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

BRENDA support

Literature summary extracted from

  • Lee, S.J.; Lee, S.J.; Lee, S.K.; Yoon, H.J.; Lee, H.H.; Kim, K.K.; Lee, B.J.; Lee, B.I.; Suh, S.W.
    Structures of Staphylococcus aureus peptide deformylase in complex with two classes of new inhibitors (2012), Acta Crystallogr. Sect. D, 68, 784-793.
    View publication on PubMed

Cloned(Commentary)

EC Number Cloned (Comment) Organism
3.5.1.88 recombinant overexpression of C-terminally His6-tagged enzyme in Escherichia coli strain C41 (DE3) Staphylococcus aureus

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
3.5.1.88 purified recombinant His6-tagged enzyme in complex with four hydroxamate inhibitors, hanging drop vapour-diffusion method, mixing of 30 mg/ml protein in 20 mM Tris-HCl, pH 7.5, and 120 mM NaCl, with reservoir solution consisting of 23% w/v PEG 4000, 50 mM Tris-HCl pH 8.5, 15% v/v glycerol, 100 mM MgCl2, 20mM CaCl2, X-ray diffraction structure determination and analysis at resolutions of 1.90-2.30 A Staphylococcus aureus

Inhibitors

EC Number Inhibitors Comment Organism Structure
3.5.1.88 (2R)-N-[(2S)-1-{4-[(2H-1,3-benzodioxol-5-yl)methyl]piperazin-1-yl}-3,3-dimethyl-1-oxobutan-2-yl]-2-(cyclopentylmethyl)-3-[formyl(hydroxy)amino]propanamide
-
 Staphylococcus aureus
3.5.1.88 actinonin
-
 Staphylococcus aureus
3.5.1.88 additional information effects of inhibitors on the enzyme structure, overview Staphylococcus aureus
3.5.1.88 N-(5-fluoro-1-hydroxypyridin-1-ium-2-yl)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]prolinamide
-
 Staphylococcus aureus
3.5.1.88 N-[(2-methoxyphenyl)carbamoyl]-3-methyl-L-valyl-N2-(cyclopentylmethyl)-N-hydroxyglycinamide binding structure, overview Staphylococcus aureus
3.5.1.88 N-[(2R,4S)-2-butyl-4-[[(2-fluorophenyl)carbamoyl]amino]-5-methyl-3-oxohexyl]-N-hydroxyformamide binding structure, overview Staphylococcus aureus
3.5.1.88 N-[(2R,4S)-2-butyl-5-methyl-4-[[(5-methylpyridin-2-yl)carbamoyl]amino]-3-oxohexyl]-N-hydroxyformamide binding structure, overview Staphylococcus aureus
3.5.1.88 N-[(3,5-difluorophenyl)carbamoyl]-3-methyl-L-valyl-N2-(cyclopentylmethyl)-N-hydroxyglycinamide binding structure, overview Staphylococcus aureus

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
3.5.1.88 Zn2+ a zinc-metalloenzyme Staphylococcus aureus

Organism

EC Number Organism UniProt Comment Textmining
3.5.1.88 Staphylococcus aureus
-
-
-
3.5.1.88 Staphylococcus aureus ATCC 6538p
-
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
3.5.1.88 recombinant C-terminally His6-tagged enzyme from Escherichia coli strain C41 (DE3) by nickel affinity chromatography, gel filtration, and ultrafiltration Staphylococcus aureus

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
3.5.1.88 formyl-Met-Ala-Ser + H2O
-
 Staphylococcus aureus formate + Met-Ala-Ser
-
 ?
3.5.1.88 formyl-Met-Ala-Ser + H2O
-
 Staphylococcus aureus ATCC 6538p formate + Met-Ala-Ser
-
 ?

Synonyms

EC Number Synonyms Comment Organism
3.5.1.88 PDF
-
 Staphylococcus aureus

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
3.5.1.88 9.5
-
 assay at Staphylococcus aureus

Ki Value [mM]

EC Number Ki Value [mM] Ki Value maximum [mM] Inhibitor Comment Organism Structure
3.5.1.88 0.0000112
-
 N-[(2R,4S)-2-butyl-5-methyl-4-[[(5-methylpyridin-2-yl)carbamoyl]amino]-3-oxohexyl]-N-hydroxyformamide pH 7.0, temperature not specified in the publication Staphylococcus aureus
3.5.1.88 0.0000351
-
 N-[(2R,4S)-2-butyl-4-[[(2-fluorophenyl)carbamoyl]amino]-5-methyl-3-oxohexyl]-N-hydroxyformamide pH 7.0, temperature not specified in the publication Staphylococcus aureus
3.5.1.88 0.0000524
-
 N-[(3,5-difluorophenyl)carbamoyl]-3-methyl-L-valyl-N2-(cyclopentylmethyl)-N-hydroxyglycinamide pH 7.0, temperature not specified in the publication Staphylococcus aureus
3.5.1.88 0.0000849
-
 N-[(2-methoxyphenyl)carbamoyl]-3-methyl-L-valyl-N2-(cyclopentylmethyl)-N-hydroxyglycinamide pH 7.0, temperature not specified in the publication Staphylococcus aureus

General Information

EC Number General Information Comment Organism
3.5.1.88 physiological function peptide deformylase catalyzes the removal of the formyl group from the N-terminal methionine residue in newly synthesized polypeptides, which is an essential process in bacteria Staphylococcus aureus