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Q93LE9

- DEF_LEPIN

UniProt

Q93LE9 - DEF_LEPIN

Protein

Peptide deformylase

Gene

def

Organism
Leptospira interrogans serogroup Icterohaemorrhagiae serovar Lai (strain 56601)
Status
Reviewed - Annotation score: 3 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 86 (01 Oct 2014)
      Sequence version 1 (01 Dec 2001)
      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 bindingi102 – 1021IronBy similarity
    Metal bindingi144 – 1441IronBy similarity
    Active sitei145 – 1451By similarity
    Metal bindingi148 – 1481IronBy 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

    Enzyme and pathway databases

    BioCyciLINT189518:GJBB-1994-MONOMER.

    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:pdf
    Ordered Locus Names:LA_2438
    OrganismiLeptospira interrogans serogroup Icterohaemorrhagiae serovar Lai (strain 56601)
    Taxonomic identifieri189518 [NCBI]
    Taxonomic lineageiBacteriaSpirochaetesSpirochaetalesLeptospiraceaeLeptospira
    ProteomesiUP000001408: Chromosome I

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 178178Peptide deformylasePRO_0000082795Add
    BLAST

    Proteomic databases

    PaxDbiQ93LE9.

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Protein-protein interaction databases

    STRINGi189518.LA2438.

    Structurei

    Secondary structure

    1
    178
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi12 – 154
    Helixi23 – 253
    Helixi29 – 4416
    Beta strandi48 – 514
    Helixi52 – 554
    Beta strandi59 – 646
    Beta strandi70 – 723
    Beta strandi81 – 9010
    Beta strandi95 – 1028
    Beta strandi105 – 12319
    Beta strandi129 – 1357
    Helixi136 – 14914
    Helixi154 – 1574
    Beta strandi163 – 1664
    Helixi167 – 1737

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1SV2X-ray3.00A/B2-178[»]
    1SZZX-ray3.30A/B/C/D/E/F/G/H2-178[»]
    1VEVX-ray2.51A/B2-178[»]
    1VEYX-ray3.30A/B2-178[»]
    1VEZX-ray2.30A/B2-178[»]
    1Y6HX-ray2.20A/B2-178[»]
    ProteinModelPortaliQ93LE9.
    SMRiQ93LE9. Positions 2-178.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ93LE9.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the polypeptide deformylase family.Curated

    Phylogenomic databases

    eggNOGiCOG0242.
    HOGENOMiHOG000243508.
    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.

    Q93LE9-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSVRKILRMG DPILRKISEP VTEDEIQTKE FKKLIRDMFD TMRHAEGVGL    50
    AAPQIGILKQ IVVVGSEDNE RYPGTPDVPE RIILNPVITP LTKDTSGFWE 100
    GCLSVPGMRG YVERPNQIRM QWMDEKGNQF DETIDGYKAI VYQHECDHLQ 150
    GILYVDRLKD TKLFGFNETL DSSHNVLD 178
    Length:178
    Mass (Da):20,379
    Last modified:December 1, 2001 - v1
    Checksum:i8F6F3D2449A48B10
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AY040678 Genomic DNA. Translation: AAK70806.1.
    AE010300 Genomic DNA. Translation: AAN49637.1.
    RefSeqiNP_712619.1. NC_004342.2.
    WP_000116243.1. NC_004342.2.

    Genome annotation databases

    EnsemblBacteriaiAAN49637; AAN49637; LA_2438.
    GeneIDi1151781.
    KEGGilil:LA_2438.
    PATRICi22385704. VBILepInt91350_2418.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AY040678 Genomic DNA. Translation: AAK70806.1 .
    AE010300 Genomic DNA. Translation: AAN49637.1 .
    RefSeqi NP_712619.1. NC_004342.2.
    WP_000116243.1. NC_004342.2.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1SV2 X-ray 3.00 A/B 2-178 [» ]
    1SZZ X-ray 3.30 A/B/C/D/E/F/G/H 2-178 [» ]
    1VEV X-ray 2.51 A/B 2-178 [» ]
    1VEY X-ray 3.30 A/B 2-178 [» ]
    1VEZ X-ray 2.30 A/B 2-178 [» ]
    1Y6H X-ray 2.20 A/B 2-178 [» ]
    ProteinModelPortali Q93LE9.
    SMRi Q93LE9. Positions 2-178.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 189518.LA2438.

    Proteomic databases

    PaxDbi Q93LE9.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAN49637 ; AAN49637 ; LA_2438 .
    GeneIDi 1151781.
    KEGGi lil:LA_2438.
    PATRICi 22385704. VBILepInt91350_2418.

    Phylogenomic databases

    eggNOGi COG0242.
    HOGENOMi HOG000243508.
    KOi K01462.
    OMAi PNQYAEV.
    OrthoDBi EOG664CMF.

    Enzyme and pathway databases

    BioCyci LINT189518:GJBB-1994-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei Q93LE9.

    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. "Cloning, high-level expression, purification and crystallization of peptide deformylase from Leptospira interrogans."
      Li Y., Ren S., Gong W.
      Acta Crystallogr. D 58:846-848(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], CRYSTALLIZATION.
      Strain: Lai / Serogroup Icterohaemorrhagiae / Serovar lai.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: 56601.
    3. "Unique structural characteristics of peptide deformylase from pathogenic bacterium Leptospira interrogans."
      Zhou Z., Song X., Li Y., Gong W.
      J. Mol. Biol. 339:207-215(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS), SUBUNIT.
      Strain: Lai / Serogroup Icterohaemorrhagiae / Serovar lai.

    Entry informationi

    Entry nameiDEF_LEPIN
    AccessioniPrimary (citable) accession number: Q93LE9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: September 19, 2002
    Last sequence update: December 1, 2001
    Last modified: October 1, 2014
    This is version 86 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