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Information on EC 3.5.1.88 - peptide deformylase and Organism(s) Pseudomonas aeruginosa and UniProt Accession Q9I7A8
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3.5.1.88 peptide deformylaseIUBMB 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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Word Map
- 3.5.1.88
- actinonin
- medicine
-
n-formylated
-
deformylation
- eubacteria
-
hydroxamic
- drug development
-
formyltransferase
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oxazolidinone
- catarrhalis
- linezolid
- moraxella
-
hexxh
- biotechnology
- synthesis
- agriculture
- molecular biology
- analysis
The taxonomic range for the selected organisms is: Pseudomonas aeruginosa
The enzyme appears in selected viruses and cellular organisms
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
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
deformylase, peptide N-formylmethionine
-
-
-
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hydrolase, aminoacyl-transfer ribonucleate
-
-
-
-
PDF
Polypeptide deformylase
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-
-
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PDF
-
-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
hydrolysis of amide bond
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-
-
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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
369636-51-1
-
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)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
N-formyl-L-methionine-polypeptide + H2O
formate + L-methionine-polypeptide
-
-
-
-
?
N-formyl-L-methionine-polypeptide + H2O
formate + L-methionine-polypeptide
-
-
-
?
N-formyl-L-methionine-polypeptide + H2O
formate + L-methionine-polypeptide
involved in polypeptide synthesis by removal of the formyl-group from methionine in growing polypeptides
-
-
?
N-formyl-L-methionine-polypeptide + H2O
formate + L-methionine-polypeptide
-
involved in polypeptide synthesis by removal of the formyl-group from methionine in growing polypeptides
-
-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
N-formyl-L-methionine-polypeptide + H2O
formate + L-methionine-polypeptide
-
-
-
-
?
N-formyl-L-methionine-polypeptide + H2O
formate + L-methionine-polypeptide
-
-
-
?
N-formyl-L-methionine-polypeptide + H2O
formate + L-methionine-polypeptide
involved in polypeptide synthesis by removal of the formyl-group from methionine in growing polypeptides
-
-
?
N-formyl-L-methionine-polypeptide + H2O
formate + L-methionine-polypeptide
-
involved in polypeptide synthesis by removal of the formyl-group from methionine in growing polypeptides
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-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Co2+
can replace Fe2+ without loss of activity, enhances stability
Ni2+
Ni2+
can replace Fe2+ without loss of activity, enhances stability
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
1-[(2-methoxyphenyl)carbamoyl]prolyl-N2-(cyclopentylmethyl)-N-hydroxyglycinamide
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3-methyl-N-(1,3-thiazol-2-ylcarbamoyl)-L-valyl-N2-(cyclopentylmethyl)-N-hydroxyglycinamide
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3-methyl-N-(2-methylpropanoyl)-L-valyl-N2-(cyclopentylmethyl)-N-hydroxyglycinamide
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3-methyl-N-(morpholin-4-ylcarbonyl)-L-valyl-N2-(cyclopentylmethyl)-N-hydroxyglycinamide
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3-methyl-N-(phenylcarbamoyl)-L-valyl-N2-(cyclopentylmethyl)-N-hydroxyglycinamide
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3-methyl-N-(piperidin-1-ylcarbonyl)-L-valyl-N2-(cyclopentylmethyl)-N-hydroxyglycinamide
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3-methyl-N-(pyridin-2-ylcarbamoyl)-L-valyl-N2-(cyclopentylmethyl)-N-hydroxyglycinamide
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3-methyl-N-(pyridin-3-ylcarbamoyl)-L-valyl-N2-(cyclopentylmethyl)-N-hydroxyglycinamide
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3-methyl-N-(pyridin-4-ylcarbamoyl)-L-valyl-N2-(cyclopentylmethyl)-N-hydroxyglycinamide
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3-methyl-N-(thiophen-2-ylcarbonyl)-L-valyl-N2-(cyclopentylmethyl)-N-hydroxyglycinamide
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3-methyl-N-[methyl(phenyl)carbamoyl]-L-valyl-N2-(cyclopentylmethyl)-N-hydroxyglycinamide
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N-(2-methoxybenzoyl)-3-methyl-L-valyl-N2-(cyclopentylmethyl)-N-hydroxyglycinamide
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N-(cyclohexylcarbamoyl)-3-methyl-L-valyl-N2-(cyclopentylmethyl)-N-hydroxyglycinamide
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N-benzoyl-3-methyl-L-valyl-N2-(cyclopentylmethyl)-N-hydroxyglycinamide
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N-[(2-methoxyethyl)carbamoyl]-3-methyl-L-valyl-N2-(cyclopentylmethyl)-N-hydroxyglycinamide
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N-[(2-methoxyphenyl)carbamoyl]-3-methyl-L-valyl-N-hydroxy-N2-(3-methylbutyl)glycinamide
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N-[(2-methoxyphenyl)carbamoyl]-3-methyl-L-valyl-N2-(2-cyclopentylethyl)-N-hydroxyglycinamide
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N-[(2-methoxyphenyl)carbamoyl]-3-methyl-L-valyl-N2-(cyclobutylmethyl)-N-hydroxyglycinamide
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N-[(2-methoxyphenyl)carbamoyl]-3-methyl-L-valyl-N2-(cyclopentylmethyl)-N-hydroxyglycinamide
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N-[(2-methoxyphenyl)carbamoyl]-3-methyl-L-valyl-N2-(cyclopropylmethyl)-N-hydroxyglycinamide
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N-[(2-methoxyphenyl)carbamoyl]alanyl-N2-(cyclopentylmethyl)-N-hydroxyglycinamide
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N-[(2-methoxyphenyl)carbamoyl]leucyl-N2-(cyclopentylmethyl)-N-hydroxyglycinamide
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N-[(2-methoxyphenyl)carbamoyl]norleucyl-N2-(cyclopentylmethyl)-N-hydroxyglycinamide
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N-[(2-methoxyphenyl)carbamoyl]phenylalanyl-N2-(cyclopentylmethyl)-N-hydroxyglycinamide
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N-[(2-methoxyphenyl)carbamoyl]valyl-N2-(cyclopentylmethyl)-N-hydroxyglycinamide
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IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.000116
1-[(2-methoxyphenyl)carbamoyl]prolyl-N2-(cyclopentylmethyl)-N-hydroxyglycinamide
Pseudomonas aeruginosa
pH and temperature not specified in the publication
0.000043
3-methyl-N-(1,3-thiazol-2-ylcarbamoyl)-L-valyl-N2-(cyclopentylmethyl)-N-hydroxyglycinamide
Pseudomonas aeruginosa
pH and temperature not specified in the publication
0.000052
3-methyl-N-(2-methylpropanoyl)-L-valyl-N2-(cyclopentylmethyl)-N-hydroxyglycinamide
Pseudomonas aeruginosa
pH and temperature not specified in the publication
0.000028
3-methyl-N-(morpholin-4-ylcarbonyl)-L-valyl-N2-(cyclopentylmethyl)-N-hydroxyglycinamide
Pseudomonas aeruginosa
pH and temperature not specified in the publication
0.000017
3-methyl-N-(phenylcarbamoyl)-L-valyl-N2-(cyclopentylmethyl)-N-hydroxyglycinamide
Pseudomonas aeruginosa
pH and temperature not specified in the publication
0.000047
3-methyl-N-(piperidin-1-ylcarbonyl)-L-valyl-N2-(cyclopentylmethyl)-N-hydroxyglycinamide
Pseudomonas aeruginosa
pH and temperature not specified in the publication
0.000054
3-methyl-N-(pyridin-2-ylcarbamoyl)-L-valyl-N2-(cyclopentylmethyl)-N-hydroxyglycinamide
Pseudomonas aeruginosa
pH and temperature not specified in the publication
0.000049
3-methyl-N-(pyridin-3-ylcarbamoyl)-L-valyl-N2-(cyclopentylmethyl)-N-hydroxyglycinamide
Pseudomonas aeruginosa
pH and temperature not specified in the publication
0.000065
3-methyl-N-(pyridin-4-ylcarbamoyl)-L-valyl-N2-(cyclopentylmethyl)-N-hydroxyglycinamide
Pseudomonas aeruginosa
pH and temperature not specified in the publication
0.000019
3-methyl-N-(thiophen-2-ylcarbonyl)-L-valyl-N2-(cyclopentylmethyl)-N-hydroxyglycinamide
Pseudomonas aeruginosa
pH and temperature not specified in the publication
0.00005
3-methyl-N-[methyl(phenyl)carbamoyl]-L-valyl-N2-(cyclopentylmethyl)-N-hydroxyglycinamide
Pseudomonas aeruginosa
pH and temperature not specified in the publication
0.000011
N-(2-methoxybenzoyl)-3-methyl-L-valyl-N2-(cyclopentylmethyl)-N-hydroxyglycinamide
Pseudomonas aeruginosa
pH and temperature not specified in the publication
0.000055
N-(cyclohexylcarbamoyl)-3-methyl-L-valyl-N2-(cyclopentylmethyl)-N-hydroxyglycinamide
Pseudomonas aeruginosa
pH and temperature not specified in the publication
0.000041
N-benzoyl-3-methyl-L-valyl-N2-(cyclopentylmethyl)-N-hydroxyglycinamide
Pseudomonas aeruginosa
pH and temperature not specified in the publication
0.000042
N-[(2-methoxyethyl)carbamoyl]-3-methyl-L-valyl-N2-(cyclopentylmethyl)-N-hydroxyglycinamide
Pseudomonas aeruginosa
pH and temperature not specified in the publication
0.000021
N-[(2-methoxyphenyl)carbamoyl]-3-methyl-L-valyl-N-hydroxy-N2-(3-methylbutyl)glycinamide
Pseudomonas aeruginosa
pH and temperature not specified in the publication
0.000031
N-[(2-methoxyphenyl)carbamoyl]-3-methyl-L-valyl-N2-(2-cyclopentylethyl)-N-hydroxyglycinamide
Pseudomonas aeruginosa
pH and temperature not specified in the publication
0.000013
N-[(2-methoxyphenyl)carbamoyl]-3-methyl-L-valyl-N2-(cyclobutylmethyl)-N-hydroxyglycinamide
Pseudomonas aeruginosa
pH and temperature not specified in the publication
0.000029
N-[(2-methoxyphenyl)carbamoyl]-3-methyl-L-valyl-N2-(cyclopentylmethyl)-N-hydroxyglycinamide
Pseudomonas aeruginosa
pH and temperature not specified in the publication
0.000015
N-[(2-methoxyphenyl)carbamoyl]-3-methyl-L-valyl-N2-(cyclopropylmethyl)-N-hydroxyglycinamide
Pseudomonas aeruginosa
pH and temperature not specified in the publication
0.000042
N-[(2-methoxyphenyl)carbamoyl]alanyl-N2-(cyclopentylmethyl)-N-hydroxyglycinamide
Pseudomonas aeruginosa
pH and temperature not specified in the publication
0.000032
N-[(2-methoxyphenyl)carbamoyl]leucyl-N2-(cyclopentylmethyl)-N-hydroxyglycinamide
Pseudomonas aeruginosa
pH and temperature not specified in the publication
0.000036
N-[(2-methoxyphenyl)carbamoyl]norleucyl-N2-(cyclopentylmethyl)-N-hydroxyglycinamide
Pseudomonas aeruginosa
pH and temperature not specified in the publication
0.000061
N-[(2-methoxyphenyl)carbamoyl]phenylalanyl-N2-(cyclopentylmethyl)-N-hydroxyglycinamide
Pseudomonas aeruginosa
pH and temperature not specified in the publication
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
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
PDB
SCOP
CATH
UNIPROT
ORGANISM
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystallization in presence of the inhibitor actinonin using polyethylene glycol 4000 as precipitant, hanging-drop vapour-diffusion method at 4°C. The crystal belongs to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 68.75 A, b = 74,46 A, c = 77.18 A. The asymmetric unit contains two subunits of peptide deformylase, with a corresponding crystal volume per protein mass of 2.45 A Da and a solvent content of 49.8%
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GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
OXIDATION STABILITY
ORGANISM
UNIPROT
LITERATURE
instable towards oxidation due to the oxidation of the metal ligating cysteine residue
666015
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
drug development
medicine
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peptide deformylase is a therapeutic target for antibacterial drug discovery
drug development
potential target or the development of new antibacterial agents
drug development
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potential target or the development of new antibacterial agents
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Haas, M.; Beyer, D.; Gahlmann, R.; Freiberg, C.
YkrB is the main peptide deformylase in Bacillus subtilis, a eubacterium containing two functional peptide deformylases
Microbiology
147
1783-1791
2001
Bacillus subtilis, Streptococcus pneumoniae, Pseudomonas aeruginosa, Streptococcus pyogenes
Kim, H.W.; Han, B.W.; Yoon, H.J.; Yang, J.K.; Lee, B.I.; Lee, H.H.; Ahn, H.J.; Suh, S.W.
Crystallization and preliminary X-ray crystallographic analysis of peptide deformylase from Pseudomonas aeruginosa
Acta Crystallogr. Sect. D
58
1874-1875
2002
Pseudomonas aeruginosa
Guilloteau, J.P.; Mathieu, M.; Giglione, C.; Blanc, V.; Dupuy, A.; Chevrier, M.; Gil, P.; Famechon, A.; Meinnel, T.; Mikol, V.
The crystal structures of four peptide deformylases bound to the antibiotic actinonin reveal two distinct types: a platform for the structure-based design of antibacterial agents
J. Mol. Biol.
320
951-962
2002
Geobacillus stearothermophilus (O31410), Escherichia coli (P0A6K3), Staphylococcus aureus (P68826), Staphylococcus aureus, Pseudomonas aeruginosa (Q9I7A8), Pseudomonas aeruginosa, Staphylococcus aureus RN4220 (P68826)
Kreusch, A.; Spraggon, G.; Lee, C.C.; Klock, H.; McMullan, D.; Ng, K.; Shin, T.; Vincent, J.; Warner, I.; Ericson, C.; Lesley, S.A.
Structure analysis of peptide deformylases from Streptococcus pneumoniae, Staphylococcus aureus, Thermotoga maritima and Pseudomonas aeruginosa: snapshots of the oxygen sensitivity of peptide deformylase
J. Mol. Biol.
330
309-321
2003
Escherichia coli (P0A6K3), Escherichia coli, Plasmodium falciparum, Pseudomonas aeruginosa (Q9I7A8), Pseudomonas aeruginosa, Staphylococcus aureus (P68826), Staphylococcus aureus, Staphylococcus aureus ATCC 2913 (P68826), Streptococcus pneumoniae (Q9F2F0), Streptococcus pneumoniae, Thermotoga maritima (P96113), Thermotoga maritima, Thermotoga maritima MSB8 / DSM 3109 / ATCC 43589 (P96113)
Lee, S.K.; Choi, K.H.; Lee, S.J.; Suh, S.W.; Kim, B.M.; Lee, B.J.
Peptide deformylase inhibitors with retro-amide scaffold: synthesis and structure-activity relationships
Bioorg. Med. Chem. Lett.
20
4317-4319
2010
Pseudomonas aeruginosa (Q9I7A8)
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
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