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B2RMJ1

- DEF_PORG3

UniProt

B2RMJ1 - DEF_PORG3

Protein

Peptide deformylase

Gene

def

Organism
Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / JCM 12257)
Status
Reviewed - Annotation score: 2 out of 5- Protein inferred from homologyi
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    • History
      Entry version 44 (01 Oct 2014)
      Sequence version 1 (01 Jul 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 bindingi98 – 981IronUniRule annotation
    Metal bindingi140 – 1401IronUniRule annotation
    Active sitei141 – 1411UniRule annotation
    Metal bindingi144 – 1441IronUniRule 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

    BioCyciPGIN431947:GC9J-2128-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:PGN_2068
    OrganismiPorphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / JCM 12257)
    Taxonomic identifieri431947 [NCBI]
    Taxonomic lineageiBacteriaBacteroidetesBacteroidiaBacteroidalesPorphyromonadaceaePorphyromonas
    ProteomesiUP000008842: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 189189Peptide deformylasePRO_1000097333Add
    BLAST

    Interactioni

    Protein-protein interaction databases

    STRINGi431947.PGN_2068.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the polypeptide deformylase family.UniRule annotation

    Phylogenomic databases

    eggNOGiCOG0242.
    HOGENOMiHOG000243509.
    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.

    B2RMJ1-1 [UniParc]FASTAAdd to Basket

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    MLLPIYLYGH PVLRKVAEDI TPDYPKLKEL IANMTESMYH SDGIGLAAPQ    50
    IGLPIRVLVI DADPLKEDYP ECAGFKRVMI NAHIEERGED LCTEYEGCLS 100
    LPAIHEKVER PTSIRIRYVD EDFQPHEEVL HGFAARVVQH EYDHIDGKLF 150
    IDHISPIRKQ LIKGKLQNII KGKVRTSYRV VTAPTGKRR 189
    Length:189
    Mass (Da):21,592
    Last modified:July 1, 2008 - v1
    Checksum:i8D0169D50273145E
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AP009380 Genomic DNA. Translation: BAG34586.1.
    RefSeqiWP_012458729.1. NC_010729.1.
    YP_001930183.1. NC_010729.1.

    Genome annotation databases

    EnsemblBacteriaiBAG34586; BAG34586; PGN_2068.
    GeneIDi6330572.
    KEGGipgn:PGN_2068.
    PATRICi22977099. VBIPorGin26334_2032.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AP009380 Genomic DNA. Translation: BAG34586.1 .
    RefSeqi WP_012458729.1. NC_010729.1.
    YP_001930183.1. NC_010729.1.

    3D structure databases

    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 431947.PGN_2068.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai BAG34586 ; BAG34586 ; PGN_2068 .
    GeneIDi 6330572.
    KEGGi pgn:PGN_2068.
    PATRICi 22977099. VBIPorGin26334_2032.

    Phylogenomic databases

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

    Enzyme and pathway databases

    BioCyci PGIN431947:GC9J-2128-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. "Determination of the genome sequence of Porphyromonas gingivalis strain ATCC 33277 and genomic comparison with strain W83 revealed extensive genome rearrangements in P. gingivalis."
      Naito M., Hirakawa H., Yamashita A., Ohara N., Shoji M., Yukitake H., Nakayama K., Toh H., Yoshimura F., Kuhara S., Hattori M., Hayashi T., Nakayama K.
      DNA Res. 15:215-225(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 33277 / DSM 20709 / JCM 12257.

    Entry informationi

    Entry nameiDEF_PORG3
    AccessioniPrimary (citable) accession number: B2RMJ1
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: March 24, 2009
    Last sequence update: July 1, 2008
    Last modified: October 1, 2014
    This is version 44 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