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A5VDM3

- DEF_SPHWW

UniProt

A5VDM3 - DEF_SPHWW

Protein

Peptide deformylase

Gene

def

Organism
Sphingomonas wittichii (strain RW1 / DSM 6014 / JCM 10273)
Status
Reviewed - Annotation score: 2 out of 5- Protein inferred from homologyi
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    • History
      Entry version 49 (01 Oct 2014)
      Sequence version 1 (10 Jul 2007)
      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 bindingi99 – 991IronUniRule annotation
    Metal bindingi141 – 1411IronUniRule annotation
    Active sitei142 – 1421UniRule annotation
    Metal bindingi145 – 1451IronUniRule 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

    BioCyciSWIT392499:GHZK-4094-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:Swit_4045
    OrganismiSphingomonas wittichii (strain RW1 / DSM 6014 / JCM 10273)
    Taxonomic identifieri392499 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaSphingomonadalesSphingomonadaceaeSphingomonas
    ProteomesiUP000001989: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 177177Peptide deformylasePRO_1000023135Add
    BLAST

    Interactioni

    Protein-protein interaction databases

    STRINGi392499.Swit_4045.

    Structurei

    3D structure databases

    ProteinModelPortaliA5VDM3.
    SMRiA5VDM3. Positions 2-174.
    ModBaseiSearch...
    MobiDBiSearch...

    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.

    A5VDM3-1 [UniParc]FASTAAdd to Basket

    « Hide

    MAIRLILEAP DPRLRTISTP VEAVDDELRA LIADMFETMY DAPGIGLAAI    50
    QVGVPKRVLV IDLQEEEDAE GKPIRHPRVF INPELFDPSE EQSVYNEGCL 100
    SVPEQYAEVE RPAVIHARWL DEQGAKHEER LEGLLATCLQ HEMDHLEGIL 150
    FIDHLSRLKR EMVMKKLEKA RRARKAA 177
    Length:177
    Mass (Da):20,154
    Last modified:July 10, 2007 - v1
    Checksum:i1A62E4EA8CF88867
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP000699 Genomic DNA. Translation: ABQ70389.1.
    RefSeqiWP_012050228.1. NC_009511.1.
    YP_001264527.1. NC_009511.1.

    Genome annotation databases

    EnsemblBacteriaiABQ70389; ABQ70389; Swit_4045.
    GeneIDi5198978.
    KEGGiswi:Swit_4045.
    PATRICi23687377. VBISphWit55028_4617.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP000699 Genomic DNA. Translation: ABQ70389.1 .
    RefSeqi WP_012050228.1. NC_009511.1.
    YP_001264527.1. NC_009511.1.

    3D structure databases

    ProteinModelPortali A5VDM3.
    SMRi A5VDM3. Positions 2-174.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 392499.Swit_4045.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai ABQ70389 ; ABQ70389 ; Swit_4045 .
    GeneIDi 5198978.
    KEGGi swi:Swit_4045.
    PATRICi 23687377. VBISphWit55028_4617.

    Phylogenomic databases

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

    Enzyme and pathway databases

    BioCyci SWIT392499:GHZK-4094-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: RW1 / DSM 6014 / JCM 10273.

    Entry informationi

    Entry nameiDEF_SPHWW
    AccessioniPrimary (citable) accession number: A5VDM3
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 15, 2008
    Last sequence update: July 10, 2007
    Last modified: October 1, 2014
    This is version 49 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