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P96113

- DEF_THEMA

UniProt

P96113 - DEF_THEMA

Protein

Peptide deformylase

Gene

def

Organism
Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
Status
Reviewed - Annotation score: 2 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 106 (01 Oct 2014)
      Sequence version 1 (01 May 1997)
      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 By similarity.By similarity

    Catalytic activityi

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

    Cofactori

    Binds 1 Fe2+ ion.By similarity

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi87 – 871IronBy similarity
    Metal bindingi129 – 1291IronBy similarity
    Active sitei130 – 1301By similarity
    Metal bindingi133 – 1331IronBy similarity

    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

    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
    Ordered Locus Names:TM_1661
    OrganismiThermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
    Taxonomic identifieri243274 [NCBI]
    Taxonomic lineageiBacteriaThermotogaeThermotogalesThermotogaceaeThermotoga
    ProteomesiUP000008183: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 164164Peptide deformylasePRO_0000082866Add
    BLAST

    Interactioni

    Protein-protein interaction databases

    STRINGi243274.TM1661.

    Structurei

    Secondary structure

    1
    164
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi10 – 123
    Helixi24 – 3916
    Beta strandi43 – 464
    Helixi47 – 504
    Beta strandi54 – 596
    Beta strandi61 – 633
    Beta strandi66 – 7611
    Beta strandi80 – 856
    Beta strandi95 – 10814
    Beta strandi114 – 1207
    Helixi121 – 13414
    Helixi139 – 1424

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1LMEX-ray2.20A/B1-164[»]
    ProteinModelPortaliP96113.
    SMRiP96113. Positions 1-145.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP96113.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the polypeptide deformylase family.Curated

    Phylogenomic databases

    eggNOGiCOG0242.
    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.

    P96113-1 [UniParc]FASTAAdd to Basket

    « Hide

    MYRIRVFGDP VLRKRAKPVT KFDENLKKTI ERMIETMYHY DGVGLAAPQV    50
    GISQRFFVMD VGNGPVAVIN PEILEIDPET EVAEEGCLSF PEIFVEIERS 100
    KRIKVKYQNT RGEYVEEELE GYAARVFQHE FDHLNGVLII DRISPAKRLL 150
    LRKKLMDIAR TVKR 164
    Length:164
    Mass (Da):19,024
    Last modified:May 1, 1997 - v1
    Checksum:i9FE94A206DE50842
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Y10306 Genomic DNA. Translation: CAA71356.1.
    AE000512 Genomic DNA. Translation: AAD36728.1.
    PIRiC72224.
    RefSeqiNP_229461.1. NC_000853.1.
    WP_004082176.1. NC_023151.1.
    YP_007978019.1. NC_021214.1.
    YP_008991245.1. NC_023151.1.

    Genome annotation databases

    EnsemblBacteriaiAAD36728; AAD36728; TM_1661.
    GeneIDi897909.
    KEGGitma:TM1661.
    tmi:THEMA_05940.
    tmm:Tmari_1670.
    PATRICi23938296. VBITheMar51294_1680.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Y10306 Genomic DNA. Translation: CAA71356.1 .
    AE000512 Genomic DNA. Translation: AAD36728.1 .
    PIRi C72224.
    RefSeqi NP_229461.1. NC_000853.1.
    WP_004082176.1. NC_023151.1.
    YP_007978019.1. NC_021214.1.
    YP_008991245.1. NC_023151.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1LME X-ray 2.20 A/B 1-164 [» ]
    ProteinModelPortali P96113.
    SMRi P96113. Positions 1-145.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 243274.TM1661.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAD36728 ; AAD36728 ; TM_1661 .
    GeneIDi 897909.
    KEGGi tma:TM1661.
    tmi:THEMA_05940.
    tmm:Tmari_1670.
    PATRICi 23938296. VBITheMar51294_1680.

    Phylogenomic databases

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

    Miscellaneous databases

    EvolutionaryTracei P96113.

    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. "A survey of polypeptide deformylase function throughout the eubacterial lineage."
      Mazel D., Coic E., Blanchard S., Saurin W., Marliere P.
      J. Mol. Biol. 266:939-949(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099.

    Entry informationi

    Entry nameiDEF_THEMA
    AccessioniPrimary (citable) accession number: P96113
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 15, 1998
    Last sequence update: May 1, 1997
    Last modified: October 1, 2014
    This is version 106 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