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Information on EC 3.5.1.88 - peptide deformylase and Organism(s) Geobacillus stearothermophilus and UniProt Accession O31410

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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:
Geobacillus stearothermophilus
UNIPROT: O31410
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Word Map
The taxonomic range for the selected organisms is: Geobacillus stearothermophilus
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
peptide deformylase
type I and type II
deformylase, peptide N-formylmethionine
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-
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hydrolase, aminoacyl-transfer ribonucleate
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PDF
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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-methionine-polypeptide + H2O
formate + L-methionine-polypeptide
show the reaction diagram
involved in polypeptide synthesis by removal of the formyl-group from methionine in growing polypeptides
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-
?
N-formyl-L-methionine-polypeptide + H2O
formate + L-methionine-polypeptide
show the reaction diagram
-
deformylation required for methionine aminopeptidase activity in eubacteria, highly specific
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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
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
show the reaction diagram
-
deformylation required for methionine aminopeptidase activity in eubacteria, highly specific
-
?
additional information
?
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Co2+
can replace Fe2+ without loss of activity, enhances stability
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
actinonin
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
DEF2_GEOSE
184
0
20383
Swiss-Prot
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
Ni2+ and Co2+ increase stability compared to the Fe2+ enzyme
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
drug development
potential target or the development of new antibacterial agents
medicine
the specific bacterial requirement for peptide deformylase in protein synthesis provides a rational basis for selectivity, making it an attractive potential drug discovery target
medicine
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possible target for new broad spectrum antimicrobial agents
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
Ragusa, S.; Blanquet, S.; Meinnel, T.
Control of peptide deformylase activity by metal cations
J. Mol. Biol.
280
515-523
1998
Geobacillus stearothermophilus, Escherichia coli, Thermus thermophilus
Manually annotated by BRENDA team
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)
Manually annotated by BRENDA team
Wang, Q.; Wang, J.; Cai, Z.; Xu, W.
Prediction of the binding modes between BB-83698 and peptide deformylase from Bacillus stearothermophilus by docking and molecular dynamics simulation
Biophys. Chem.
134
178-184
2008
Geobacillus stearothermophilus (O31410), Geobacillus stearothermophilus
Manually annotated by BRENDA team