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Information on EC 3.5.1.88 - peptide deformylase and Organism(s) Bacillus cereus and UniProt Accession Q819K2

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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:
Bacillus cereus
UNIPROT: Q819K2
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Word Map
The taxonomic range for the selected organisms is: Bacillus cereus
The enzyme appears in selected viruses and cellular organisms
Synonyms
peptide deformylase, hspdf, pdf-1, polypeptide deformylase, pdf1a, hppdf, pdf1b, pdf-2, tbpdf1, atdef2, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
BcPDF2
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deformylase, peptide N-formylmethionine
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hydrolase, aminoacyl-transfer ribonucleate
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peptide deformylase
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peptide deformylase 2
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Polypeptide deformylase
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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
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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
formyl-L-methionyl peptide + H2O
formate + methionyl peptide
show the reaction diagram
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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
formyl-L-methionyl peptide + H2O
formate + methionyl peptide
show the reaction diagram
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-
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1-(5-bromo-2-methyl-1H-indol-3-yl)-N-hydroxymethanamine
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1-[5-bromo-2-methyl-1-(phenylsulfonyl)-1H-indol-3-yl]-N-hydroxymethanamine
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2-(4-fluoro-1H-indol-3-yl)-N-hydroxyacetamide
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2-(5-bromo-1H-indol-3-yl)-N-hydroxyacetamide
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2-(5-bromo-2-methyl-1H-indol-3-yl)-N-hydroxyacetamide
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2-(5-chloro-1H-indol-3-yl)-N-hydroxyacetamide
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2-(5-fluoro-1H-indol-3-yl)-N-hydroxyacetamide
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2-(6-bromo-1H-indol-3-yl)-N-hydroxyacetamide
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benzyl 5-bromo-3-[2-(hydroxyamino)-2-oxoethyl]-1H-indole-1-carboxylate
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N-hydroxy-2-(1H-indol-3-yl)acetamide
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N-hydroxy-2-(5-methoxy-1H-indol-3-yl)acetamide
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N-[[5-bromo-2-methyl-1-(phenylsulfonyl)-1H-indol-3-yl]methyl]-N-hydroxyformamide
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actinonin
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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Uniprot
Manually annotated by BRENDA team
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
inhibitor free structure, 1.7 A resolution - peptide deformylase-actinonin complex, 2.0 A resolution
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inhibitor free structure, resolution range 50-1.7 A - peptide deformylase-actinonin complex, resolution 50-2.0 A
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sitting-drop vapor diffusion method, crystallization of a BcPDF2-actinonin complex. BcPDF2 is found as a dimer in the crystal form with two additional actinonin bound at that interface
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
using a Ni2+-chelated Hi-trap chelating column and gelfiltation on a Superdex-75 prep-grade column
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
into pET28a vector for overexpression of the recombinant protein in Escherichia BL21(DE3) cells
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overexpressed in Escherichia coli BL21(DE3) cells
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
medicine
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peptide deformylase has been considered as a potential target in antimicrobial chemotherapy
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Park, J.K.; Moon, J.H.; Kim, J.H.; Kim, E.E.
Crystallization and preliminary X-ray crystallographic analysis of peptide deformylase (PDF) from Bacillus cereus in ligand-free and actinonin-bound forms
Acta Crystallogr. Sect. F
61
150-152
2005
Bacillus cereus
Manually annotated by BRENDA team
Moon, J.H.; Park, J.K.; Kim, E.E.
Structure analysis of peptide deformylase from Bacillus cereus
Proteins
61
217-220
2005
Bacillus cereus
Manually annotated by BRENDA team
Park, J.K.; Kim, K.H.; Moon, J.H.; Kim, E.E.
Characterization of peptide deformylase 2 from B. cereus
J. Biochem. Mol. Biol.
40
1050-1057
2007
Bacillus cereus
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)
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Manually annotated by BRENDA team