formyl-Nle-Leu(NH2) + H2O
-
Escherichia coli formate + Nle-Leu(NH2)
-
?
3.5.1.88 N-formyl-Nle-Leu(NH2) + H2O
-
Arabidopsis thaliana formate + Nle-Leu(NH2)
-
?
3.5.1.88 N-formyl-Nle-NH(CH3) + H2O
-
Escherichia coli formate + Nle-NH(CH3)
-
?
3.5.1.88 N-formyl-Nle-NH(CH3) + H2O
-
Arabidopsis thaliana formate + Nle-NH(CH3)
-
?
3.5.1.88 N-formyl-Nle-NH2 + H2O
-
Escherichia coli formate + Nle-Nle-NH2
-
?
3.5.1.88 N-formyl-Nle-NH2 + H2O
-
Arabidopsis thaliana formate + Nle-Nle-NH2
-
?
3.5.1.88 N-formyl-Nle-Ser(NH2) + H2O
-
Escherichia coli formate + Nle-Ser(NH2)
-
?
3.5.1.88 N-formyl-Nle-Ser(NH2) + H2O
-
Arabidopsis thaliana formate + Nle-Ser(NH2)
-
?
3.5.1.88 N-formyl-Nva-Ala-Ser + H2O
-
Escherichia coli formate + Nva-Ala-Ser
-
?
3.5.1.88 N-formyl-Nva-Ala-Ser + H2O
-
Arabidopsis thaliana formate + Nva-Ala-Ser
-
?
3.5.1.88 N-formyl-Phe-Ala-Ser + H2O
-
Escherichia coli formate + Phe-Ala-Ser
-
?
3.5.1.88 N-formyl-Phe-Ala-Ser + H2O
-
Arabidopsis thaliana formate + Phe-Ala-Ser
-
?
3.5.1.88 N-formyl-Ser(NH2) + H2O
-
Arabidopsis thaliana ?
-
?

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
3.5.1.88 additional information
-
additional information
-
Arabidopsis thaliana
3.5.1.88 0.36
-
N-formyl-Nle-Leu(NH2) enzyme form PDF1A Arabidopsis thaliana
3.5.1.88 0.4
-
N-formyl-Nle-Asp(NH2) enzyme form PDF1A Arabidopsis thaliana
3.5.1.88 0.6
-
N-formyl-Phe-Ala-Ser enzyme form PDF1A Arabidopsis thaliana
3.5.1.88 0.7
-
N-Formyl-Met-Leu-Phe enzyme form PDF1A Arabidopsis thaliana
3.5.1.88 1.1
-
N-formyl-Met-Leu-Glu enzyme form PDF1A Arabidopsis thaliana
3.5.1.88 1.4
-
N-formyl-Nle-Gly(NH2) enzyme form PDF1A Arabidopsis thaliana
3.5.1.88 1.9
-
N-formyl-Met-Ser-Asn-Glu enzyme form Ni-PDF1B Arabidopsis thaliana
3.5.1.88 5
-
N-formyl-Nle-Arg(NH2) enzyme form PDF1A Arabidopsis thaliana
3.5.1.88 6.4
-
N-formyl-Nle-Asp(NH2) enzyme form Ni-PDF1B Arabidopsis thaliana
3.5.1.88 9.2
-
N-formyl-Met-Leu-Glu enzyme form Ni-PDF1B Arabidopsis thaliana
3.5.1.88 10
-
N-formyl-Nle-Ser(NH2) enzyme form PDF1A Arabidopsis thaliana
3.5.1.88 11
-
N-formyl-Met-Ser-Asn-Glu enzyme form PDF1A Arabidopsis thaliana
3.5.1.88 13
-
N-formyl-Met-Ala-Ser enzyme form Ni-PDF1B Arabidopsis thaliana
3.5.1.88 15
-
N-formyl-Met-Ala-Ser enzyme form PDF1A Solanum lycopersicum
3.5.1.88 18
-
N-formyl-Nva-Ala-Ser enzyme form PDF1A Arabidopsis thaliana
3.5.1.88 22
-
N-formyl-Met-Ala-Ser enzyme form PDF1A Arabidopsis thaliana
3.5.1.88 26
-
N-formyl-Nle-Ala-Ser enzyme form PDF1A Arabidopsis thaliana
3.5.1.88 51
-
N-formyl-Nle-Ser(NH2) enzyme form Ni-PDF1B Arabidopsis thaliana
3.5.1.88 75
-
N-formyl-Met-Ala-Ser enzyme form Ni-PDF1B Arabidopsis thaliana
3.5.1.88 136
-
N-formyl-Nle-Ala-Ser enzyme form Ni-PDF1B Arabidopsis thaliana
3.5.1.88 138
-
N-formyl-Nle-Arg(NH2) enzyme form Ni-PDF1B Arabidopsis thaliana