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    PDF1B peptide deformylase 1B [ Arabidopsis thaliana (thale cress) ]

    Gene ID: 831318, updated on 18-Sep-2024

    Summary

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    Official Symbol
    PDF1B
    Official Full Name
    peptide deformylase 1B
    Primary source
    TAIR:AT5G14660
    Locus tag
    AT5G14660
    See related
    Araport:AT5G14660
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Arabidopsis thaliana (ecotype: Columbia)
    Lineage
    Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
    Also known as
    ATDEF2; DEF2; peptide deformylase 1B
    Summary
    Encodes a peptide deformylase PDF1B. The crystal structure has been determined at a resolution of 0.24 nm (Biochem J, 2008, vol 413:417-427).
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    Genomic context

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    See PDF1B in Genome Data Viewer
    Location:
    chromosome: 5
    Exon count:
    7
    Sequence:
    Chromosome: 5; NC_003076.8 (4726641..4728746, complement)

    Chromosome 5 - NC_003076.8Genomic Context describing neighboring genes Neighboring gene ncRNA Neighboring gene ncRNA Neighboring gene Pectin lyase-like superfamily protein Neighboring gene ADP-ribosylation factor A1B Neighboring gene Adenine nucleotide alpha hydrolases-like superfamily protein Neighboring gene uncharacterized protein

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003076.8

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Trapping conformational states along ligand-binding dynamics of peptide deformylase: the impact of induced fit on enzyme catalysis. Fieulaine S, et al. PLoS Biol, 2011 May. PMID 21629676, Free PMC Article
    2. Insights into the substrate specificity of plant peptide deformylase, an essential enzyme with potential for the development of novel biotechnology applications in agriculture. Dirk LM, et al. Biochem J, 2008 Aug 1. PMID 18412546
    3. Interplay between N-terminal methionine excision and FtsH protease is essential for normal chloroplast development and function in Arabidopsis. Adam Z, et al. Plant Cell, 2011 Oct. PMID 22010036, Free PMC Article
    4. Arabidopsis G-protein interactome reveals connections to cell wall carbohydrates and morphogenesis. Klopffleisch K, et al. Mol Syst Biol, 2011 Sep 27. PMID 21952135, Free PMC Article
    5. Sorting signals, N-terminal modifications and abundance of the chloroplast proteome. Zybailov B, et al. PLoS One, 2008 Apr 23. PMID 18431481, Free PMC Article

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. PDF1B acts upstream of the FtsH protease in a common pathway.
      Title: Interplay between N-terminal methionine excision and FtsH protease is essential for normal chloroplast development and function in Arabidopsis.
    2. Trapping conformational states along ligand-binding dynamics of peptide deformylase: the impact of induced fit on enzyme catalysis
      Title: Trapping conformational states along ligand-binding dynamics of peptide deformylase: the impact of induced fit on enzyme catalysis.
    Submit: New GeneRIF Correction

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    NM_001343352.1
    NM_121470.3
    NM_180490.1

    Gene Ontology Provided by TAIR

    Function Evidence Code Pubs
    enables peptide deformylase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in chloroplast HDA PubMed 
    located_in chloroplast ISM
    Inferred from Sequence Model
    more info
    		  
    located_in plastid HDA PubMed 

    General protein information

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    Preferred Names
    peptide deformylase 1B
    NP_196970.1
    • peptide deformylase 1B (PDF1B); FUNCTIONS IN: peptide deformylase activity; INVOLVED IN: translation; LOCATED IN: chloroplast; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Formylmethionine deformylase (InterPro:IPR000181); BEST Arabidopsis thaliana protein match is: peptide deformylase 1A (TAIR:AT1G15390.1); Has 11015 Blast hits to 11012 proteins in 2634 species: Archae - 4; Bacteria - 7821; Metazoa - 125; Fungi - 0; Plants - 121; Viruses - 2; Other Eukaryotes - 2942 (source: NCBI BLink).
    NP_850821.1
    • peptide deformylase 1B (PDF1B); FUNCTIONS IN: peptide deformylase activity; INVOLVED IN: translation; LOCATED IN: chloroplast; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Formylmethionine deformylase (InterPro:IPR000181); BEST Arabidopsis thaliana protein match is: peptide deformylase 1A (TAIR:AT1G15390.1); Has 11057 Blast hits to 11054 proteins in 2650 species: Archae - 4; Bacteria - 7863; Metazoa - 125; Fungi - 0; Plants - 121; Viruses - 2; Other Eukaryotes - 2942 (source: NCBI BLink).

    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_003076.8 Reference assembly

      Range
      4726641..4728746 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_121470.3 → NP_196970.1  peptide deformylase 1B [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_196970.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q8LEH0, Q949U8, Q9FUZ2, Q9LYJ4
      UniProtKB/TrEMBL
      A0A178U947, A0A5S9Y4V3, A0A654G1P3
      Conserved Domains (1) summary
      cd00487
      Location:83 → 223
      Pep_deformylase; Polypeptide or peptide deformylase; a family of metalloenzymes that catalyzes the removal of the N-terminal formyl group in a growing polypeptide chain following translation initiation during protein synthesis in prokaryotes. These enzymes utilize Fe(II) ...

    2. NM_180490.1 → NP_850821.1  peptide deformylase 1B [Arabidopsis thaliana]

      See identical proteins and their annotated locations for NP_850821.1

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q8LEH0, Q949U8, Q9FUZ2, Q9LYJ4
      UniProtKB/TrEMBL
      A0A178U947, A0A5S9Y4V3, A0A654G1P3
      Conserved Domains (1) summary
      cd00487
      Location:83 → 223
      Pep_deformylase; Polypeptide or peptide deformylase; a family of metalloenzymes that catalyzes the removal of the N-terminal formyl group in a growing polypeptide chain following translation initiation during protein synthesis in prokaryotes. These enzymes utilize Fe(II) ...

    3. NM_001343352.1 → NP_001332718.1  peptide deformylase 1B [Arabidopsis thaliana]

      Status: REVIEWED

      UniProtKB/Swiss-Prot
      Q8LEH0, Q949U8, Q9FUZ2, Q9LYJ4
      UniProtKB/TrEMBL
      A0A178U947, A0A5S9Y4V3, A0A654G1P3
      Conserved Domains (1) summary
      cd00487
      Location:83 → 223
      Pep_deformylase; Polypeptide or peptide deformylase; a family of metalloenzymes that catalyzes the removal of the N-terminal formyl group in a growing polypeptide chain following translation initiation during protein synthesis in prokaryotes. These enzymes utilize Fe(II) ...
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9FUZ2.2

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