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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)DescriptionActionsGraphical viewLength
    Active sitei72Proton acceptorSequence analysis1
    Binding sitei178S-adenosyl-L-methionine; via amide nitrogen1 Publication1
    Metal bindingi196MagnesiumSequence analysis1
    Binding sitei202S-adenosyl-L-methionine1 Publication1
    Metal bindingi223MagnesiumSequence analysis1
    Metal bindingi224MagnesiumSequence analysis1

    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)DescriptionActionsGraphical viewLength
    ChainiPRO_00004240041 – 262Demethyldecarbamoylnovobiocin O-methyltransferaseAdd BLAST262

    Interactioni

    Subunit structurei

    Homodimer.1 Publication

    Structurei

    Secondary structure

    1262
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi15 – 26Combined sources12
    Turni27 – 32Combined sources6
    Helixi49 – 53Combined sources5
    Beta strandi59 – 61Combined sources3
    Helixi67 – 83Combined sources17
    Beta strandi89 – 93Combined sources5
    Helixi99 – 110Combined sources12
    Beta strandi118 – 122Combined sources5
    Helixi136 – 141Combined sources6
    Helixi143 – 146Combined sources4
    Helixi147 – 150Combined sources4
    Helixi154 – 163Combined sources10
    Beta strandi171 – 176Combined sources6
    Helixi178 – 181Combined sources4
    Beta strandi190 – 195Combined sources6
    Helixi200 – 210Combined sources11
    Helixi211 – 213Combined sources3
    Beta strandi214 – 224Combined sources11
    Helixi229 – 241Combined sources13
    Beta strandi252 – 254Combined sources3
    Beta strandi256 – 259Combined sources4

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2WK1X-ray1.40A1-262[»]
    SMRiQ9L9F2.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni64 – 65S-adenosyl-L-methionine binding1 Publication2
    Regioni92 – 96S-adenosyl-L-methionine binding1 Publication5
    Regioni122 – 126S-adenosyl-L-methionine binding1 Publication5
    Regioni196 – 197S-adenosyl-L-methionine binding1 Publication2

    Sequence similaritiesi

    Belongs to the methyltransferase TylF/MycF family.Curated

    Phylogenomic databases

    KOiK12712.

    Family and domain databases

    Gene3Di3.40.50.150. 1 hit.
    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
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2WK1X-ray1.40A1-262[»]
    SMRiQ9L9F2.
    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

    Gene3Di3.40.50.150. 1 hit.
    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 30, 2016
    This is version 41 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.