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P0A6K3

- DEF_ECOLI

UniProt

P0A6K3 - DEF_ECOLI

Protein

Peptide deformylase

Gene

def

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 90 (01 Oct 2014)
      Sequence version 2 (23 Jan 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.

    Catalytic activityi

    Formyl-L-methionyl peptide + H2O = formate + methionyl peptide.

    Cofactori

    Binds 1 Fe2+ ion per monomer.1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi91 – 911Iron
    Metal bindingi133 – 1331Iron
    Active sitei134 – 1341
    Metal bindingi137 – 1371Iron

    GO - Molecular functioni

    1. ferrous iron binding Source: EcoCyc
    2. hydrolase activity Source: EcoliWiki
    3. peptide deformylase activity Source: EcoCyc
    4. protein binding Source: EcoCyc
    5. ribosome binding Source: EcoCyc
    6. zinc ion binding Source: EcoliWiki

    GO - Biological processi

    1. co-translational protein modification Source: EcoCyc
    2. N-terminal protein amino acid modification Source: EcoCyc
    3. translation Source: UniProtKB-HAMAP

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Biological processi

    Protein biosynthesis

    Keywords - Ligandi

    Iron, Metal-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:EG11440-MONOMER.
    ECOL316407:JW3248-MONOMER.
    MetaCyc:EG11440-MONOMER.
    SABIO-RKP0A6K3.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Peptide deformylase (EC:3.5.1.88)
    Short name:
    PDF
    Alternative name(s):
    Polypeptide deformylase
    Gene namesi
    Name:def
    Synonyms:fms
    Ordered Locus Names:b3287, JW3248
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG11440. def.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Initiator methioninei1 – 11Removed
    Chaini2 – 169168Peptide deformylasePRO_0000082779Add
    BLAST

    Proteomic databases

    PaxDbiP0A6K3.
    PRIDEiP0A6K3.

    Expressioni

    Gene expression databases

    GenevestigatoriP0A6K3.

    Interactioni

    Subunit structurei

    Monomer.

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    rplDP607231EBI-548913,EBI-545597
    usgP083901EBI-548913,EBI-548921
    yaeBP286341EBI-548913,EBI-1114692

    Protein-protein interaction databases

    DIPiDIP-47953N.
    IntActiP0A6K3. 13 interactions.
    STRINGi511145.b3287.

    Structurei

    Secondary structure

    1
    169
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi12 – 154
    Helixi26 – 4116
    Beta strandi45 – 484
    Helixi49 – 524
    Beta strandi56 – 616
    Beta strandi65 – 684
    Beta strandi71 – 8212
    Beta strandi85 – 895
    Beta strandi92 – 943
    Beta strandi99 – 1035
    Beta strandi105 – 1128
    Beta strandi114 – 1163
    Beta strandi118 – 1236
    Helixi125 – 13814
    Helixi143 – 1464
    Helixi149 – 16517

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1BS4X-ray1.90A/B/C2-169[»]
    1BS5X-ray2.50A/B/C2-169[»]
    1BS6X-ray2.10A/B/C2-169[»]
    1BS7X-ray2.50A/B/C2-169[»]
    1BS8X-ray2.20A/B/C2-169[»]
    1BSJX-ray3.00A2-169[»]
    1BSKX-ray3.00A2-169[»]
    1BSZX-ray1.90A/B/C2-169[»]
    1DEFNMR-A2-148[»]
    1DFFX-ray2.88A2-165[»]
    1DTFmodel-A1-169[»]
    1G27X-ray2.10A/B/C2-169[»]
    1G2AX-ray1.75A/B/C2-169[»]
    1ICJX-ray1.90A/B/C2-169[»]
    1LRUX-ray2.10A/B/C2-169[»]
    1XEMX-ray1.76A2-169[»]
    1XENX-ray1.85A2-169[»]
    1XEOX-ray1.30A2-169[»]
    2AI8X-ray1.70A/B/C2-169[»]
    2DEFNMR-A3-148[»]
    2DTFmodel-A1-169[»]
    2KMNNMR-A2-148[»]
    2VHMX-ray3.745147-162[»]
    2W3TX-ray1.69A2-169[»]
    2W3UX-ray1.96A2-169[»]
    3K6LX-ray2.15A/B/C1-169[»]
    4AL2X-ray2.60A/B/C2-169[»]
    4AL3X-ray1.98A2-169[»]
    ProteinModelPortaliP0A6K3.
    SMRiP0A6K3. Positions 2-168.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP0A6K3.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the polypeptide deformylase family.Curated

    Phylogenomic databases

    eggNOGiCOG0242.
    HOGENOMiHOG000243509.
    KOiK01462.
    OMAiELLAICI.
    OrthoDBiEOG664CMF.
    PhylomeDBiP0A6K3.

    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.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P0A6K3-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSVLQVLHIP DERLRKVAKP VEEVNAEIQR IVDDMFETMY AEEGIGLAAT    50
    QVDIHQRIIV IDVSENRDER LVLINPELLE KSGETGIEEG CLSIPEQRAL 100
    VPRAEKVKIR ALDRDGKPFE LEADGLLAIC IQHEMDHLVG KLFMDYLSPL 150
    KQQRIRQKVE KLDRLKARA 169
    Length:169
    Mass (Da):19,328
    Last modified:January 23, 2007 - v2
    Checksum:iC485EB6C1D2D91B8
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X77800 Genomic DNA. Translation: CAA54826.1.
    X63666 Genomic DNA. Translation: CAA45206.1.
    X65946 Genomic DNA. No translation available.
    X77091 Genomic DNA. Translation: CAA54367.1.
    U18997 Genomic DNA. Translation: AAA58084.1.
    U00096 Genomic DNA. Translation: AAC76312.1.
    AP009048 Genomic DNA. Translation: BAE78005.1.
    PIRiS23107.
    RefSeqiNP_417745.1. NC_000913.3.
    YP_492146.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC76312; AAC76312; b3287.
    BAE78005; BAE78005; BAE78005.
    GeneIDi12934422.
    947780.
    KEGGiecj:Y75_p3890.
    eco:b3287.
    PATRICi32122006. VBIEscCol129921_3380.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X77800 Genomic DNA. Translation: CAA54826.1 .
    X63666 Genomic DNA. Translation: CAA45206.1 .
    X65946 Genomic DNA. No translation available.
    X77091 Genomic DNA. Translation: CAA54367.1 .
    U18997 Genomic DNA. Translation: AAA58084.1 .
    U00096 Genomic DNA. Translation: AAC76312.1 .
    AP009048 Genomic DNA. Translation: BAE78005.1 .
    PIRi S23107.
    RefSeqi NP_417745.1. NC_000913.3.
    YP_492146.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1BS4 X-ray 1.90 A/B/C 2-169 [» ]
    1BS5 X-ray 2.50 A/B/C 2-169 [» ]
    1BS6 X-ray 2.10 A/B/C 2-169 [» ]
    1BS7 X-ray 2.50 A/B/C 2-169 [» ]
    1BS8 X-ray 2.20 A/B/C 2-169 [» ]
    1BSJ X-ray 3.00 A 2-169 [» ]
    1BSK X-ray 3.00 A 2-169 [» ]
    1BSZ X-ray 1.90 A/B/C 2-169 [» ]
    1DEF NMR - A 2-148 [» ]
    1DFF X-ray 2.88 A 2-165 [» ]
    1DTF model - A 1-169 [» ]
    1G27 X-ray 2.10 A/B/C 2-169 [» ]
    1G2A X-ray 1.75 A/B/C 2-169 [» ]
    1ICJ X-ray 1.90 A/B/C 2-169 [» ]
    1LRU X-ray 2.10 A/B/C 2-169 [» ]
    1XEM X-ray 1.76 A 2-169 [» ]
    1XEN X-ray 1.85 A 2-169 [» ]
    1XEO X-ray 1.30 A 2-169 [» ]
    2AI8 X-ray 1.70 A/B/C 2-169 [» ]
    2DEF NMR - A 3-148 [» ]
    2DTF model - A 1-169 [» ]
    2KMN NMR - A 2-148 [» ]
    2VHM X-ray 3.74 5 147-162 [» ]
    2W3T X-ray 1.69 A 2-169 [» ]
    2W3U X-ray 1.96 A 2-169 [» ]
    3K6L X-ray 2.15 A/B/C 1-169 [» ]
    4AL2 X-ray 2.60 A/B/C 2-169 [» ]
    4AL3 X-ray 1.98 A 2-169 [» ]
    ProteinModelPortali P0A6K3.
    SMRi P0A6K3. Positions 2-168.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-47953N.
    IntActi P0A6K3. 13 interactions.
    STRINGi 511145.b3287.

    Chemistry

    BindingDBi P0A6K3.
    ChEMBLi CHEMBL4976.

    Proteomic databases

    PaxDbi P0A6K3.
    PRIDEi P0A6K3.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC76312 ; AAC76312 ; b3287 .
    BAE78005 ; BAE78005 ; BAE78005 .
    GeneIDi 12934422.
    947780.
    KEGGi ecj:Y75_p3890.
    eco:b3287.
    PATRICi 32122006. VBIEscCol129921_3380.

    Organism-specific databases

    EchoBASEi EB1410.
    EcoGenei EG11440. def.

    Phylogenomic databases

    eggNOGi COG0242.
    HOGENOMi HOG000243509.
    KOi K01462.
    OMAi ELLAICI.
    OrthoDBi EOG664CMF.
    PhylomeDBi P0A6K3.

    Enzyme and pathway databases

    BioCyci EcoCyc:EG11440-MONOMER.
    ECOL316407:JW3248-MONOMER.
    MetaCyc:EG11440-MONOMER.
    SABIO-RK P0A6K3.

    Miscellaneous databases

    EvolutionaryTracei P0A6K3.
    PROi P0A6K3.

    Gene expression databases

    Genevestigatori P0A6K3.

    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. "Genetic characterization of polypeptide deformylase, a distinctive enzyme of eubacterial translation."
      Mazel D., Pochet S., Marliere P.
      EMBO J. 13:914-923(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], CHARACTERIZATION.
      Strain: K12.
    2. "Disruption of the gene for Met-tRNA(fMet) formyltransferase severely impairs growth of Escherichia coli."
      Guillon J.-M., Mechulam Y., Schmitter J.-M., Blanquet S., Fayat G.
      J. Bacteriol. 174:4294-4301(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: K12 / K37.
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
      Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
      Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    5. "The Escherichia coli fmt gene, encoding methionyl-tRNA(fMet) formyltransferase, escapes metabolic control."
      Meinnel T., Guillon J.-M., Mechulam Y., Blanquet S.
      J. Bacteriol. 175:993-1000(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-16.
      Strain: K12 / K37.
    6. "Enzymatic properties of Escherichia coli peptide deformylase."
      Meinnel T., Blanquet S.
      J. Bacteriol. 177:1883-1887(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: CHARACTERIZATION.
    7. "Isolation and crystallization of functionally competent Escherichia coli peptide deformylase forms containing either iron or nickel in the active site."
      Groche D., Becker A., Schlichting I., Kabsch W., Schultz S., Wagner A.F.
      Biochem. Biophys. Res. Commun. 246:342-346(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: COFACTOR.
    8. "A new subclass of the zinc metalloproteases superfamily revealed by the solution structure of peptide deformylase."
      Meinnel T., Blanquet S., Dardel F.
      J. Mol. Biol. 262:375-386(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: STRUCTURE BY NMR.
    9. Cited for: STRUCTURE BY NMR.
    10. "Crystal structure of the Escherichia coli peptide deformylase."
      Chan M.K., Gong W., Rajagopalan P.T.R., Hao B., Tsai C.M., Pei D.
      Biochemistry 36:13904-13909(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.9 ANGSTROMS).
    11. Erratum
      Chan M.K., Gong W., Rajagopalan P.T.R., Hao B., Tsai C.M., Pei D.
      Biochemistry 37:13042-13042(1998)
    12. "Structure of peptide deformylase and identification of the substrate binding site."
      Becker A., Schlichting I., Kabsch W., Schultz S., Wagner A.F.
      J. Biol. Chem. 273:11413-11416(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
    13. "Iron center, substrate recognition and mechanism of peptide deformylase."
      Becker A., Schlichting I., Kabsch W., Groche D., Schultz S., Wagner A.F.
      Nat. Struct. Biol. 5:1053-1058(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS).
    14. "Structural basis for the design of antibiotics targeting peptide deformylase."
      Hao B., Gong W., Rajagopalan P.T.R., Zhou Y., Pei D., Chan M.K.
      Biochemistry 38:4712-4719(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY.

    Entry informationi

    Entry nameiDEF_ECOLI
    AccessioniPrimary (citable) accession number: P0A6K3
    Secondary accession number(s): P27251, Q2M6V1
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: March 29, 2005
    Last sequence update: January 23, 2007
    Last modified: October 1, 2014
    This is version 90 of the entry and version 2 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. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3