Literature summary for 3.5.1.88 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.

Cloned(Commentary)

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

Crystallization (Commentary)

Crystallization (Comment)	Organism
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

Crystallization (Comment)

Organism

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

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

Metals/Ions

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

Organism

Organism	UniProt	Comment	Textmining
Staphylococcus aureus	-	-	-
Staphylococcus aureus ATCC 6538p	-	-	-

Purification (Commentary)

Purification (Comment)	Organism
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)

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

Synonyms

Synonyms	Comment	Organism
PDF	-	Staphylococcus aureus

pH Optimum

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

Ki Value [mM]

Ki Value [mM]	Ki Value maximum [mM]	Inhibitor	Comment	Organism
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
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
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
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

General Information	Comment	Organism
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