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B2GBA3

- DEF_LACF3

UniProt

B2GBA3 - DEF_LACF3

Protein

Peptide deformylase

Gene

def

Organism
Lactobacillus fermentum (strain NBRC 3956 / LMG 18251)
Status
Reviewed - Annotation score: 2 out of 5- Protein inferred from homologyi
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    • History
      Entry version 40 (01 Oct 2014)
      Sequence version 1 (10 Jun 2008)
      Previous versions | rss
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    Functioni

    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.UniRule annotation

    Catalytic activityi

    Formyl-L-methionyl peptide + H2O = formate + methionyl peptide.UniRule annotation

    Cofactori

    Binds 1 Fe2+ ion.UniRule annotation

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi116 – 1161IronUniRule annotation
    Metal bindingi159 – 1591IronUniRule annotation
    Active sitei160 – 1601UniRule annotation
    Metal bindingi163 – 1631IronUniRule annotation

    GO - Molecular functioni

    1. iron ion binding Source: InterPro
    2. peptide deformylase activity Source: UniProtKB-HAMAP

    GO - Biological processi

    1. translation Source: UniProtKB-HAMAP

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Biological processi

    Protein biosynthesis

    Keywords - Ligandi

    Iron, Metal-binding

    Enzyme and pathway databases

    BioCyciLFER334390:GJ2S-643-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Peptide deformylaseUniRule annotation (EC:3.5.1.88UniRule annotation)
    Short name:
    PDFUniRule annotation
    Alternative name(s):
    Polypeptide deformylaseUniRule annotation
    Gene namesi
    Name:defUniRule annotation
    Ordered Locus Names:LAF_0599
    OrganismiLactobacillus fermentum (strain NBRC 3956 / LMG 18251)
    Taxonomic identifieri334390 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesLactobacillaceaeLactobacillus
    ProteomesiUP000001697: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 189189Peptide deformylasePRO_1000097319Add
    BLAST

    Interactioni

    Protein-protein interaction databases

    STRINGi334390.LAF_0599.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the polypeptide deformylase family.UniRule annotation

    Phylogenomic databases

    eggNOGiCOG0242.
    HOGENOMiHOG000243507.
    KOiK01462.
    OMAiSQDPKIA.
    OrthoDBiEOG6PZXGQ.

    Family and domain databases

    Gene3Di3.90.45.10. 1 hit.
    HAMAPiMF_00163. Pep_deformylase.
    InterProiIPR000181. Fmet_deformylase.
    IPR023635. Peptide_deformylase.
    [Graphical view]
    PANTHERiPTHR10458. PTHR10458. 1 hit.
    PfamiPF01327. Pep_deformylase. 1 hit.
    [Graphical view]
    PIRSFiPIRSF004749. Pep_def. 1 hit.
    PRINTSiPR01576. PDEFORMYLASE.
    SUPFAMiSSF56420. SSF56420. 1 hit.
    TIGRFAMsiTIGR00079. pept_deformyl. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    B2GBA3-1 [UniParc]FASTAAdd to Basket

    « Hide

    MILMKDIVRD DQEGTVLRDY AAKVSFPLTE EEQQLAKDLM EYLEISQDEE    50
    LAEKYGLRAG VGLAAPQVNV SKQMAAVLVP SDDEEDDTPI FKDVIINPVI 100
    ISESVQMGAL TEGEGCLSVD RDIAGYVPRH DRITLKYQDV QGETHKVRLK 150
    HYPAIVCQHE IDHLHGVLFY DHINKDNPFE APEGTVFFG 189
    Length:189
    Mass (Da):21,240
    Last modified:June 10, 2008 - v1
    Checksum:i9C1F7E60ECA3172B
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AP008937 Genomic DNA. Translation: BAG26935.1.
    RefSeqiYP_001843415.1. NC_010610.1.

    Genome annotation databases

    EnsemblBacteriaiBAG26935; BAG26935; LAF_0599.
    GeneIDi6231795.
    KEGGilfe:LAF_0599.
    PATRICi22225316. VBILacFer15497_0645.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AP008937 Genomic DNA. Translation: BAG26935.1 .
    RefSeqi YP_001843415.1. NC_010610.1.

    3D structure databases

    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 334390.LAF_0599.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai BAG26935 ; BAG26935 ; LAF_0599 .
    GeneIDi 6231795.
    KEGGi lfe:LAF_0599.
    PATRICi 22225316. VBILacFer15497_0645.

    Phylogenomic databases

    eggNOGi COG0242.
    HOGENOMi HOG000243507.
    KOi K01462.
    OMAi SQDPKIA.
    OrthoDBi EOG6PZXGQ.

    Enzyme and pathway databases

    BioCyci LFER334390:GJ2S-643-MONOMER.

    Family and domain databases

    Gene3Di 3.90.45.10. 1 hit.
    HAMAPi MF_00163. Pep_deformylase.
    InterProi IPR000181. Fmet_deformylase.
    IPR023635. Peptide_deformylase.
    [Graphical view ]
    PANTHERi PTHR10458. PTHR10458. 1 hit.
    Pfami PF01327. Pep_deformylase. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF004749. Pep_def. 1 hit.
    PRINTSi PR01576. PDEFORMYLASE.
    SUPFAMi SSF56420. SSF56420. 1 hit.
    TIGRFAMsi TIGR00079. pept_deformyl. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "Comparative genome analysis of Lactobacillus reuteri and Lactobacillus fermentum reveal a genomic island for reuterin and cobalamin production."
      Morita H., Toh H., Fukuda S., Horikawa H., Oshima K., Suzuki T., Murakami M., Hisamatsu S., Kato Y., Takizawa T., Fukuoka H., Yoshimura T., Itoh K., O'Sullivan D.J., McKay L.L., Ohno H., Kikuchi J., Masaoka T., Hattori M.
      DNA Res. 15:151-161(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: NBRC 3956 / LMG 18251.

    Entry informationi

    Entry nameiDEF_LACF3
    AccessioniPrimary (citable) accession number: B2GBA3
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: March 24, 2009
    Last sequence update: June 10, 2008
    Last modified: October 1, 2014
    This is version 40 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3