Peptide deformylase (P0A6K3)

Identification
Name:Peptide deformylase
Synonyms:
  • PDF
  • Polypeptide deformylase
Gene Name:def
Enzyme Class:
Biological Properties
General Function:Involved in iron ion binding
Specific Function:Removes the formyl group from the N-terminal Met of newly synthesized proteins. 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
Cellular Location:Cytoplasmic
SMPDB Pathways:Not Available
KEGG Pathways:Not Available
KEGG Reactions:
1.0Formyl-L-methionyl peptide+1.0Thumb ↔ 1.0Thumb+1.0Methionyl peptide
1.0Formyl-L-methionyl peptide + 1.0Water ↔ 1.0Formic acid + 1.0Methionyl peptide
ReactionCard
EcoCyc Reactions:
1.0Thumb+1.0formyl-L-methionyl peptide → 1.0Thumb+1.0methionyl peptide+1.0Thumb
1.0Water + 1.0formyl-L-methionyl peptide → 1.0Hydrogen ion + 1.0methionyl peptide + 1.0Formic acid
ReactionCard
Complex Reactions:
1.0Formyl-L-methionyl peptide+1.0Thumb → 1.0Thumb+1.0methionyl peptide
1.0Formyl-L-methionyl peptide + 1.0Water → 1.0Formic acid + 1.0methionyl peptide
ReactionCard
Metabolites:
ECMDB IDNameView
ECMDB00142Formic acidMetaboCard
ECMDB21225Hydrogen ionMetaboCard
ECMDB00494WaterMetaboCard
GO Classification:
Function
binding
catalytic activity
cation binding
hydrolase activity
hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds
hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
ion binding
iron ion binding
metal ion binding
peptide deformylase activity
transition metal ion binding
Process
biosynthetic process
cellular macromolecule biosynthetic process
macromolecule biosynthetic process
metabolic process
translation
Gene Properties
Blattner:b3287
Gene OrientationClockwise
Centisome Percentage:73.96
Left Sequence End3431712
Right Sequence End3432221
Gene Sequence:
>510 bp
ATGAATCTACAACGATTTGATGACAGCACCCTAATCCGTATCTTTGCCCTTCATGAGTTA
CATCGACTGAAAGAACATGGCTTAACGCGCGGGGCGCTTCTCGATTATCACAGCCGCTAT
AAACTCGTCTTTCTGGCGCATTCTCAGCCGGAGTACCGCAAACTTGGCCCGTTCGTGGCT
GATATTCACCAGTGGCAAAATCTGGATGACTATTACAACCAGTACCGCCAACGCGTAGTT
GTTTTGCTTTCTCACCCCGCCAACCCGCGCGATCACACCAATGTTTTGATGCACGTTCAG
GGTTATTTTCGCCCGCATATTGATTCCACAGAACGCCAGCAGCTGGCTGCGCTTATCGAC
AGTTATCGCCGTGGCGAGCAACCACTTCTTGCGCCGCTGATGCGTATCAAACACTATATG
GCGCTTTATCCTGACGCCTGGCTTTCAGGGCAGCGTTATTTCGAACTTTGGCCGCGTGTG
ATTAACTTGCGCCATTCAGGAGTTTTATGA
Protein Properties
Pfam Domain Function:
Protein Residues:169
Protein Molecular Weight:19328
Protein Theoretical pI:5
PDB File:1XEO
Signaling Regions:
  • None
Transmembrane Regions:
  • None
Protein Sequence:
>Peptide deformylase
MSVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIV
IDVSENRDERLVLINPELLEKSGETGIEEGCLSIPEQRALVPRAEKVKIRALDRDGKPFE
LEADGLLAICIQHEMDHLVGKLFMDYLSPLKQQRIRQKVEKLDRLKARA
References
External Links:
ResourceLink
Uniprot ID:P0A6K3
Uniprot Name:DEF_ECOLI
GenBank Gene ID:AP009048
Genebank Protein ID:4062300
PDB ID:1XEO
Ecogene ID:EG11440
Ecocyc:EG11440
ColiBase:b3287
Kegg Gene:b3287
EchoBASE ID:EB1410
CCDB:DEF_ECOLI
BacMap:16131166
General Reference:
  • Becker, A., Schlichting, I., Kabsch, W., Groche, D., Schultz, S., Wagner, A. F. (1998). "Iron center, substrate recognition and mechanism of peptide deformylase." Nat Struct Biol 5:1053-1058. Pubmed: 9846875
  • Becker, A., Schlichting, I., Kabsch, W., Schultz, S., Wagner, A. F. (1998). "Structure of peptide deformylase and identification of the substrate binding site." J Biol Chem 273:11413-11416. Pubmed: 9565550
  • Blattner, F. R., Plunkett, G. 3rd, Bloch, C. A., Perna, N. T., Burland, V., Riley, M., Collado-Vides, J., Glasner, J. D., Rode, C. K., Mayhew, G. F., Gregor, J., Davis, N. W., Kirkpatrick, H. A., Goeden, M. A., Rose, D. J., Mau, B., Shao, Y. (1997). "The complete genome sequence of Escherichia coli K-12." Science 277:1453-1462. Pubmed: 9278503
  • Chan, M. K., Gong, W., Rajagopalan, P. T., Hao, B., Tsai, C. M., Pei, D. (1997). "Crystal structure of the Escherichia coli peptide deformylase." Biochemistry 36:13904-13909. Pubmed: 9374869
  • Dardel, F., Ragusa, S., Lazennec, C., Blanquet, S., Meinnel, T. (1998). "Solution structure of nickel-peptide deformylase." J Mol Biol 280:501-513. Pubmed: 9665852
  • Groche, D., Becker, A., Schlichting, I., Kabsch, W., Schultz, S., Wagner, A. F. (1998). "Isolation and crystallization of functionally competent Escherichia coli peptide deformylase forms containing either iron or nickel in the active site." Biochem Biophys Res Commun 246:342-346. Pubmed: 9610360
  • Guillon, J. M., Mechulam, Y., Schmitter, J. M., Blanquet, S., Fayat, G. (1992). "Disruption of the gene for Met-tRNA(fMet) formyltransferase severely impairs growth of Escherichia coli." J Bacteriol 174:4294-4301. Pubmed: 1624424
  • Hao, B., Gong, W., Rajagopalan, P. T., Zhou, Y., Pei, D., Chan, M. K. (1999). "Structural basis for the design of antibiotics targeting peptide deformylase." Biochemistry 38:4712-4719. Pubmed: 10200158
  • Hayashi, K., Morooka, N., Yamamoto, Y., Fujita, K., Isono, K., Choi, S., Ohtsubo, E., Baba, T., Wanner, B. L., Mori, H., Horiuchi, T. (2006). "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Mol Syst Biol 2:2006.0007. Pubmed: 16738553
  • Mazel, D., Pochet, S., Marliere, P. (1994). "Genetic characterization of polypeptide deformylase, a distinctive enzyme of eubacterial translation." EMBO J 13:914-923. Pubmed: 8112305
  • Meinnel, T., Blanquet, S. (1995). "Enzymatic properties of Escherichia coli peptide deformylase." J Bacteriol 177:1883-1887. Pubmed: 7896716
  • Meinnel, T., Blanquet, S., Dardel, F. (1996). "A new subclass of the zinc metalloproteases superfamily revealed by the solution structure of peptide deformylase." J Mol Biol 262:375-386. Pubmed: 8845003
  • Meinnel, T., Guillon, J. M., Mechulam, Y., Blanquet, S. (1993). "The Escherichia coli fmt gene, encoding methionyl-tRNA(fMet) formyltransferase, escapes metabolic control." J Bacteriol 175:993-1000. Pubmed: 8432722