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Information on EC 3.5.1.88 - peptide deformylase and Organism(s) Arabidopsis thaliana and UniProt Accession Q9FV53

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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:
Arabidopsis thaliana
UNIPROT: Q9FV53
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The taxonomic range for the selected organisms is: Arabidopsis thaliana
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
-
-
-
-
hydrolase, aminoacyl-transfer ribonucleate
-
-
-
-
PDF1B
peptide deformylase
-
-
Polypeptide deformylase
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hydrolysis of amide bond
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
-
37289-08-0
-
9032-86-4
-
9054-98-2
-
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-Met-Leu-p-nitroanilide + H2O
formate + Met-Leu-p-nitroanilide
show the reaction diagram
-
-
-
?
formyl-L-methionyl peptide + H2O
formate + methionyl peptide
show the reaction diagram
-
-
-
-
?
formyl-Met-Ala-Ser + H2O
formate + Met-Ala-Ser
show the reaction diagram
-
-
-
?
formylmethionine + H2O
formate + methionine
show the reaction diagram
the smallest efficient substrate of PDF
-
-
?
N-formyl-Asp(NH2) + H2O
?
show the reaction diagram
-
-
-
-
?
N-formyl-Gly(NH2) + H2O
?
show the reaction diagram
-
-
-
-
?
N-formyl-L-Arg(NH2) + H2O
?
show the reaction diagram
-
-
-
-
?
N-formyl-L-Arg-amide + H2O
?
show the reaction diagram
-
-
-
-
?
N-formyl-L-methionine-polypeptide + H2O
formate + L-methionine-polypeptide
show the reaction diagram
N-formyl-Leu(NH2) + H2O
?
show the reaction diagram
-
-
-
-
?
N-formyl-Met-Ala + H2O
formate + Met-Ala
show the reaction diagram
-
-
-
-
?
N-formyl-Met-Ala(OCH3) + H2O
formate + Met-Ala(OCH3)
show the reaction diagram
-
-
-
-
?
N-formyl-Met-Ala-Ser + H2O
formate + Met-Ala-Ser
show the reaction diagram
N-formyl-Met-Leu-Glu + H2O
formate + Met-Leu-Glu
show the reaction diagram
-
-
-
-
?
N-formyl-Met-Leu-p-nitroanilide + H2O
formate + Met-Leu-p-nitroanilide
show the reaction diagram
-
-
-
-
?
N-formyl-Met-Leu-Phe + H2O
formate + Met-Leu-Phe
show the reaction diagram
-
-
-
-
?
N-formyl-Met-Ser-Asn-Glu + H2O
formate + Met-Ser-Asn-Glu
show the reaction diagram
-
-
-
-
?
N-formyl-Nle-Ala(NH2) + H2O
formate + Nle-Ala(NH2)
show the reaction diagram
-
-
-
-
?
N-formyl-Nle-Ala-Ser + H2O
formate + Nle-Ala-Ser
show the reaction diagram
-
-
-
-
?
N-formyl-Nle-Arg(NH2) + H2O
formate + Nle-Arg(NH2)
show the reaction diagram
-
-
-
-
?
N-formyl-Nle-Asp(NH2) + H2O
formate + Nle-Asp(NH2)
show the reaction diagram
-
-
-
-
?
N-formyl-Nle-Gly(NH2) + H2O
formate + Nle-Gly(NH2)
show the reaction diagram
-
-
-
-
?
N-formyl-Nle-Leu(NH2) + H2O
formate + Nle-Leu(NH2)
show the reaction diagram
-
-
-
-
?
N-formyl-Nle-NH(CH3) + H2O
formate + Nle-NH(CH3)
show the reaction diagram
-
-
-
-
?
N-formyl-Nle-NH2 + H2O
formate + Nle-Nle-NH2
show the reaction diagram
-
-
-
-
?
N-formyl-Nle-Ser(NH2) + H2O
formate + Nle-Ser(NH2)
show the reaction diagram
-
-
-
-
?
N-formyl-Nva-Ala-Ser + H2O
formate + Nva-Ala-Ser
show the reaction diagram
-
-
-
-
?
N-formyl-Phe-Ala-Ser + H2O
formate + Phe-Ala-Ser
show the reaction diagram
-
-
-
-
?
N-formyl-Ser(NH2) + H2O
?
show the reaction diagram
-
-
-
-
?
additional information
?
-
coupled enzyme activity assay with formate dehydrogenase
-
-
-
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
formyl-L-methionyl peptide + H2O
formate + methionyl peptide
show the reaction diagram
-
-
-
-
?
N-formyl-L-methionine-polypeptide + H2O
formate + L-methionine-polypeptide
show the reaction diagram
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Fe
-
PDF1B is an iron enzyme
Zn
-
PDF1A is a zinc enzyme, contains 0.8 mol of Zn per mol of enzyme
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(1-hydroxycarbamoylmethyl-2-phenylethyl)carbamic acid tert-butyl ester
-
1-(5-bromo-1H-indol-3-yl)-3-hydroxypropan-2-one
-
2-(5-bromo-1H-indol-3-yl)-N-hydroxyacetamide
-
2-(5-bromo-2-methyl-1H-indolyl)-N-hydroxyacetamide
-
2-(5-chloro-1H-indol-3-yl)-N-hydroxyacetamide
-
2-(5-fluoro-1H-indol-3-yl)-N-hydroxyacetamide
-
2-(6-bromo-1H-indol-3-yl)-N-hydroxyacetamide
-
3-(3-acetylsulfanyl-2-oxopropyl)indole-1-carboxylic acid benzyl ester
-
5-bromo-3-hydroxycarbamoylmethylindole-1-carboxylic acid benzyl ester
-
N-((5-bromo-2-methyl-1(phenylsulfonyl)-1H-indol-3-yl)methyl) hydroxylamine
-
N-(1-benzenesulfonyl-5-bromo-2-methyl-1H-indol-3-ylmethyl)-N-hydroxyformamide
-
thioacetic acid S-[3-(5-bromo-1H-indol-3-yl)-2-oxopropyl] ester
-
(1-hydroxyaminomethyl-2-phenylethyl)carbamic acid tert-butyl ester
(1-hydroxycarbamoylmethyl-2-phenylethyl)carbamic acid tert-butyl ester
(3R)-3-[3-[(1,3-benzothiazol-2-yl)methyl]-1,2,4-oxadiazol-5-yl]-N-hydroxyheptanamide
-
(3R)-3-[3-[(1-benzofuran-3-yl)methyl]-1,2,4-oxadiazol-5-yl]-5-cyclopentyl-N-hydroxypentanamide
-
(3R)-3-[3-[(1-benzofuran-3-yl)methyl]-1,2,4-oxadiazol-5-yl]-N-hydroxyheptanamide
-
(3R)-3-[3-[(2H-1,3-benzodioxol-5-yl)methyl]-1,2,4-oxadiazol-5-yl]-5-cyclopentyl-N-hydroxypentanamide
-
(3R)-3-[3-[(2H-1,3-benzodioxol-5-yl)methyl]-1,2,4-oxadiazol-5-yl]-N-hydroxyheptanamide
-
(3R)-3-[3-[(4-fluorophenyl)methyl]-1,2,4-oxadiazol-5-yl]-N-hydroxyheptanamide
-
(3R)-3-[3-[([1,1'-biphenyl]-4-yl)methyl]-1,2,4-oxadiazol-5-yl]-N-hydroxyheptanamide
-
(3R)-N-hydroxy-3-(3-phenyl-1,2,4-oxadiazol-5-yl)heptanamide
-
(3R)-N-hydroxy-3-(3-[[4-(trifluoromethoxy)phenyl]methyl]-1,2,4-oxadiazol-5-yl)heptanamide
-
(3R)-N-hydroxy-3-(3-[[4-(trifluoromethyl)phenyl]methyl]-1,2,4-oxadiazol-5-yl)heptanamide
-
(3R)-N-hydroxy-3-(4-phenyl-1,3-oxazol-2-yl)heptanamide
-
(3R)-N-hydroxy-3-[3-(4-nitrophenyl)-1,2,4-oxadiazol-5-yl]heptanamide
-
(3R)-N-hydroxy-3-[3-[(4-methylphenyl)methyl]-1,2,4-oxadiazol-5-yl]heptanamide
-
(3R)-N-hydroxy-3-[3-[4-(trifluoromethyl)phenyl]-1,2,4-oxadiazol-5-yl]heptanamide
-
1-(5-bromo-1H-indol-3-yl)-3-hydroxypropan-2-one
1-(5-bromo-2-methyl-1H-indol-3-yl)-N-hydroxymethanamine
-
1-[5-bromo-2-methyl-1-(phenylsulfonyl)-1H-indol-3-yl]-N-hydroxymethanamine
-
2-(1-benzyl-5-bromo-1H-indol-3-yl)-N-hydroxyacetamide
-
2-(3-benzyl-5-bromo-1H-indol-1-yl)-N-hydroxyacetamide
-
2-(4-fluoro-1H-indol-3-yl)-N-hydroxyacetamide
2-(5-bromo-1H-indol-3-yl)-N-hydroxyacetamide
2-(5-bromo-2-methyl-1H-indol-3-yl)-N-hydroxyacetamide
-
2-(5-bromo-2-methyl-1H-indolyl)-N-hydroxyacetamide
2-(5-chloro-1H-indol-3-yl)-N-hydroxyacetamide
2-(5-fluoro-1H-indol-3-yl)-N-hydroxyacetamide
2-(5-methoxy-1H-indol-3-yl)-N-hydroxyacetamide
2-(6-bromo-1H-indol-3-yl)-N-hydroxyacetamide
2-(indol-3-yl)-N-hydroxyacetamide
2-[(3R)-1-(hydroxyamino)-1-oxoheptan-3-yl]-1,3-oxazole-4-carboxamide
-
3,3,3-trifluoro-N-[(2S)-1-[formyl(hydroxy)amino]-3-phenylpropan-2-yl]propanamide
-
3-(3-acetylsulfanyl-2-oxopropyl)indole-1-carboxylic acid benzyl ester
3-carboxymethylindol-1-carboxylic acid benzyl ester
4-([5-[(3R)-1-(hydroxyamino)-1-oxoheptan-3-yl]-1,2,4-oxadiazol-3-yl]methyl)phenyl hydrogen carbonate
-
4-([5-[(3R)-1-(hydroxyamino)-1-oxoheptan-3-yl]-1,2,4-oxadiazol-3-yl]methyl)phenyl methyl carbonate
-
5-bromo-3-hydroxycarbamoylmethylindole-1-carboxylic acid benzyl ester
actinonin
benzyl 5-bromo-3-[2-(hydroxyamino)-2-oxoethyl]-1H-indole-1-carboxylate
-
ethyl 2-[(3R)-1-(hydroxyamino)-1-oxoheptan-3-yl]-1,3-oxazole-4-carboxylate
-
imino[(5-methoxy-5-oxo-4-[2-(sulfanylmethyl)hexanoyl]aminopentyl)amino]methaneamine
-
-
methyl N-[2-[(3R)-1-(hydroxyamino)-1-oxoheptan-3-yl]-1,3-oxazole-4-carbonyl]-L-valinate
-
methyl-1-(sulfanylmethyl)hexanoate
-
-
N-((5-bromo-2-methyl-1(phenylsulfonyl)-1H-indol-3-yl)methyl) hydroxylamine
N-(1-benzenesulfonyl-5-bromo-2-methyl-1H-indol-3-ylmethyl)-N-hydroxyformamide
N-hydroxy-2-(1H-indol-3-yl)acetamide
-
N-hydroxy-2-(5-methoxy-1H-indol-3-yl)acetamide
-
N-[2-(5-bromo-2-methyl-1H-indole-3-yl)methyl]hydroxylamine
N-[[5-bromo-2-methyl-1-(phenylsulfonyl)-1H-indol-3-yl]methyl]-N-hydroxyformamide
-
N2-[2-[(3R)-1-(hydroxyamino)-1-oxoheptan-3-yl]-1,3-oxazole-4-carbonyl]-L-valinamide
-
Phe-Arg-beta-naphthylamide
-
-
thioacetic acid S-[3-(5-bromo-1H-indol-3-yl)-2-oxopropyl] ester
thioacetic acid S-[3-(indol-3-yl)-2-oxopropyl] ester
additional information
inhibitor design with the enzyme as model, structure-activity relationship analysis, overview. Design and synthesis of effective specific bacterial PDF inhibitors of an oxadiazole series with potent antimicrobial activity against a multidrug-resistant clinical isolate. Determination of minimal inhibitory concentrations of oxadiazole compounds for antibacterial activity on Escherichia coli strains. Three-dimensional comparison of the binding between various PDF inhibitors and actinonin
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.42
N-formyl-Arg(NH2)
-
enzyme form PDF1A
0.74 - 1
N-formyl-Asp(NH2)
2.9 - 4.3
N-formyl-Gly(NH2)
0.5
N-formyl-L-Arg-amide
-
enzyme form Ni-PDF1B
-
0.79
N-formyl-Leu(NH2)
-
enzyme form PDF1A
0.25 - 8.2
N-formyl-Met-Ala-Ser
8 - 12
N-formyl-Met-Leu-Glu
0.23
N-Formyl-Met-Leu-Phe
-
enzyme form PDF1A
2 - 4.1
N-formyl-Met-Ser-Asn-Glu
0.6 - 11
N-formyl-Nle-Ala-Ser
9.4
N-formyl-Nva-Ala-Ser
-
enzyme form PDF1A
3
N-formyl-Phe-Ala-Ser
-
enzyme form PDF1A
0.42 - 1
N-formyl-Ser(NH2)
additional information
additional information
-
-
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
13 - 75
N-formyl-Met-Ala-Ser
1.1 - 9.2
N-formyl-Met-Leu-Glu
0.7
N-Formyl-Met-Leu-Phe
-
enzyme form PDF1A
1.9 - 11
N-formyl-Met-Ser-Asn-Glu
26 - 136
N-formyl-Nle-Ala-Ser
5 - 138
N-formyl-Nle-Arg(NH2)
0.4 - 6.4
N-formyl-Nle-Asp(NH2)
1.4
N-formyl-Nle-Gly(NH2)
-
enzyme form PDF1A
0.36
N-formyl-Nle-Leu(NH2)
-
enzyme form PDF1A
10 - 51
N-formyl-Nle-Ser(NH2)
18
N-formyl-Nva-Ala-Ser
-
enzyme form PDF1A
0.6
N-formyl-Phe-Ala-Ser
-
enzyme form PDF1A
additional information
additional information
-
-
-
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.083 - 0.15
(1-hydroxycarbamoylmethyl-2-phenylethyl)carbamic acid tert-butyl ester
0.79
1-(5-bromo-1H-indol-3-yl)-3-hydroxypropan-2-one
-
0.13
2-(5-bromo-1H-indol-3-yl)-N-hydroxyacetamide
-
0.45
2-(5-bromo-2-methyl-1H-indolyl)-N-hydroxyacetamide
-
0.25
2-(5-chloro-1H-indol-3-yl)-N-hydroxyacetamide
-
0.7
2-(5-fluoro-1H-indol-3-yl)-N-hydroxyacetamide
-
0.25
2-(6-bromo-1H-indol-3-yl)-N-hydroxyacetamide
-
0.5
3-(3-acetylsulfanyl-2-oxopropyl)indole-1-carboxylic acid benzyl ester
-
0.014
5-bromo-3-hydroxycarbamoylmethylindole-1-carboxylic acid benzyl ester
-
0.000027
actinonin
-
0.5
N-((5-bromo-2-methyl-1(phenylsulfonyl)-1H-indol-3-yl)methyl) hydroxylamine
-
0.035
N-(1-benzenesulfonyl-5-bromo-2-methyl-1H-indol-3-ylmethyl)-N-hydroxyformamide
-
0.17
thioacetic acid S-[3-(5-bromo-1H-indol-3-yl)-2-oxopropyl] ester
-
0.052 - 0.11
(1-hydroxyaminomethyl-2-phenylethyl)carbamic acid tert-butyl ester
0.000044 - 0.0004
(1-hydroxycarbamoylmethyl-2-phenylethyl)carbamic acid tert-butyl ester
0.000263
(3R)-3-[3-[(1-benzofuran-3-yl)methyl]-1,2,4-oxadiazol-5-yl]-5-cyclopentyl-N-hydroxypentanamide
pH 7.5, 37°C, recombinant enzyme
0.000238
(3R)-3-[3-[(2H-1,3-benzodioxol-5-yl)methyl]-1,2,4-oxadiazol-5-yl]-5-cyclopentyl-N-hydroxypentanamide
pH 7.5, 37°C, recombinant enzyme
0.25 - 0.56
1-(5-bromo-1H-indol-3-yl)-3-hydroxypropan-2-one
0.000909
2-(1-benzyl-5-bromo-1H-indol-3-yl)-N-hydroxyacetamide
pH 7.5, 37°C, recombinant enzyme
0.001
2-(3-benzyl-5-bromo-1H-indol-1-yl)-N-hydroxyacetamide
pH 7.5, 37°C, recombinant enzyme
0.0001 - 0.002
2-(4-fluoro-1H-indol-3-yl)-N-hydroxyacetamide
0.000013 - 0.000455
2-(5-bromo-1H-indol-3-yl)-N-hydroxyacetamide
0.0001 - 0.003
2-(5-bromo-2-methyl-1H-indolyl)-N-hydroxyacetamide
0.000015 - 0.00008
2-(5-chloro-1H-indol-3-yl)-N-hydroxyacetamide
0.00002 - 0.00016
2-(5-fluoro-1H-indol-3-yl)-N-hydroxyacetamide
0.00033 - 0.009
2-(5-methoxy-1H-indol-3-yl)-N-hydroxyacetamide
0.00003 - 0.00021
2-(6-bromo-1H-indol-3-yl)-N-hydroxyacetamide
0.0003 - 0.0014
2-(indol-3-yl)-N-hydroxyacetamide
0.002
3,3,3-trifluoro-N-[(2S)-1-[formyl(hydroxy)amino]-3-phenylpropan-2-yl]propanamide
pH 7.5, 37°C, recombinant enzyme
0.1 - 0.35
3-(3-acetylsulfanyl-2-oxopropyl)indole-1-carboxylic acid benzyl ester
0.28 - 0.3
3-carboxymethylindol-1-carboxylic acid benzyl ester
0.001111
4-([5-[(3R)-1-(hydroxyamino)-1-oxoheptan-3-yl]-1,2,4-oxadiazol-3-yl]methyl)phenyl methyl carbonate
pH 7.5, 37°C, recombinant enzyme
0.000018 - 0.000027
5-bromo-3-hydroxycarbamoylmethylindole-1-carboxylic acid benzyl ester
0.00001 - 0.00014
actinonin
0.0004 - 0.006
N-((5-bromo-2-methyl-1(phenylsulfonyl)-1H-indol-3-yl)methyl) hydroxylamine
0.000025 - 0.00003
N-(1-benzenesulfonyl-5-bromo-2-methyl-1H-indol-3-ylmethyl)-N-hydroxyformamide
0.001 - 0.05
N-[2-(5-bromo-2-methyl-1H-indole-3-yl)methyl]hydroxylamine
0.12
thioacetic acid S-[3-(5-bromo-1H-indol-3-yl)-2-oxopropyl] ester
0.2
thioacetic acid S-[3-(indol-3-yl)-2-oxopropyl] ester
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.000077
(3R)-3-[3-[(1-benzofuran-3-yl)methyl]-1,2,4-oxadiazol-5-yl]-5-cyclopentyl-N-hydroxypentanamide
Arabidopsis thaliana
pH 7.5, 37°C, recombinant enzyme
0.0003
(3R)-3-[3-[(1-benzofuran-3-yl)methyl]-1,2,4-oxadiazol-5-yl]-N-hydroxyheptanamide
Arabidopsis thaliana
pH 7.5, 37°C, recombinant enzyme
0.000119
(3R)-3-[3-[(2H-1,3-benzodioxol-5-yl)methyl]-1,2,4-oxadiazol-5-yl]-5-cyclopentyl-N-hydroxypentanamide
Arabidopsis thaliana
pH 7.5, 37°C, recombinant enzyme
0.000058
(3R)-3-[3-[(4-fluorophenyl)methyl]-1,2,4-oxadiazol-5-yl]-N-hydroxyheptanamide
Arabidopsis thaliana
pH 7.5, 37°C, recombinant enzyme
0.00055
(3R)-3-[3-[([1,1'-biphenyl]-4-yl)methyl]-1,2,4-oxadiazol-5-yl]-N-hydroxyheptanamide
Arabidopsis thaliana
pH 7.5, 37°C, recombinant enzyme
0.0005
(3R)-N-hydroxy-3-(3-[[4-(trifluoromethoxy)phenyl]methyl]-1,2,4-oxadiazol-5-yl)heptanamide
Arabidopsis thaliana
pH 7.5, 37°C, recombinant enzyme
0.000909
(3R)-N-hydroxy-3-(3-[[4-(trifluoromethyl)phenyl]methyl]-1,2,4-oxadiazol-5-yl)heptanamide
Arabidopsis thaliana
pH 7.5, 37°C, recombinant enzyme
0.00046
(3R)-N-hydroxy-3-[3-[(4-methylphenyl)methyl]-1,2,4-oxadiazol-5-yl]heptanamide
Arabidopsis thaliana
pH 7.5, 37°C, recombinant enzyme
0.006
(3R)-N-hydroxy-3-[3-[4-(trifluoromethyl)phenyl]-1,2,4-oxadiazol-5-yl]heptanamide
Arabidopsis thaliana
pH 7.5, 37°C, recombinant enzyme
0.0004
2-(1-benzyl-5-bromo-1H-indol-3-yl)-N-hydroxyacetamide
Arabidopsis thaliana
pH 7.5, 37°C, recombinant enzyme
0.000703
2-(3-benzyl-5-bromo-1H-indol-1-yl)-N-hydroxyacetamide
Arabidopsis thaliana
pH 7.5, 37°C, recombinant enzyme
0.00036
2-(5-bromo-1H-indol-3-yl)-N-hydroxyacetamide
Arabidopsis thaliana
pH 7.5, 37°C, recombinant enzyme
0.000251
3,3,3-trifluoro-N-[(2S)-1-[formyl(hydroxy)amino]-3-phenylpropan-2-yl]propanamide
Arabidopsis thaliana
pH 7.5, 37°C, recombinant enzyme
0.0082
4-([5-[(3R)-1-(hydroxyamino)-1-oxoheptan-3-yl]-1,2,4-oxadiazol-3-yl]methyl)phenyl hydrogen carbonate
Arabidopsis thaliana
pH 7.5, 37°C, recombinant enzyme
0.00065
4-([5-[(3R)-1-(hydroxyamino)-1-oxoheptan-3-yl]-1,2,4-oxadiazol-3-yl]methyl)phenyl methyl carbonate
Arabidopsis thaliana
pH 7.5, 37°C, recombinant enzyme
0.0000075
actinonin
Arabidopsis thaliana
pH 7.5, 37°C, recombinant enzyme
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
-
the enzyme belongs to the type 1B subclass.PDFs are a subclass of the metalloprotease superfamily of enzymes known as the clan MA and MB metalloproteases. Proteins from this family share a common structure containing a three-stranded beta strand facing a catalytic metal and a HEXXH motif-containing alpha helix
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
DEF1A_ARATH
269
0
29996
Swiss-Prot
Chloroplast (Reliability: 4)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
25000
-
x * 25000, mature enzyme, SDS-PAGE
40000
-
gel filtration
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimer
AtPDF1B exists as a symmetric dimer
?
-
x * 25000, mature enzyme, SDS-PAGE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystals of AtPDF1Bt were grown by hanging drop vapor diffusion. The structure is determined a resolution of 2.4 A
purified recombinant enzyme, X-ray diffraction structure determination and analysis at 1.95 A resolution
-
sitting drop vapor diffusion method, using 15%-20% (w/v) PEG-3350 and either 0.1 or 0.2 M zinc acetate
using the sitting drop vapor diffusion method, two crystal forms diffract with a resolution of 2.8-2.9 A, third form yield a data set at 3.4 A resolution
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Y178A
the mutant shows an increase in Km for f-MTA substrate
Y178F
mutant shows a decrease in Km as well as an increase in kcat, indicating tighter binding of the substrate
G41A
the mutant shows strongly reduced Km and kcat values compared to the wild type enzyme
G41M
the kcat/Km value is reduced by three orders of magnitude due to large decrease in the kcat value (to 1%) compared to the wild type enzyme
G41Q
the kcat/Km value is reduced by three orders of magnitude due to large decrease in the kcat value (to 0.4%) compared to the wild type enzyme
I130A
the mutant protein exhibits strongly reduced kcat and Km values but shows no change in overall stability compared to the wild type
I130F
the mutant protein exhibits strongly reduced kcat and Km values but shows no change in overall stability compared to the wild type
I42A
the mutant shows increased Km and reduced kcat values compared to the wild type enzyme
I42F
the mutant shows increased Km and reduced kcat values compared to the wild type enzyme
I42N
the mutant shows decreased Km and kcat values compared to the wild type enzyme
I42W
the mutant shows decreased Km and kcat values compared to the wild type enzyme
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
limited proteolysis of AtPDF1B with trypsin results in the relatively slow formation of a lower molecular mass form (AtPDF1Bt) reduced by approximately 3 kDa. Although small reductions in molecular mass are observed after prolonged incubation, the proteolyzed AtPDF1B generated was largely resistant to further digestion. Recombinant AtPDF1B has a requirement for 0.5 M NaCl for solubility at concentrations of 0.5 mg/ml. After proteolysis with trypsin, AtPDF1B loses this characteristic and is soluble without NaCl at concentrations of 30 mg/ml
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20°C, PDF1A is stable for at least 6 months
-
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
Ni-nitrilotriacetate agarose chromatography
-
Q-Sepharose column chromatography, Superdex-75 gel filtration, and Mono Q column chromatography
recombinant isozyme 1B
two classes of PDF: PDF1A and PDF1B
-
using a Hi-Trap chelating HP nickel affinity column
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
DNA and amino acid sequence determination and analysis, recombinant expression
-
expressed in Nicotiana tabacum chloroplasts
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for over-expression in Escherichia coli
-
gene DEF2, recombinant expression of isozyme 1B
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
drug development
peptide deformylase (PDF) is considered an excellent target to develop antibiotics
medicine
-
peptide deformylase inhibitors have a strong potential to be used as antibiotics
additional information
-
PDF1B is not an appropriate selective marker for chloroplast transformation
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Giglione, C.; Pierre, M.; Meinnel, T.
Peptide deformylase as a target for new generation, broad spectrum antimicrobial agents
Mol. Microbiol.
36
1197-1205
2000
Arabidopsis thaliana, Geobacillus stearothermophilus, Escherichia coli, Enterococcus faecalis, Solanum lycopersicum, Staphylococcus aureus, no activity in Caenorhabditis elegans, no activity in Saccharomyces cerevisiae, Plasmodium falciparum, Trypanosoma sp.
Manually annotated by BRENDA team
Serero, A.; Giglione, C.; Meinnel, T.
Distinctive features of the two classes of eukaryotic peptide deformylases
J. Mol. Biol.
314
695-708
2001
Arabidopsis thaliana, Escherichia coli, Solanum lycopersicum
Manually annotated by BRENDA team
Fieulaine, S.; Juillan-Binard, C.; Serero, A.; Dardel, F.; Giglione, C.; Meinnel, T.; Ferrer, J.L.
The crystal structure of mitochondrial (Type 1A) peptide deformylase provides clear guidelines for the design of inhibitors specific for the bacterial forms
J. Biol. Chem.
280
42315-42324
2005
Arabidopsis thaliana
Manually annotated by BRENDA team
Dirk, L.M.; Schmidt, J.J.; Cai, Y.; Barnes, J.C.; Hanger, K.M.; Nayak, N.R.; Williams, M.A.; Grossman, R.B.; Houtz, R.L.; Rodgers, D.
Insights into substrate specificity of plant peptide deformylase, an essential enzyme with potential for the development of novel biotechnology applications in agriculture
Biochem. J.
413
417-427
2008
Arabidopsis thaliana (Q9FV53)
Manually annotated by BRENDA team
Boularot, A.; Giglione, C.; Petit, S.; Duroc, Y.; Alves de Sousa, R.; Larue, V.; Cresteil, T.; Dardel, F.; Artaud, I.; Meinnel, T.
Discovery and refinement of a new structural class of potent peptide deformylase inhibitors
J. Med. Chem.
50
10-20
2007
Arabidopsis thaliana, Arabidopsis thaliana (Q9FUZ2), Arabidopsis thaliana (Q9FV53), Bacillus subtilis, Escherichia coli, Homo sapiens
Manually annotated by BRENDA team
Chikhi, A.; Bensegueni, A.
In silico study of the selective inhibition of bacterial peptide deformylases by several drugs
J. Proteomics Bioinform.
3
61-65
2010
Escherichia coli (P0A6K3), Bacillus cereus (Q819K2), Arabidopsis thaliana (Q9FUZ2), Homo sapiens (Q9HBH1)
-
Manually annotated by BRENDA team
Fieulaine, S.; Boularot, A.; Artaud, I.; Desmadril, M.; Dardel, F.; Meinnel, T.; Giglione, C.
Trapping conformational states along ligand-binding dynamics of peptide deformylase: the impact of induced fit on enzyme catalysis
PLoS Biol.
9
e1001066
2011
Arabidopsis thaliana (Q9FUZ2)
Manually annotated by BRENDA team
Fernandez-San Millan, A.; Obregon, P.; Veramendi, J.
Over-expression of peptide deformylase in chloroplasts confers actinonin resistance, but is not a suitable selective marker system for plastid transformation
Transgenic Res.
20
613-624
2011
Arabidopsis thaliana
Manually annotated by BRENDA team
Frank, J.A.; Lorimer, D.; Youle, M.; Witte, P.; Craig, T.; Abendroth, J.; Rohwer, F.; Edwards, R.A.; Segall, A.M.; Burgin, A.B.
Structure and function of a cyanophage-encoded peptide deformylase
ISME J.
7
1150-1160
2013
Arabidopsis thaliana, Synechococcus phage S-SSM7 (E3SLL2)
Manually annotated by BRENDA team
Fieulaine, S.; Alves de Sousa, R.; Maigre, L.; Hamiche, K.; Alimi, M.; Bolla, J.M.; Taleb, A.; Denis, A.; Pages, J.M.; Artaud, I.; Meinnel, T.; Giglione, C.
A unique peptide deformylase platform to rationally design and challenge novel active compounds
Sci. Rep.
6
35429
2016
Escherichia coli (P0A6K3), Streptococcus agalactiae (Q8E378), Streptococcus agalactiae, Arabidopsis thaliana (Q9FUZ2), Streptococcus agalactiae NEM316 (Q8E378)
Manually annotated by BRENDA team