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Protein

Demethyldecarbamoylnovobiocin O-methyltransferase

Gene

novP

Organism
Streptomyces niveus (Streptomyces spheroides)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

S-adenosyl-L-methionine-dependent O-methyltransferase that methylates at 4-OH of the noviose moiety, the penultimate step in the novobiocin biosynthesis pathway. Novobiocin is an aminocoumarin family antibiotic that targets bacterial DNA gyrases.2 Publications

Catalytic activityi

S-adenosyl-L-methionine + demethyldecarbamoylnovobiocin = S-adenosyl-L-homocysteine + decarbamoylnovobiocin.1 Publication

Cofactori

Mg2+Curated

Kineticsi

kcat is 0.4 min(-1) with demethyldecarbamoylnovobiocin as substrate.

  1. KM=9.5 µM for demethyldecarbamoylnovobiocin1 Publication

    Pathwayi: novobiocin biosynthesis

    This protein is involved in the pathway novobiocin biosynthesis, which is part of Antibiotic biosynthesis.1 Publication
    View all proteins of this organism that are known to be involved in the pathway novobiocin biosynthesis and in Antibiotic biosynthesis.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei72 – 721Proton acceptorSequence analysis
    Binding sitei178 – 1781S-adenosyl-L-methionine; via amide nitrogen1 Publication
    Metal bindingi196 – 1961MagnesiumSequence analysis
    Binding sitei202 – 2021S-adenosyl-L-methionine1 Publication
    Metal bindingi223 – 2231MagnesiumSequence analysis
    Metal bindingi224 – 2241MagnesiumSequence analysis

    GO - Molecular functioni

    • metal ion binding Source: UniProtKB-KW
    • methyltransferase activity Source: UniProtKB

    GO - Biological processi

    • methylation Source: UniProtKB
    • novobiocin biosynthetic process Source: UniProtKB
    Complete GO annotation...

    Keywords - Molecular functioni

    Methyltransferase, Transferase

    Keywords - Biological processi

    Antibiotic biosynthesis

    Keywords - Ligandi

    Magnesium, Metal-binding, S-adenosyl-L-methionine

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-18053.
    BRENDAi2.1.1.285. 6099.
    UniPathwayiUPA01035.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Demethyldecarbamoylnovobiocin O-methyltransferaseCurated (EC:2.1.1.2851 Publication)
    Alternative name(s):
    Novobiocin biosynthesis protein P
    Gene namesi
    Name:novP
    OrganismiStreptomyces niveus (Streptomyces spheroides)
    Taxonomic identifieri193462 [NCBI]
    Taxonomic lineageiBacteriaActinobacteriaStreptomycetalesStreptomycetaceaeStreptomyces

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 262262Demethyldecarbamoylnovobiocin O-methyltransferasePRO_0000424004Add
    BLAST

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Structurei

    Secondary structure

    1
    262
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi15 – 2612Combined sources
    Turni27 – 326Combined sources
    Helixi49 – 535Combined sources
    Beta strandi59 – 613Combined sources
    Helixi67 – 8317Combined sources
    Beta strandi89 – 935Combined sources
    Helixi99 – 11012Combined sources
    Beta strandi118 – 1225Combined sources
    Helixi136 – 1416Combined sources
    Helixi143 – 1464Combined sources
    Helixi147 – 1504Combined sources
    Helixi154 – 16310Combined sources
    Beta strandi171 – 1766Combined sources
    Helixi178 – 1814Combined sources
    Beta strandi190 – 1956Combined sources
    Helixi200 – 21011Combined sources
    Helixi211 – 2133Combined sources
    Beta strandi214 – 22411Combined sources
    Helixi229 – 24113Combined sources
    Beta strandi252 – 2543Combined sources
    Beta strandi256 – 2594Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2WK1X-ray1.40A1-262[»]
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni64 – 652S-adenosyl-L-methionine binding1 Publication
    Regioni92 – 965S-adenosyl-L-methionine binding1 Publication
    Regioni122 – 1265S-adenosyl-L-methionine binding1 Publication
    Regioni196 – 1972S-adenosyl-L-methionine binding1 Publication

    Sequence similaritiesi

    Belongs to the methyltransferase TylF/MycF family.Curated

    Phylogenomic databases

    KOiK12712.

    Family and domain databases

    InterProiIPR029063. SAM-dependent_MTases.
    IPR008884. TylF_MeTrfase.
    [Graphical view]
    PfamiPF05711. TylF. 1 hit.
    [Graphical view]
    SUPFAMiSSF53335. SSF53335. 2 hits.

    Sequencei

    Sequence statusi: Complete.

    Q9L9F2-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MAPIVETAKE TNSDSSLYLD LMIKVLAGTV YEDPAHRENF SHRDSTYREE
    60 70 80 90 100
    VRNEGRDWPA NAHTMIGIKR LENIRQCVED VIGNNVPGDL VETGVWRGGA
    110 120 130 140 150
    CILMRGILRA HDVRDRTVWV ADSFQGIPDV GEDGYAGDRK MALHRRNSVL
    160 170 180 190 200
    AVSEEEVRRN FRNYDLLDEQ VRFLPGWFKD TLPTAPIDTL AVLRMDGDLY
    210 220 230 240 250
    ESTWDTLTNL YPKVSVGGYV IVDDYMMCPP CKDAVDEYRA KFDIADELIT
    260
    IDRDGVYWQR TR
    Length:262
    Mass (Da):29,967
    Last modified:October 1, 2000 - v1
    Checksum:i2FC79BADAC4E0184
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AF170880 Genomic DNA. Translation: AAF67509.1.

    Genome annotation databases

    KEGGiag:AAF67509.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AF170880 Genomic DNA. Translation: AAF67509.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2WK1X-ray1.40A1-262[»]
    ModBaseiSearch...
    MobiDBiSearch...

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    KEGGiag:AAF67509.

    Phylogenomic databases

    KOiK12712.

    Enzyme and pathway databases

    UniPathwayiUPA01035.
    BioCyciMetaCyc:MONOMER-18053.
    BRENDAi2.1.1.285. 6099.

    Family and domain databases

    InterProiIPR029063. SAM-dependent_MTases.
    IPR008884. TylF_MeTrfase.
    [Graphical view]
    PfamiPF05711. TylF. 1 hit.
    [Graphical view]
    SUPFAMiSSF53335. SSF53335. 2 hits.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiNOVP_STRNV
    AccessioniPrimary (citable) accession number: Q9L9F2
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 16, 2013
    Last sequence update: October 1, 2000
    Last modified: November 11, 2015
    This is version 39 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

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.