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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
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