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Information on EC 3.5.1.88 - peptide deformylase and Organism(s) Staphylococcus epidermidis and UniProt Accession Q5HQ78

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EC Tree
     3 Hydrolases
         3.5 Acting on carbon-nitrogen bonds, other than peptide bonds
             3.5.1 In linear amides
                3.5.1.88 peptide deformylase
IUBMB Comments
Requires Fe(II). Also requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions. Differs in substrate specifity from EC 3.5.1.31 (formylmethionine deformylase).
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This record set is specific for:
Staphylococcus epidermidis
UNIPROT: Q5HQ78
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The taxonomic range for the selected organisms is: Staphylococcus epidermidis
The enzyme appears in selected viruses and cellular organisms
Synonyms
peptide deformylase, hspdf, pdf-1, polypeptide deformylase, pdf1a, hppdf, pdf1b, pdf-2, vp16 pdf, tbpdf1, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
deformylase, peptide N-formylmethionine
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hydrolase, aminoacyl-transfer ribonucleate
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PDF-2
isoform without peptide deformylase activity
peptide deformylase
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Polypeptide deformylase
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hydrolysis of amide bond
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SYSTEMATIC NAME
IUBMB Comments
formyl-L-methionyl peptide amidohydrolase
Requires Fe(II). Also requires at least a dipeptide for an efficient rate of reaction. N-terminal L-methionine is a prerequisite for activity but the enzyme has broad specificity at other positions. Differs in substrate specifity from EC 3.5.1.31 (formylmethionine deformylase).
CAS REGISTRY NUMBER
COMMENTARY hide
369636-51-1
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37289-08-0
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9032-86-4
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9054-98-2
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SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
N-formyl-L-Met-L-Ala-L-Ser + H2O
formate + L-Met-L-Ala-L-Ser
show the reaction diagram
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?
N-formyl-L-methionine-polypeptide + H2O
formate + L-methionine-polypeptide
show the reaction diagram
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?
N-formyl-L-methionine-polypeptide + H2O
formate + L-methionine-polypeptide
show the reaction diagram
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?
additional information
?
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
N-formyl-L-methionine-polypeptide + H2O
formate + L-methionine-polypeptide
show the reaction diagram
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-
?
N-formyl-L-methionine-polypeptide + H2O
formate + L-methionine-polypeptide
show the reaction diagram
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?
additional information
?
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peptide deformylase is responsible for the removal of the N-formyl group from the terminal methionine residue in bacterial protein synthesis
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?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Co2+
Co2+-substituted isoform PDF-1 exhibits much higher enzymatic activity than that of Ni2+ and Zn2+ substituted PDF-1
Ni2+
isoform PDF-1 shows much weaker binding ability towards Ni2+ than towards Co2+ and Zn2+
Zn2+
compared with Co2+-substituted PDF-1, the enzymatic activity of Zn2+-substituted PDF-1 shows a 4fold decrease, PDF-1 binds more Zn2+ (1.36 mol Zn per mol protein) than Co2+ (0.87 mol Co per mol protein), though the activity of Zn-PDF is much lower
additional information
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(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
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(2S)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-(4-methoxyphenyl)-2,5-dihydro-1H-pyrrole-2-carboxamide
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(2S)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-(4-nitrophenyl)-2,5-dihydro-1H-pyrrole-2-carboxamide
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(2S)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-(5-methyl-1,3-thiazol-2-yl)-2,5-dihydro-1H-pyrrole-2-carboxamide
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(2S)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-(pyridin-2-yl)-2,5-dihydro-1H-pyrrole-2-carboxamide
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(2S)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-phenyl-2,5-dihydro-1H-pyrrole-2-carboxamide
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(2S)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-[(1R)-1-phenylethyl]-2,5-dihydro-1H-pyrrole-2-carboxamide
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(2S)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-[(1S)-1-phenylethyl]-2,5-dihydro-1H-pyrrole-2-carboxamide
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(2S)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-[5-(trifluoromethyl)-1,3,4-thiadiazol-2-yl]-2,5-dihydro-1H-pyrrole-2-carboxamide
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(2S)-N-(2-bromophenyl)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-2,5-dihydro-1H-pyrrole-2-carboxamide
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(2S)-N-(2-chlorophenyl)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-2,5-dihydro-1H-pyrrole-2-carboxamide
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(2S)-N-(3-bromophenyl)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-2,5-dihydro-1H-pyrrole-2-carboxamide
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(2S)-N-(4-bromophenyl)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-2,5-dihydro-1H-pyrrole-2-carboxamide
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(2S)-N-(4-chlorophenyl)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-2,5-dihydro-1H-pyrrole-2-carboxamide
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(2S)-N-(4-fluorophenyl)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-2,5-dihydro-1H-pyrrole-2-carboxamide
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(2S)-N-(5-fluoro-1-oxidopyridin-2-yl)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-2,5-dihydro-1H-pyrrole-2-carboxamide
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(2S)-N-(5-fluoropyridin-2-yl)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-2,5-dihydro-1H-pyrrole-2-carboxamide
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(2S)-N-cyclopropyl-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-2,5-dihydro-1H-pyrrole-2-carboxamide
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(2S,3aR,7aS)-1-((R)-2-((N-hydroxyformamido)methyl)hexanoyl)-N-(5-methylpyridin-2-yl)octahydro-1H-indole-2-carboxamide
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(2S,3aR,7aS)-1-((R)-2-((N-hydroxyformamido)methyl)hexanoyl)-N-(5-methylthiazol-2-yl)octahydro-1H-indole-2-carboxamide
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(2S,3aR,7aS)-1-((R)-3-cyclopentyl-2-((N-hydroxyformamido)methyl)propanoyl)-N-(5-fluoropyridin-2-yl)octahydro-1H-indole-2-carboxamide
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(2S,3aR,7aS)-1-((R)-3-cyclopentyl-2-((N-hydroxyformamido)methyl)propanoyl)-N-(5-methylpyridin-2-yl)octahydro-1H-indole-2-carboxamide
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(2S,3aR,7aS)-1-((R)-3-cyclopentyl-2-((N-hydroxyformamido)methyl)propanoyl)-N-(5-methylthiazol-2-yl)octahydro-1H-indole-2-carboxamide
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(2S,4S)-1-((R)-3-cyclopentyl-2-((N-hydroxyformamido)methyl)propanoyl)-4-fluoro-N-(5-methylthiazol-2-yl)pyrrolidine-2-carboxamide
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(2S,4S)-1-((R)-3-cyclopentyl-2-((N-hydroxyformamido)methyl)propanoyl)-4-methyl-N-(5-methylthiazol-2-yl)pyrrolidine-2-carboxamide
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(2S,4S)-4-fluoro-1-((R)-2-((N-hydroxyformamido)methyl)hexanoyl)-N-(5-methylthiazol-2-yl)pyrrolidine-2-carboxamide
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(S)-1-((R)-2-(((formyl-hydroxyamino)methyl)hexanoyl)-N-(5-fluoro-1-oxido-pyridin)-2-yl)-2,5-dihydro-1H-pyrrole-2-carboxamide
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(S)-1-((R)-2-((formyl(hydroxy)amino)methyl)hexanoyl)-N-(2-bromophenyl)-2,5-dihydro-1H-pyrrole-2-carboxamide
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(S)-1-((R)-2-((formyl(hydroxy)amino)methyl)hexanoyl)-N-(2-chlorophenyl)-2,5-dihydro-1H-pyrrole-2-carboxamide
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(S)-1-((R)-2-((formyl(hydroxy)amino)methyl)hexanoyl)-N-(3-bromophenyl)-2,5-dihydro-1H-pyrrole-2-carboxamide
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(S)-1-((R)-2-((formyl(hydroxy)amino)methyl)hexanoyl)-N-(4-bromophenyl)-2,5-dihydro-1H-pyrrole-2-carboxamide
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(S)-1-((R)-2-((formyl(hydroxy)amino)methyl)hexanoyl)-N-(4-chlorophenyl)-2,5-dihydro-1H-pyrrole-2-carboxamide
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(S)-1-((R)-2-((formyl-hydroxyamino)methyl)hexanoyl)-N-(5-fluoropyridin-2-yl)-2,5-dihydro-1H-pyrrole-2-carboxamide
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(S)-1-((R)-2-((N-hydroxyformamido)methyl)hexanoyl)-4-methylene-N-(5-methylthiazol-2-yl)pyrrolidine-2-carboxamide
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(S)-1-((R)-2-((N-hydroxyformamido)methyl)hexanoyl)-4-methylene-N-phenylpyrrolidine-2-carboxamide
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(S)-1-((R)-2-((N-hydroxyformamido)methyl)hexanoyl)-N-((R)-1-phenylethyl)-2,5-dihydro-1H-pyrrole-2-carboxamide
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(S)-1-((R)-2-((N-hydroxyformamido)methyl)hexanoyl)-N-((S)-1-phenylethyl)-2,5-dihydro-1H-pyrrole-2-carboxamide
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(S)-1-((R)-2-((N-hydroxyformamido)methyl)hexanoyl)-N-(4-methoxyphenyl)-2,5-dihydro-1H-pyrrole-2-carboxamide
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(S)-1-((R)-2-((N-hydroxyformamido)methyl)hexanoyl)-N-(4-nitrophenyl)-2,5-dihydro-1H-pyrrole-2-carboxamide
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(S)-1-((R)-2-((N-hydroxyformamido)methyl)hexanoyl)-N-(5-(trifluoromethyl)-1,3,4-thiadiazol-2-yl)-2,5-dihydro-1H-pyrrole-2-carboxamide
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(S)-1-((R)-2-((N-hydroxyformamido)methyl)hexanoyl)-N-(5-methylthiazol-2-yl)-2,5-dihydro-1H-pyrrole-2-carboxamide
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(S)-1-((R)-2-((N-hydroxyformamido)methyl)hexanoyl)-N-(pyridin-2-yl)-2,5-dihydro-1H-pyrrole-2-carboxamide
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(S)-1-((R)-2-((N-hydroxyformamido)methyl)hexanoyl)-Nphenyl-2,5-dihydro-1H-pyrrole-2-carboxamide
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(S)-1-((R)-3-cyclopentyl-2-((N-hydroxyformamido)methyl)propanoyl)-N-((S)-1-phenylethyl)-2,5-dihydro-1H-pyrrole-2-carboxamide
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(S)-1-((R)-3-cyclopentyl-2-((N-hydroxyformamido)methyl)propanoyl)-N-(4-fluorophenyl)-2,5-dihydro-1H-pyrrole-2-carboxamide
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(S)-1-((R)-3-cyclopentyl-2-((N-hydroxyformamido)methyl)propanoyl)-N-(5-fluoropyridin-2-yl)-2,5-dihydro-1H-pyrrole-2-carboxamide
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(S)-1-((R)-3-cyclopentyl-2-((N-hydroxyformamido)methyl)propanoyl)-N-(5-methylthiazol-2-yl)-2,5-dihydro-1H-pyrrole-2-carboxamide
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(S)-1-((R)-3-cyclopentyl-2-((N-hydroxyformamido)methyl)propanoyl)-N-phenyl-2,5-dihydro-1H-pyrrole-2-carboxamide
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(S)-N-(4-fluorophenyl)-1-((R)-2-((N-hydroxyformamido)methyl)hexanoyl)-2,5-dihydro-1H-pyrrole-2-carboxamide
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(S)-N-(4-fluorophenyl)-1-((R)-2-((N-hydroxyformamido)methyl)hexanoyl)-4-methylenepyrrolidine-2-carboxamide
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(S)-N-(5-fluoropyridin-2-yl)-1-((R)-2-((N-hydroxyformamido)methyl)hexanoyl)-4-methylenepyrrolidine-2-carboxamide
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(S)-N-cyclopropyl-1-((R)-2-((N-hydroxyformamido)methyl)hexanoyl)-2,5-dihydro-1H-pyrrole-2-carboxamide
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1-(2-[[formyl(hydroxy)amino]methyl]hexanoyl)-4-methylidene-N,N-dimorpholin-4-yl-L-prolinamide
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1-(3-cyclopentyl-2-[[formyl(hydroxy)amino]methyl]propanoyl)-4-methylidene-N,N-dimorpholin-4-yl-L-prolinamide
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1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-(2-methylphenyl)-L-prolinamide
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1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-(3-methylphenyl)-L-prolinamide
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1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-(4-methoxyphenyl)-L-prolinamide
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1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-(4-methylphenyl)-L-prolinamide
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1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-(4-morpholin-4-ylphenyl)-L-prolinamide
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1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-(4-piperidin-1-ylphenyl)-L-prolinamide
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1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-(4-pyrrolidin-1-ylphenyl)-L-prolinamide
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1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-[4-(1H-pyrrol-1-yl)phenyl]-L-prolinamide
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1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-[4-(4-methylpiperazin-1-yl)phenyl]-L-prolinamide
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1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-[4-(4-oxidomorpholin-4-yl)phenyl]-L-prolinamide
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2-((2S,4S)-1-((R)-3-cyclopentyl-2-((N-hydroxyformamido)methyl)propanoyl)-4-fluoropyrrolidine-2-carboxamido)-5-fluoropyridine 1-oxide
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2-((2S,4S)-1-((R)-3-cyclopentyl-2-((N-hydroxyformamido)methyl)propanoyl)-4-methylpyrrolidine-2-carboxamido)-5-fluoropyridine 1-oxide
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2-((S)-1-((R)-3-cyclopentyl-2-((N-hydroxyformamido)methyl)propanoyl)-2,5-dihydro-1H-pyrrole-2-carboxamido)-5-fluoropyridine 1-oxide
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5-fluoro-2-((2S,4S)-1-((R)-2-((N-hydroxyformamido)methyl)hexanoyl)-4-methylpyrrolidine-2-carboxamido)pyridine 1-oxide
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5-fluoro-2-((2S,4S)-4-fluoro-1-((R)-2-((N-hydroxyformamido)methyl)hexanoyl)pyrrolidine-2-carboxamido)pyridine1-oxide
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5-fluoro-2-((S)-1-((R)-2-((N-hydroxyformamido)methyl)hexanoyl)-4-methylenepyrrolidine-2-carboxamido)pyridine 1-oxide
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N-((R)-2-(cyclopentylmethyl)-3-((S)-2-(morpholine-4-carbonyl)-2,5-dihydro-1H-pyrrol-1-yl)-3-oxopropyl)-N-hydroxyformamide
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N-(2-[[(2S)-2-[[1,3-bis(4-fluorophenyl)triazan-2-yl]carbonyl]-4-methylidenepyrrolidin-1-yl]carbonyl]hexyl)-N-hydroxyformamide
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N-(2-[[(2S)-2-[[1,3-bis(4-hydroxyphenyl)triazan-2-yl]carbonyl]-4-methylidenepyrrolidin-1-yl]carbonyl]hexyl)-N-hydroxyformamide
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N-(2-[[(2S)-2-[[1,3-bis(5-fluoro-1-oxidopyridin-2-yl)triazan-2-yl]carbonyl]-4-methylidenepyrrolidin-1-yl]carbonyl]hexyl)-N-hydroxyformamide
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N-(2-[[(2S)-2-[[1,3-bis(5-fluoropyridin-2-yl)triazan-2-yl]carbonyl]-4-methylidenepyrrolidin-1-yl]carbonyl]hexyl)-N-hydroxyformamide
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N-(2-[[(2S)-2-[[1,3-bis(5-methyl-1,3-thiazol-2-yl)triazan-2-yl]carbonyl]-4-methylidenepyrrolidin-1-yl]carbonyl]hexyl)-N-hydroxyformamide
-
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N-(3,4-difluorophenyl)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
-
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N-(3-chloro-4-morpholin-4-ylphenyl)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
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N-(3-chloro-4-piperidin-1-ylphenyl)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
-
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N-(3-chloro-4-pyrrolidin-1-ylphenyl)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
-
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N-(3-fluoro-4-morpholin-4-ylphenyl)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
-
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N-(3-fluoro-4-piperidin-1-ylphenyl)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
-
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N-(3-fluoro-4-pyrrolidin-1-ylphenyl)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
-
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N-(4-chlorophenyl)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
-
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N-(4-fluorophenyl)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
-
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N-(5-fluoro-1-hydroxypyridin-1-ium-2-yl)-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]prolinamide
-
-
N-hydroxy-N-((R)-2-((S)-2-(morpholine-4-carbonyl)-2,5-dihydro-1H-pyrrole-1-carbonyl)hexyl)formamide
-
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N-hydroxy-N-((R)-2-((S)-4-methylene-2-(morpholine-4-carbonyl)pyrrolidine-1-carbonyl)hexyl)formamide
-
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N-hydroxy-N-[(2R)-2-[[(2S)-2-(morpholin-4-ylcarbonyl)-2,5-dihydro-1H-pyrrol-1-yl]carbonyl]hexyl]formamide
-
-
N-[(2R)-2-(cyclopentylmethyl)-3-(2-{5-fluoro-6-[(9aS)-hexahydropyrazino[2,1-c][1,4]oxazin-8(1H)-yl]-2-methylpyrimidin-4-yl}hydrazinyl)-3-oxopropyl]-N-hydroxyformamide
-
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N-[2-(cyclopentylmethyl)-3-[(2S)-2-[(1,3-dicyclopropyltriazan-2-yl)carbonyl]-4-methylidenepyrrolidin-1-yl]-3-oxopropyl]-N-hydroxyformamide
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N-[2-([(2S)-2-[(1,3-diphenyltriazan-2-yl)carbonyl]-4-methylidenepyrrolidin-1-yl]carbonyl)hexyl]-N-hydroxyformamide
-
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N-[3-chloro-4-(4-oxidomorpholin-4-yl)phenyl]-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
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N-[3-fluoro-4-(1-oxidopiperidin-1-yl)phenyl]-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
-
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N-[3-fluoro-4-(1H-pyrrol-1-yl)phenyl]-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
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N-[3-fluoro-4-(4-methyl-1,4-diazepan-1-yl)phenyl]-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
-
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N-[3-fluoro-4-(4-oxidomorpholin-4-yl)phenyl]-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
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N-[3-[(2S)-2-[[1,3-bis(4-fluorophenyl)triazan-2-yl]carbonyl]-4-methylidenepyrrolidin-1-yl]-2-(cyclopentylmethyl)-3-oxopropyl]-N-hydroxyformamide
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N-[3-[(2S)-2-[[1,3-bis(5-fluoro-1-oxidopyridin-2-yl)triazan-2-yl]carbonyl]-4-methylidenepyrrolidin-1-yl]-2-(cyclopentylmethyl)-3-oxopropyl]-N-hydroxyformamide
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N-[3-[(2S)-2-[[1,3-bis(5-fluoropyridin-2-yl)triazan-2-yl]carbonyl]-4-methylidenepyrrolidin-1-yl]-2-(cyclopentylmethyl)-3-oxopropyl]-N-hydroxyformamide
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N-[3-[(2S)-2-[[1,3-bis(5-methyl-1,3-thiazol-2-yl)triazan-2-yl]carbonyl]-4-methylidenepyrrolidin-1-yl]-2-(cyclopentylmethyl)-3-oxopropyl]-N-hydroxyformamide
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N-[4-(4-ethylpiperazin-1-yl)-3-fluorophenyl]-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
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N-[4-(4-ethylpiperazin-1-yl)phenyl]-1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-L-prolinamide
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VIC-104959
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LBM415
additional information
-
synthesis, antibacterial activity, and biological evaluation of formyl hydroxyamino derivatives as novel potent peptide deformylase inhibitors against drug-resistant bacteria, MIC values, structure-activity relationships, overview
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2.227
N-formyl-L-Met-L-Ala-L-Ser
Co2+-substituted PDF-1, in 50 mM HEPES, pH 7.5, at 37°C
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
140
N-formyl-L-Met-L-Ala-L-Ser
Co2+-substituted PDF-1, in 50 mM HEPES, pH 7.5, at 37°C
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
63
N-formyl-L-Met-L-Ala-L-Ser
Co2+-substituted PDF-1, in 50 mM HEPES, pH 7.5, at 37°C
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
additional information
1-[(2R)-2-[[formyl(hydroxy)amino]methyl]hexanoyl]-N-(2-methylphenyl)-L-prolinamide
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
isoform PDF-1; strain ATCC35984/RP62A
UniProt
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
-
PDF plays a critical role in mediating the maturation process of the nascent polypeptides partly due to the necessity of removing the N-formyl group to render nascent polypeptides available for cleavage of the N-terminal methionine residue by methionine amino peptidase
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
21800
1 * 21800, gel filtration
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
monomer
1 * 21800, gel filtration
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
Co2+-PDF1-complex hanging drop vapor diffusion method, using 0.2 M ammonium acetate, 0.1 M tri-sodium citrate dihydrate pH 5.6, and 30% (v/v) PEG 4000
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
Ni-NTA column chromatography, the purification buffers for PDFs expressed using Ni2+ fortified medium are compensated with 0.1 mM NiCl2 to avoid possible Ni2+ competition between Ni-NTA and PDFs
Ni-NTA column chromatography
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli BL21(DE3) cells
expressed in Escherichia coli BL21(DE3) cells
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
medicine
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Wang, Z.; Zhou, W.
Synthesis and in vitro antibacterial activity of (2S)-N-(substitutedphenyl)-1-[(2R)-2-[(formylhydroxyamino)methyl]-1-oxohexyl]-2-pyrrolidinecarboxamides as potential peptide deformylase inhibitors
Chem. Biol. Drug Des.
73
142-146
2009
Streptococcus pneumoniae, Staphylococcus aureus, Staphylococcus epidermidis, Staphylococcus enteridis, Staphylococcus non-hemolyticus
Manually annotated by BRENDA team
Shi, W.; Duan, Y.; Qian, Y.; Li, M.; Yang, L.; Hu, W.
Design, synthesis, and antibacterial activity of 2,5-dihydropyrrole formyl hydroxyamino derivatives as novel peptide deformylase inhibitors
Bioorg. Med. Chem. Lett.
20
3592-3595
2010
Escherichia coli, Staphylococcus aureus, Staphylococcus epidermidis
Manually annotated by BRENDA team
Sharma, A.; Khuller, G.K.; Sharma, S.
Peptide deformylase--a promising therapeutic target for tuberculosis and antibacterial drug discovery
Expert Opin. Ther. Targets
13
753-765
2009
Bacillus subtilis, Bacteroides fragilis, Enterobacter cloacae, Enterococcus sp., Escherichia coli, Homo sapiens, Klebsiella pneumoniae, Moraxella catarrhalis, Mycobacterium tuberculosis, Mycobacterium tuberculosis variant bovis, Neisseria gonorrhoeae, Plasmodium falciparum, Pseudomonas aeruginosa, Staphylococcus aureus, Staphylococcus epidermidis, Stenotrophomonas maltophilia, Streptococcus pneumoniae
Manually annotated by BRENDA team
Lin, P.; Hu, T.; Hu, J.; Yu, W.; Han, C.; Zhang, J.; Qin, G.; Yu, K.; Gotz, F.; Shen, X.; Jiang, H.; Qu, D.
Characterization of peptide deformylase homologs from Staphylococcus epidermidis
Microbiology
156
3194-3202
2010
Staphylococcus epidermidis (Q5HPX6), Staphylococcus epidermidis (Q5HQ78), Staphylococcus epidermidis
Manually annotated by BRENDA team
Shi, W.; Ma, H.; Duan, Y.; Aubart, K.; Fang, Y.; Zonis, R.; Yang, L.; Hu, W.
Design, synthesis and antibacterial activity of 3-methylenepyrrolidine formyl hydroxyamino derivatives as novel peptide deformylase inhibitors
Bioorg. Med. Chem. Lett.
21
1060-1063
2011
Staphylococcus aureus, Staphylococcus aureus ATCC 25923, Staphylococcus aureus ATCC 29213, Staphylococcus aureus ATCC 43300, Staphylococcus epidermidis, Staphylococcus epidermidis ATCC 12228
Manually annotated by BRENDA team
Yang, S.; Shi, W.; Xing, D.; Zhao, Z.; Lv, F.; Yang, L.; Yang, Y.; Hu, W.
Synthesis, antibacterial activity, and biological evaluation of formyl hydroxyamino derivatives as novel potent peptide deformylase inhibitors against drug-resistant bacteria
Eur. J. Med. Chem.
86
133-152
2014
Escherichia coli, Staphylococcus aureus, Staphylococcus epidermidis
Manually annotated by BRENDA team