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B5FCW6

- DEF_VIBFM

UniProt

B5FCW6 - DEF_VIBFM

Protein

Peptide deformylase

Gene

def

Organism
Vibrio fischeri (strain MJ11)
Status
Reviewed - Annotation score: 2 out of 5- Protein inferred from homologyi
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    • History
      Entry version 37 (01 Oct 2014)
      Sequence version 1 (14 Oct 2008)
      Previous versions | rss
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    • Comment

    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 bindingi91 – 911IronUniRule annotation
    Metal bindingi133 – 1331IronUniRule annotation
    Active sitei134 – 1341UniRule annotation
    Metal bindingi137 – 1371IronUniRule 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

    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:VFMJ11_2674
    OrganismiVibrio fischeri (strain MJ11)
    Taxonomic identifieri388396 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeAliivibrio
    ProteomesiUP000001857: Chromosome I

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 170170Peptide deformylasePRO_1000097359Add
    BLAST

    Proteomic databases

    PRIDEiB5FCW6.

    Interactioni

    Protein-protein interaction databases

    STRINGi388396.VFMJ11_2674.

    Structurei

    3D structure databases

    ProteinModelPortaliB5FCW6.
    SMRiB5FCW6. Positions 2-168.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the polypeptide deformylase family.UniRule annotation

    Phylogenomic databases

    eggNOGiCOG0242.
    HOGENOMiHOG000243509.
    KOiK01462.
    OMAiELLAICI.
    OrthoDBiEOG664CMF.

    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.

    B5FCW6-1 [UniParc]FASTAAdd to Basket

    « Hide

    MALLEVLTFP DDRLRTVAKP VEAVTPEIQK FVDDMIETMY DEEGIGLAAT    50
    QVDFHQRIVV IDVSETRDEP MVLINPVITQ KSGDDGIEEG CLSVPGAKGL 100
    VPRSAEVSVS ALDRDGNEFS FDADDLLAIC VQHELDHLDG KLFVDYLSPL 150
    KRKRIKEKLE KIKKFNAKNQ 170
    Length:170
    Mass (Da):18,997
    Last modified:October 14, 2008 - v1
    Checksum:iB603540B0E20FC28
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP001139 Genomic DNA. Translation: ACH65039.1.
    RefSeqiYP_002157326.1. NC_011184.1.

    Genome annotation databases

    EnsemblBacteriaiACH65039; ACH65039; VFMJ11_2674.
    GeneIDi6807350.
    KEGGivfm:VFMJ11_2674.
    PATRICi20123840. VBIVibFis37164_2556.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP001139 Genomic DNA. Translation: ACH65039.1 .
    RefSeqi YP_002157326.1. NC_011184.1.

    3D structure databases

    ProteinModelPortali B5FCW6.
    SMRi B5FCW6. Positions 2-168.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 388396.VFMJ11_2674.

    Proteomic databases

    PRIDEi B5FCW6.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai ACH65039 ; ACH65039 ; VFMJ11_2674 .
    GeneIDi 6807350.
    KEGGi vfm:VFMJ11_2674.
    PATRICi 20123840. VBIVibFis37164_2556.

    Phylogenomic databases

    eggNOGi COG0242.
    HOGENOMi HOG000243509.
    KOi K01462.
    OMAi ELLAICI.
    OrthoDBi EOG664CMF.

    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. "Complete sequence of Vibrio fischeri strain MJ11."
      Mandel M.J., Stabb E.V., Ruby E.G., Ferriera S., Johnson J., Kravitz S., Beeson K., Sutton G., Rogers Y.-H., Friedman R., Frazier M., Venter J.C.
      Submitted (AUG-2008) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: MJ11.

    Entry informationi

    Entry nameiDEF_VIBFM
    AccessioniPrimary (citable) accession number: B5FCW6
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: March 24, 2009
    Last sequence update: October 14, 2008
    Last modified: October 1, 2014
    This is version 37 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

    Documents

    1. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3