Peptide deformylase

NamePeptide deformylase
Synonyms
  • 3.5.1.88
  • fms
  • PDF
  • Polypeptide deformylase
Gene Namedef
OrganismEscherichia coli (strain K12)
Amino acid sequence
>lcl|BSEQ0011040|Peptide deformylase
MSVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIV
IDVSENRDERLVLINPELLEKSGETGIEEGCLSIPEQRALVPRAEKVKIRALDRDGKPFE
LEADGLLAICIQHEMDHLVGKLFMDYLSPLKQQRIRQKVEKLDRLKARA
Number of residues169
Molecular Weight19328.23
Theoretical pI5.0
GO Classification
Functions
  • hydrolase activity
  • zinc ion binding
  • ferrous iron binding
  • peptide deformylase activity
  • ribosome binding
Processes
  • co-translational protein modification
  • N-terminal protein amino acid modification
  • translation
Components
  • cytosol
General FunctionZinc ion binding
Specific FunctionRemoves 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.
Pfam Domain Function
Transmembrane RegionsNot Available
GenBank Protein ID471304
UniProtKB IDP0A6K3
UniProtKB Entry NameDEF_ECOLI
Cellular LocationCytoplasmic
Gene sequence
>lcl|BSEQ0011041|Peptide deformylase (def)
ATGTCAGTTTTGCAAGTGTTACATATTCCGGACGAGCGGCTTCGCAAAGTTGCTAAACCG
GTAGAAGAAGTGAATGCAGAAATTCAGCGTATCGTCGATGATATGTTCGAGACGATGTAC
GCAGAAGAAGGTATTGGCCTGGCGGCAACCCAGGTTGATATCCATCAACGTATCATTGTT
ATTGATGTTTCGGAAAACCGTGACGAACGGCTAGTGTTAATCAATCCAGAGCTTTTAGAA
AAAAGCGGCGAAACAGGCATTGAAGAAGGTTGCCTGTCGATCCCTGAACAACGTGCTTTA
GTGCCGCGCGCAGAGAAAGTTAAAATTCGCGCCCTTGACCGCGACGGTAAACCATTTGAA
CTGGAAGCAGACGGTCTGTTAGCCATCTGTATTCAGCATGAGATGGATCACCTGGTCGGC
AAACTGTTTATGGATTATCTGTCACCGCTGAAACAACAACGTATTCGTCAGAAAGTTGAA
AAACTGGATCGTCTGAAAGCCCGGGCTTAA
GenBank Gene IDX77800
GeneCard IDNot Available
GenAtlas IDNot Available
HGNC IDNot Available
Chromosome LocationNot Available
LocusNot Available
References
  1. Mazel D, Pochet S, Marliere P: Genetic characterization of polypeptide deformylase, a distinctive enzyme of eubacterial translation. EMBO J. 1994 Feb 15;13(4):914-23. 8112305
  2. Guillon JM, Mechulam Y, Schmitter JM, Blanquet S, Fayat G: Disruption of the gene for Met-tRNA(fMet) formyltransferase severely impairs growth of Escherichia coli. J Bacteriol. 1992 Jul;174(13):4294-301. 1624424
  3. Blattner FR, Plunkett G 3rd, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y: The complete genome sequence of Escherichia coli K-12. Science. 1997 Sep 5;277(5331):1453-62. 9278503
  4. Hayashi K, Morooka N, Yamamoto Y, Fujita K, Isono K, Choi S, Ohtsubo E, Baba T, Wanner BL, Mori H, Horiuchi T: Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110. Mol Syst Biol. 2006;2:2006.0007. Epub 2006 Feb 21. 16738553
  5. Meinnel T, Guillon JM, Mechulam Y, Blanquet S: The Escherichia coli fmt gene, encoding methionyl-tRNA(fMet) formyltransferase, escapes metabolic control. J Bacteriol. 1993 Feb;175(4):993-1000. 8432722
  6. Meinnel T, Blanquet S: Enzymatic properties of Escherichia coli peptide deformylase. J Bacteriol. 1995 Apr;177(7):1883-7. 7896716
  7. Groche D, Becker A, Schlichting I, Kabsch W, Schultz S, Wagner AF: Isolation and crystallization of functionally competent Escherichia coli peptide deformylase forms containing either iron or nickel in the active site. Biochem Biophys Res Commun. 1998 May 19;246(2):342-6. 9610360
  8. Meinnel T, Blanquet S, Dardel F: A new subclass of the zinc metalloproteases superfamily revealed by the solution structure of peptide deformylase. J Mol Biol. 1996 Sep 27;262(3):375-86. 8845003
  9. Dardel F, Ragusa S, Lazennec C, Blanquet S, Meinnel T: Solution structure of nickel-peptide deformylase. J Mol Biol. 1998 Jul 17;280(3):501-13. 9665852
  10. Chan MK, Gong W, Rajagopalan PT, Hao B, Tsai CM, Pei D: Crystal structure of the Escherichia coli peptide deformylase. Biochemistry. 1997 Nov 11;36(45):13904-9. 9374869
  11. Becker A, Schlichting I, Kabsch W, Schultz S, Wagner AF: Structure of peptide deformylase and identification of the substrate binding site. J Biol Chem. 1998 May 8;273(19):11413-6. 9565550
  12. Becker A, Schlichting I, Kabsch W, Groche D, Schultz S, Wagner AF: Iron center, substrate recognition and mechanism of peptide deformylase. Nat Struct Biol. 1998 Dec;5(12):1053-8. 9846875
  13. Hao B, Gong W, Rajagopalan PT, Zhou Y, Pei D, Chan MK: Structural basis for the design of antibiotics targeting peptide deformylase. Biochemistry. 1999 Apr 13;38(15):4712-9. 10200158