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A4XNB3

- DEF_PSEMY

UniProt

A4XNB3 - DEF_PSEMY

Protein

Peptide deformylase

Gene

def

Organism
Pseudomonas mendocina (strain ymp)
Status
Reviewed - Annotation score: 2 out of 5- Protein inferred from homologyi
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    • History
      Entry version 48 (01 Oct 2014)
      Sequence version 1 (29 May 2007)
      Previous versions | rss
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    • Comment

    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

    BioCyciPMEN399739:GHR6-54-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:Pmen_0055
    OrganismiPseudomonas mendocina (strain ymp)
    Taxonomic identifieri399739 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas
    ProteomesiUP000000229: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 168168Peptide deformylasePRO_1000023132Add
    BLAST

    Interactioni

    Protein-protein interaction databases

    STRINGi399739.Pmen_0055.

    Structurei

    3D structure databases

    ProteinModelPortaliA4XNB3.
    SMRiA4XNB3. Positions 1-167.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the polypeptide deformylase family.UniRule annotation

    Phylogenomic databases

    eggNOGiCOG0242.
    HOGENOMiHOG000243509.
    KOiK01462.
    OMAiDMYDTMD.
    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.

    A4XNB3-1 [UniParc]FASTAAdd to Basket

    « Hide

    MAILNILEFP DPRLRTIAKP VDVVDDSIRQ LVDDMFETMY DAPGIGLAAT    50
    QVNVHKRVVV MDLSEDKSEP RVFINPEFES LTDEMDQYQE GCLSVPGFYE 100
    NVDRPQKVKI KALDRDGQPF ELIAEGLLAV CIQHECDHLN GKLFVDYLSN 150
    LKRDRIKKKL EKQHRQRA 168
    Length:168
    Mass (Da):19,326
    Last modified:May 29, 2007 - v1
    Checksum:i57444DC876B39BF4
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP000680 Genomic DNA. Translation: ABP82829.1.
    RefSeqiYP_001185561.1. NC_009439.1.

    Genome annotation databases

    EnsemblBacteriaiABP82829; ABP82829; Pmen_0055.
    GeneIDi5106240.
    KEGGipmy:Pmen_0055.
    PATRICi19906507. VBIPseMen131592_0054.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP000680 Genomic DNA. Translation: ABP82829.1 .
    RefSeqi YP_001185561.1. NC_009439.1.

    3D structure databases

    ProteinModelPortali A4XNB3.
    SMRi A4XNB3. Positions 1-167.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 399739.Pmen_0055.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai ABP82829 ; ABP82829 ; Pmen_0055 .
    GeneIDi 5106240.
    KEGGi pmy:Pmen_0055.
    PATRICi 19906507. VBIPseMen131592_0054.

    Phylogenomic databases

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

    Enzyme and pathway databases

    BioCyci PMEN399739:GHR6-54-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: ymp.

    Entry informationi

    Entry nameiDEF_PSEMY
    AccessioniPrimary (citable) accession number: A4XNB3
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 15, 2008
    Last sequence update: May 29, 2007
    Last modified: October 1, 2014
    This is version 48 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