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Q9KVU3

- DEF1_VIBCH

UniProt

Q9KVU3 - DEF1_VIBCH

Protein

Peptide deformylase 1

Gene

def1

Organism
Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 84 (01 Oct 2014)
      Sequence version 1 (01 Oct 2000)
      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 bindingi91 – 911IronUniRule annotation
    Metal bindingi133 – 1331IronUniRule annotation
    Active sitei134 – 1341UniRule annotation
    Metal bindingi137 – 1371IronUniRule annotation

    GO - Molecular functioni

    1. formylmethionine deformylase activity Source: TIGR
    2. iron ion binding Source: InterPro
    3. peptide deformylase activity Source: UniProtKB-HAMAP

    GO - Biological processi

    1. cellular protein modification process Source: TIGR
    2. translation Source: UniProtKB-HAMAP

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Biological processi

    Protein biosynthesis

    Keywords - Ligandi

    Iron, Metal-binding

    Enzyme and pathway databases

    BioCyciVCHO:VC0046-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Peptide deformylase 1UniRule annotation (EC:3.5.1.88UniRule annotation)
    Short name:
    PDF 1UniRule annotation
    Alternative name(s):
    Polypeptide deformylase 1UniRule annotation
    Gene namesi
    Name:def1UniRule annotation
    Ordered Locus Names:VC_0046
    OrganismiVibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
    Taxonomic identifieri243277 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaVibrionalesVibrionaceaeVibrio
    ProteomesiUP000000584: Chromosome 1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 169169Peptide deformylase 1PRO_0000082873Add
    BLAST

    Interactioni

    Protein-protein interaction databases

    STRINGi243277.VC0046.

    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 strandi71 – 8313
    Beta strandi85 – 895
    Beta strandi99 – 1035
    Beta strandi105 – 1128
    Beta strandi118 – 1236
    Helixi125 – 13814
    Helixi143 – 1464
    Helixi149 – 16315

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3FWXX-ray2.00A/B1-169[»]
    ProteinModelPortaliQ9KVU3.
    SMRiQ9KVU3. Positions 2-168.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9KVU3.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the polypeptide deformylase family.UniRule annotation

    Phylogenomic databases

    eggNOGiCOG0242.
    KOiK01462.
    OMAiASHINGA.
    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.

    Q9KVU3-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSVLQVLTFP DDRLRTVAKP VEQVTPEIQQ IVDDMLETMY AEEGIGLAAT    50
    QVDIHQRIVV IDISETRDQP MVLINPEIIE KRGEDGIEEG CLSVPGARAL 100
    VPRAAEVTVK ALDRNGQEYQ FDADDLLAIC VQHELDHLAG KLFVDYLSPL 150
    KRNRIKEKLE KIKRFNEKK 169
    Length:169
    Mass (Da):19,147
    Last modified:October 1, 2000 - v1
    Checksum:i16DB00B08CA40FC7
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE003852 Genomic DNA. Translation: AAF93224.1.
    PIRiA82373.
    RefSeqiNP_229705.1. NC_002505.1.

    Genome annotation databases

    EnsemblBacteriaiAAF93224; AAF93224; VC_0046.
    GeneIDi2614445.
    KEGGivch:VC0046.
    PATRICi20079140. VBIVibCho83274_0045.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE003852 Genomic DNA. Translation: AAF93224.1 .
    PIRi A82373.
    RefSeqi NP_229705.1. NC_002505.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    3FWX X-ray 2.00 A/B 1-169 [» ]
    ProteinModelPortali Q9KVU3.
    SMRi Q9KVU3. Positions 2-168.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 243277.VC0046.

    Protocols and materials databases

    DNASUi 2614445.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAF93224 ; AAF93224 ; VC_0046 .
    GeneIDi 2614445.
    KEGGi vch:VC0046.
    PATRICi 20079140. VBIVibCho83274_0045.

    Phylogenomic databases

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

    Enzyme and pathway databases

    BioCyci VCHO:VC0046-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei Q9KVU3.

    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 39315 / El Tor Inaba N16961.

    Entry informationi

    Entry nameiDEF1_VIBCH
    AccessioniPrimary (citable) accession number: Q9KVU3
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: December 5, 2001
    Last sequence update: October 1, 2000
    Last modified: October 1, 2014
    This is version 84 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