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B1XSN2

- DEF_POLNS

UniProt

B1XSN2 - DEF_POLNS

Protein

Peptide deformylase

Gene

def

Organism
Polynucleobacter necessarius subsp. necessarius (strain STIR1)
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 (20 May 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 bindingi92 – 921IronUniRule annotation
    Metal bindingi134 – 1341IronUniRule annotation
    Active sitei135 – 1351UniRule annotation
    Metal bindingi138 – 1381IronUniRule 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

    BioCyciPNEC452638:GI4T-1774-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:Pnec_1778
    OrganismiPolynucleobacter necessarius subsp. necessarius (strain STIR1)
    Taxonomic identifieri452638 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesBurkholderiaceaePolynucleobacter
    ProteomesiUP000006582: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 171171Peptide deformylasePRO_1000097332Add
    BLAST

    Interactioni

    Protein-protein interaction databases

    STRINGi452638.Pnec_1778.

    Structurei

    3D structure databases

    ProteinModelPortaliB1XSN2.
    SMRiB1XSN2. Positions 2-166.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the polypeptide deformylase family.UniRule annotation

    Phylogenomic databases

    eggNOGiCOG0242.
    HOGENOMiHOG000243509.
    KOiK01462.
    OMAiWATCAQH.
    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.

    B1XSN2-1 [UniParc]FASTAAdd to Basket

    « Hide

    MALLTVLCYP DSRLHKVAKP VAQVDARIKK IVADMADTMY EAPGVGLAAT    50
    QVDIHERIVV IDVSDEQNEL MVFINPEIVW TSSETKSWRE GCLSVPEFYD 100
    EVERPAEIRV KALDIDGKEF EIEADGSLAV CLQHELDHLQ GKVFVEYLSI 150
    FKRTRISQKM KKRAKELIGQ R 171
    Length:171
    Mass (Da):19,429
    Last modified:May 20, 2008 - v1
    Checksum:i08FE68FC24DF4974
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP001010 Genomic DNA. Translation: ACB44831.1.
    RefSeqiYP_001798445.1. NC_010531.1.

    Genome annotation databases

    EnsemblBacteriaiACB44831; ACB44831; Pnec_1778.
    GeneIDi6184595.
    KEGGipne:Pnec_1778.
    PATRICi22972894. VBIPolNec8289_2040.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP001010 Genomic DNA. Translation: ACB44831.1 .
    RefSeqi YP_001798445.1. NC_010531.1.

    3D structure databases

    ProteinModelPortali B1XSN2.
    SMRi B1XSN2. Positions 2-166.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 452638.Pnec_1778.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai ACB44831 ; ACB44831 ; Pnec_1778 .
    GeneIDi 6184595.
    KEGGi pne:Pnec_1778.
    PATRICi 22972894. VBIPolNec8289_2040.

    Phylogenomic databases

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

    Enzyme and pathway databases

    BioCyci PNEC452638:GI4T-1774-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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: STIR1.

    Entry informationi

    Entry nameiDEF_POLNS
    AccessioniPrimary (citable) accession number: B1XSN2
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: March 24, 2009
    Last sequence update: May 20, 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