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B6JJP8

- DEF_OLICO

UniProt

B6JJP8 - DEF_OLICO

Protein

Peptide deformylase

Gene

def

Organism
Oligotropha carboxidovorans (strain ATCC 49405 / DSM 1227 / OM5)
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 (16 Dec 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 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

    Enzyme and pathway databases

    BioCyciOCAR504832:GJPZ-600-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:OCAR_7540, OCA5_c06000
    OrganismiOligotropha carboxidovorans (strain ATCC 49405 / DSM 1227 / OM5)
    Taxonomic identifieri504832 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesBradyrhizobiaceaeOligotropha
    ProteomesiUP000001678: Chromosome, UP000007730: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 171171Peptide deformylasePRO_1000097327Add
    BLAST

    Interactioni

    Protein-protein interaction databases

    STRINGi504832.OCAR_7540.

    Structurei

    3D structure databases

    ProteinModelPortaliB6JJP8.
    SMRiB6JJP8. Positions 2-170.
    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.

    B6JJP8-1 [UniParc]FASTAAdd to Basket

    « Hide

    MAIREIISIP DKRLRRVSEP VEKITSEVRA LAEDMFETMY DAPGIGLAAI    50
    QVAVPLRLIT MDLAKKEGES APRVFINPEI LSKSEDIAVY EEGCLSIPEY 100
    YEEVERPASV RVRFMDLEGE VHEEDAEGLF ATCIQHEIDH LNGVLFIDYL 150
    SKLKRDRVMK KFTKAAKLAA K 171
    Length:171
    Mass (Da):19,367
    Last modified:December 16, 2008 - v1
    Checksum:iEB0D04A8BF41330E
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP001196 Genomic DNA. Translation: ACI94642.1.
    CP002826 Genomic DNA. Translation: AEI05324.1.
    RefSeqiYP_002290507.1. NC_011386.1.
    YP_004631565.1. NC_015684.1.

    Genome annotation databases

    EnsemblBacteriaiACI94642; ACI94642; OCAR_7540.
    AEI05324; AEI05324; OCA5_c06000.
    GeneIDi10845732.
    6990043.
    KEGGioca:OCAR_7540.
    ocg:OCA5_c06000.
    PATRICi22808857. VBIOliCar134280_3371.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP001196 Genomic DNA. Translation: ACI94642.1 .
    CP002826 Genomic DNA. Translation: AEI05324.1 .
    RefSeqi YP_002290507.1. NC_011386.1.
    YP_004631565.1. NC_015684.1.

    3D structure databases

    ProteinModelPortali B6JJP8.
    SMRi B6JJP8. Positions 2-170.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 504832.OCAR_7540.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai ACI94642 ; ACI94642 ; OCAR_7540 .
    AEI05324 ; AEI05324 ; OCA5_c06000 .
    GeneIDi 10845732.
    6990043.
    KEGGi oca:OCAR_7540.
    ocg:OCA5_c06000.
    PATRICi 22808857. VBIOliCar134280_3371.

    Phylogenomic databases

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

    Enzyme and pathway databases

    BioCyci OCAR504832:GJPZ-600-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. "Genome sequence of the chemolithoautotrophic bacterium Oligotropha carboxidovorans OM5T."
      Paul D., Bridges S., Burgess S.C., Dandass Y., Lawrence M.L.
      J. Bacteriol. 190:5531-5532(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 49405 / DSM 1227 / OM5.
    2. "Complete genome sequences of the chemolithoautotrophic Oligotropha carboxidovorans strains OM4 and OM5."
      Volland S., Rachinger M., Strittmatter A., Daniel R., Gottschalk G., Meyer O.
      J. Bacteriol. 193:5043-5043(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 49405 / DSM 1227 / OM5.

    Entry informationi

    Entry nameiDEF_OLICO
    AccessioniPrimary (citable) accession number: B6JJP8
    Secondary accession number(s): F8BWX2
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: March 24, 2009
    Last sequence update: December 16, 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, Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3