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P63917

- DEF_XYLFA

UniProt

P63917 - DEF_XYLFA

Protein

Peptide deformylase

Gene

def

Organism
Xylella fastidiosa (strain 9a5c)
Status
Reviewed - Annotation score: 2 out of 5- Protein inferred from homologyi
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    • History
      Entry version 56 (01 Oct 2014)
      Sequence version 1 (11 Oct 2004)
      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 bindingi94 – 941IronUniRule annotation
    Metal bindingi136 – 1361IronUniRule annotation
    Active sitei137 – 1371UniRule annotation
    Metal bindingi140 – 1401IronUniRule 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:XF_0926
    OrganismiXylella fastidiosa (strain 9a5c)
    Taxonomic identifieri160492 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaXanthomonadalesXanthomonadaceaeXylella
    ProteomesiUP000000812: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 170170Peptide deformylasePRO_0000082887Add
    BLAST

    Interactioni

    Protein-protein interaction databases

    STRINGi160492.XF0926.

    Structurei

    3D structure databases

    ProteinModelPortaliP63917.
    SMRiP63917. Positions 1-168.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the polypeptide deformylase family.UniRule annotation

    Phylogenomic databases

    eggNOGiCOG0242.
    KOiK01462.
    OMAiEETGEEW.
    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.

    P63917-1 [UniParc]FASTAAdd to Basket

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    MALLPILEFP DPRLRTKAVR VGVAEVVSSS FQTLLDDMFE TMYAAPGIGL    50
    AATQVNVHQR FMVIDVSEEK NVPMVFINPE IVTREGDQVF QEGCLSVPGI 100
    HADVTRALSI VVRFLDRHGD EQQLTAEGLL AVCIQHEMDH LDGKLFIDYL 150
    SPLKRDMVRR KLEKQRRRAS 170
    Length:170
    Mass (Da):19,200
    Last modified:October 11, 2004 - v1
    Checksum:i4F87A555C8BB76D8
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE003849 Genomic DNA. Translation: AAF83736.1.
    PIRiH82746.
    RefSeqiNP_298216.1. NC_002488.3.

    Genome annotation databases

    EnsemblBacteriaiAAF83736; AAF83736; XF_0926.
    GeneIDi1126462.
    KEGGixfa:XF0926.
    PATRICi24131906. VBIXylFas578_0992.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE003849 Genomic DNA. Translation: AAF83736.1 .
    PIRi H82746.
    RefSeqi NP_298216.1. NC_002488.3.

    3D structure databases

    ProteinModelPortali P63917.
    SMRi P63917. Positions 1-168.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 160492.XF0926.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAF83736 ; AAF83736 ; XF_0926 .
    GeneIDi 1126462.
    KEGGi xfa:XF0926.
    PATRICi 24131906. VBIXylFas578_0992.

    Phylogenomic databases

    eggNOGi COG0242.
    KOi K01462.
    OMAi EETGEEW.
    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. "The genome sequence of the plant pathogen Xylella fastidiosa."
      Simpson A.J.G., Reinach F.C., Arruda P., Abreu F.A., Acencio M., Alvarenga R., Alves L.M.C., Araya J.E., Baia G.S., Baptista C.S., Barros M.H., Bonaccorsi E.D., Bordin S., Bove J.M., Briones M.R.S., Bueno M.R.P., Camargo A.A., Camargo L.E.A.
      , Carraro D.M., Carrer H., Colauto N.B., Colombo C., Costa F.F., Costa M.C.R., Costa-Neto C.M., Coutinho L.L., Cristofani M., Dias-Neto E., Docena C., El-Dorry H., Facincani A.P., Ferreira A.J.S., Ferreira V.C.A., Ferro J.A., Fraga J.S., Franca S.C., Franco M.C., Frohme M., Furlan L.R., Garnier M., Goldman G.H., Goldman M.H.S., Gomes S.L., Gruber A., Ho P.L., Hoheisel J.D., Junqueira M.L., Kemper E.L., Kitajima J.P., Krieger J.E., Kuramae E.E., Laigret F., Lambais M.R., Leite L.C.C., Lemos E.G.M., Lemos M.V.F., Lopes S.A., Lopes C.R., Machado J.A., Machado M.A., Madeira A.M.B.N., Madeira H.M.F., Marino C.L., Marques M.V., Martins E.A.L., Martins E.M.F., Matsukuma A.Y., Menck C.F.M., Miracca E.C., Miyaki C.Y., Monteiro-Vitorello C.B., Moon D.H., Nagai M.A., Nascimento A.L.T.O., Netto L.E.S., Nhani A. Jr., Nobrega F.G., Nunes L.R., Oliveira M.A., de Oliveira M.C., de Oliveira R.C., Palmieri D.A., Paris A., Peixoto B.R., Pereira G.A.G., Pereira H.A. Jr., Pesquero J.B., Quaggio R.B., Roberto P.G., Rodrigues V., de Rosa A.J.M., de Rosa V.E. Jr., de Sa R.G., Santelli R.V., Sawasaki H.E., da Silva A.C.R., da Silva A.M., da Silva F.R., Silva W.A. Jr., da Silveira J.F., Silvestri M.L.Z., Siqueira W.J., de Souza A.A., de Souza A.P., Terenzi M.F., Truffi D., Tsai S.M., Tsuhako M.H., Vallada H., Van Sluys M.A., Verjovski-Almeida S., Vettore A.L., Zago M.A., Zatz M., Meidanis J., Setubal J.C.
      Nature 406:151-159(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: 9a5c.

    Entry informationi

    Entry nameiDEF_XYLFA
    AccessioniPrimary (citable) accession number: P63917
    Secondary accession number(s): Q9PEV2
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 11, 2004
    Last sequence update: October 11, 2004
    Last modified: October 1, 2014
    This is version 56 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