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Q8DP79

- DEF_STRR6

UniProt

Q8DP79 - DEF_STRR6

Protein

Peptide deformylase

Gene

def

Organism
Streptococcus pneumoniae (strain ATCC BAA-255 / R6)
Status
Reviewed - Annotation score: 2 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 83 (01 Oct 2014)
      Sequence version 1 (01 Mar 2003)
      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 bindingi130 – 1301IronUniRule annotation
    Metal bindingi173 – 1731IronUniRule annotation
    Active sitei174 – 1741UniRule annotation
    Metal bindingi177 – 1771IronUniRule 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

    BioCyciSPNE171101:GJC8-1323-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:spr1310
    OrganismiStreptococcus pneumoniae (strain ATCC BAA-255 / R6)
    Taxonomic identifieri171101 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliLactobacillalesStreptococcaceaeStreptococcus
    ProteomesiUP000000586: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 203203Peptide deformylasePRO_0000082858Add
    BLAST

    Interactioni

    Protein-protein interaction databases

    STRINGi171101.spr1310.

    Structurei

    Secondary structure

    1
    203
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi3 – 75
    Helixi16 – 183
    Helixi25 – 284
    Helixi40 – 5617
    Helixi59 – 657
    Beta strandi71 – 744
    Helixi75 – 784
    Beta strandi82 – 909
    Beta strandi103 – 11715
    Beta strandi119 – 1246
    Beta strandi143 – 1453
    Beta strandi147 – 1526
    Beta strandi158 – 1636
    Helixi165 – 17814
    Helixi183 – 1864
    Beta strandi189 – 1913
    Beta strandi199 – 2024

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2AI7X-ray2.00A1-202[»]
    2AIAX-ray1.70A1-202[»]
    2AIEX-ray1.70P1-202[»]
    4EOXX-ray1.78P1-203[»]
    ProteinModelPortaliQ8DP79.
    SMRiQ8DP79. Positions 2-203.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ8DP79.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the polypeptide deformylase family.UniRule annotation

    Phylogenomic databases

    eggNOGiCOG0242.
    HOGENOMiHOG000243507.
    KOiK01462.
    OMAiIISCKIL.
    OrthoDBiEOG6PZXGQ.

    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.

    Q8DP79-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSAIERITKA AHLIDMNDII REGNPTLRTV AEEVTFPLSD QEIILGEKMM    50
    QFLKHSQDPV MAEKMGLRGG VGLAAPQLDI SKRIIAVLVP NIVEEGETPQ 100
    EAYDLEAIMY NPKIVSHSVQ DAALGEGEGC LSVDRNVPGY VVRHARVTVD 150
    YFDKDGEKHR IKLKGYNSIV VQHEIDHING IMFYDRINEK DPFAVKDGLL 200
    ILE 203
    Length:203
    Mass (Da):22,692
    Last modified:March 1, 2003 - v1
    Checksum:iE332956982A67161
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE007317 Genomic DNA. Translation: AAL00114.1.
    PIRiE98035.
    RefSeqiNP_358903.1. NC_003098.1.

    Genome annotation databases

    EnsemblBacteriaiAAL00114; AAL00114; spr1310.
    GeneIDi934523.
    KEGGispr:spr1310.
    PATRICi19702614. VBIStrPne107296_1422.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE007317 Genomic DNA. Translation: AAL00114.1 .
    PIRi E98035.
    RefSeqi NP_358903.1. NC_003098.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2AI7 X-ray 2.00 A 1-202 [» ]
    2AIA X-ray 1.70 A 1-202 [» ]
    2AIE X-ray 1.70 P 1-202 [» ]
    4EOX X-ray 1.78 P 1-203 [» ]
    ProteinModelPortali Q8DP79.
    SMRi Q8DP79. Positions 2-203.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 171101.spr1310.

    Chemistry

    BindingDBi Q8DP79.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAL00114 ; AAL00114 ; spr1310 .
    GeneIDi 934523.
    KEGGi spr:spr1310.
    PATRICi 19702614. VBIStrPne107296_1422.

    Phylogenomic databases

    eggNOGi COG0242.
    HOGENOMi HOG000243507.
    KOi K01462.
    OMAi IISCKIL.
    OrthoDBi EOG6PZXGQ.

    Enzyme and pathway databases

    BioCyci SPNE171101:GJC8-1323-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei Q8DP79.

    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: ATCC BAA-255 / R6.

    Entry informationi

    Entry nameiDEF_STRR6
    AccessioniPrimary (citable) accession number: Q8DP79
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: December 15, 2003
    Last sequence update: March 1, 2003
    Last modified: October 1, 2014
    This is version 83 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

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3