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    def peptide deformylase [ Escherichia coli str. K-12 substr. MG1655 ]

    Gene ID: 947780, updated on 3-Dec-2024

    Summary

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    Official Symbol
    def
    Official Full Name
    peptide deformylase
    Primary source
    ECOCYC:EG11440
    Locus tag
    b3287
    See related
    ASAP:ABE-0010779
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Escherichia coli str. K-12 substr. MG1655 (strain: K-12, substrain: MG1655)
    Lineage
    Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Escherichia
    Also known as
    ECK3273; fms
    Summary
    The def gene is essential unless the fmt formylase gene is also inactivated. [More information is available at EcoGene: EG11440]. Peptide deformylase releases the formyl group from the amino terminal methionine residue of most nascent proteins . [More information is available at EcoCyc: EG11440].
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    Genomic context

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    Sequence:
    NC_000913.3 (3433690..3434199)

    NC_000913.3Genomic Context describing neighboring genes Neighboring gene putative DNA topoisomerase Neighboring gene DUF494 domain-containing protein Smg Neighboring gene protein Smf Neighboring gene 10-formyltetrahydrofolate:L-methionyl-tRNA(fMet) N-formyltransferase Neighboring gene 16S rRNA m(5)C967 methyltransferase

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_000913.3

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. H-phosphonate derivatives as novel peptide deformylase inhibitors. Hu YJ, et al. Bioorg Med Chem Lett, 1998 Sep 22. PMID 9873565
    2. N-terminal labeling of proteins using initiator tRNA. Olejnik J, et al. Methods, 2005 Jul. PMID 16076451
    3. Structures of E. coli peptide deformylase bound to formate: insight into the preference for Fe2+ over Zn2+ as the active site metal. Jain R, et al. J Am Chem Soc, 2005 Apr 6. PMID 15796505
    4. Oxygen-mediated inactivation of peptide deformylase. Rajagopalan PT, et al. J Biol Chem, 1998 Aug 28. PMID 9712848
    5. Mechanism of time-dependent inhibition of polypeptide deformylase by actinonin. Van Aller GS, et al. Biochemistry, 2005 Jan 11. PMID 15628866

    See all (70) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Structural insights into the interplay of protein biogenesis factors with the 70S ribosome.
      Title: Structural insights into the interplay of protein biogenesis factors with the 70S ribosome.
    2. Peptide deformylase has very fast association & dissociation kinetics which allows it to frequently sample ribosomes & ensure the processing of nascent chains after emergence. It competes with methionine aminopeptidase for ribosomal tunnel-exit binding sites.
      Title: Dynamic enzyme docking to the ribosome coordinates N-terminal processing with polypeptide folding.
    3. Data show that peptide deformylase, threonine dehydrogenase, and cytosine deaminase are very sensitve to hydrogen peroxide.
      Title: Mononuclear iron enzymes are primary targets of hydrogen peroxide stress.
    4. N-terminus verified by Edman degradation on mature peptide
      Title: Evidence that peptide deformylase and methionyl-tRNA(fMet) formyltransferase are encoded within the same operon in Escherichia coli.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    Gene Ontology Provided by EcoCyc

    Function Evidence Code Pubs
    enables ferrous iron binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables hydrolase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables peptide deformylase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables peptide deformylase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables peptide deformylase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables ribosome binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables zinc ion binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in co-translational protein modification IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in co-translational protein modification IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    involved_in translation IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    peptide deformylase
    NP_417745.1

    NCBI Reference Sequences (RefSeq)

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    Genome Annotation

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference assembly

    Genomic

    1. NC_000913.3 Reference assembly

      Range
      3433690..3434199
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NP_417745.1 peptide deformylase [Escherichia coli str. K-12 substr. MG1655]

      See identical proteins and their annotated locations for NP_417745.1

      Status: PROVISIONAL

      UniProtKB/TrEMBL
      A0A376JRD5
      Conserved Domains (1) summary
      PRK00150
      Location:1 → 163
      def; peptide deformylase; Reviewed
    Nucleotide Protein
    Heading Accession and Version

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