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Q5N5L5

- Q5N5L5_SYNP6

UniProt

Q5N5L5 - Q5N5L5_SYNP6

Protein

Peptide deformylase

Gene

def

Organism
Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1) (Anacystis nidulans)
Status
Unreviewed - Annotation score: 2 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 63 (01 Oct 2014)
      Sequence version 1 (01 Feb 2005)
      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 annotationSAAS annotation

    Cofactori

    Binds 1 Fe2+ ion.UniRule annotation

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi109 – 1091IronUniRule annotation
    Metal bindingi109 – 1091ZincImported
    Metal bindingi151 – 1511IronUniRule annotation
    Metal bindingi151 – 1511Zinc; via tele nitrogenImported
    Active sitei152 – 1521UniRule annotation
    Metal bindingi155 – 1551IronUniRule annotation
    Metal bindingi155 – 1551Zinc; via tele nitrogenImported

    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

    HydrolaseUniRule annotationSAAS annotation

    Keywords - Biological processi

    Protein biosynthesisUniRule annotationSAAS annotation

    Keywords - Ligandi

    IronUniRule annotation, Metal-bindingUniRule annotationSAAS annotationImported, ZincImported

    Enzyme and pathway databases

    BioCyciSELO269084:GCDQ-219-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:syc0213_dImported
    OrganismiSynechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1) (Anacystis nidulans)Imported
    Taxonomic identifieri269084 [NCBI]
    Taxonomic lineageiBacteriaCyanobacteriaOscillatoriophycideaeChroococcalesSynechococcus
    ProteomesiUP000001175: Chromosome

    Interactioni

    Protein-protein interaction databases

    STRINGi269084.syc0213_d.

    Structurei

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    4DR8X-ray1.55A/B/C/D2-192[»]
    4DR9X-ray1.90A/B/C/D2-192[»]
    ProteinModelPortaliQ5N5L5.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the polypeptide deformylase family.UniRule annotation

    Phylogenomic databases

    eggNOGiCOG0242.
    HOGENOMiHOG000243509.
    KOiK01462.
    OMAiPNQYAEV.
    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.

    Q5N5L5-1 [UniParc]FASTAAdd to Basket

    « Hide

    MTAAVAIRVA KKKLAKPPLD LHYLGDRVLR QPAKRVSRID DELRQTIRQM    50
    LQTMYSADGI GLAAPQVGIN KQLIVIDLEL EDEQAPPLVL INPKIERTAG 100
    DLEQCQEGCL SIPGVYLDVE RPEIVEVSYK DENGRPQRLV ADGLLARCIQ 150
    HEMDHLNGVL FVDRVENRLE LNEALDKKGF AVQAVRPVAA AS 192
    Length:192
    Mass (Da):21,350
    Last modified:February 1, 2005 - v1
    Checksum:i7F8107DD9B120FB7
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AP008231 Genomic DNA. Translation: BAD78403.1.
    RefSeqiYP_170923.1. NC_006576.1.

    Genome annotation databases

    EnsemblBacteriaiBAD78403; BAD78403; syc0213_d.
    GeneIDi3199121.
    KEGGisyc:syc0213_d.
    PATRICi32485956. VBISynElo117686_0255.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AP008231 Genomic DNA. Translation: BAD78403.1 .
    RefSeqi YP_170923.1. NC_006576.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    4DR8 X-ray 1.55 A/B/C/D 2-192 [» ]
    4DR9 X-ray 1.90 A/B/C/D 2-192 [» ]
    ProteinModelPortali Q5N5L5.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 269084.syc0213_d.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai BAD78403 ; BAD78403 ; syc0213_d .
    GeneIDi 3199121.
    KEGGi syc:syc0213_d.
    PATRICi 32485956. VBISynElo117686_0255.

    Phylogenomic databases

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

    Enzyme and pathway databases

    BioCyci SELO269084:GCDQ-219-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. "Complete nucleotide sequence of the freshwater unicellular cyanobacterium Synechococcus elongatus PCC 6301 chromosome: gene content and organization."
      Sugita C., Ogata K., Shikata M., Jikuya H., Takano J., Furumichi M., Kanehisa M., Omata T., Sugiura M., Sugita M.
      Photosyn. Res. 93:55-67(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 27144 / PCC 6301 / SAUG 1402/1Imported.
    2. "Structure and function of a cyanophage-encoded peptide deformylase."
      Frank J.A., Lorimer D., Youle M., Witte P., Craig T., Abendroth J., Rohwer F., Edwards R.A., Segall A.M., Burgin A.B.
      ISME J. 7:1150-1160(2013) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.55 ANGSTROMS) OF 2-192 IN COMPLEX WITH ZINC.

    Entry informationi

    Entry nameiQ5N5L5_SYNP6
    AccessioniPrimary (citable) accession number: Q5N5L5
    Entry historyi
    Integrated into UniProtKB/TrEMBL: February 1, 2005
    Last sequence update: February 1, 2005
    Last modified: October 1, 2014
    This is version 63 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiUnreviewed (UniProtKB/TrEMBL)

    Miscellaneousi

    Keywords - Technical termi

    3D-structureImported, Complete proteomeImported

    External Data

    Dasty 3