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Protein

dTDP-3-amino-3,4,6-trideoxy-alpha-D-glucopyranose

Gene

desVI

Organism
Streptomyces venezuelae
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

S-adenosyl-L-methionine-dependent methyltransferase involved in the biosynthesis of desosamine, found in certain macrolide antibiotics such as erthyromycin, azithromycin, and clarithromycin. Catalyzes the last step in the biosynthesis of dTDP-desosamine.1 Publication

Catalytic activityi

2 S-adenosyl-L-methionine + dTDP-3-amino-3,4,6-trideoxy-alpha-D-glucopyranose = 2 S-adenosyl-L-homocysteine + dTDP-3-dimethylamino-3,4,6-trideoxy-alpha-D-glucopyranose.1 Publication

Kineticsi

kcat is 92 min(-1) with dTDP-3-amino-3,4,6-trideoxy-alpha-D-glucopyranose as substrate. kcat is 4.2 min(-1) with dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose as substrate.

  1. KM=307.4 µM for dTDP-3-amino-3,4,6-trideoxy-alpha-D-glucopyranose1 Publication
  2. KM=276.6 µM for dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose1 Publication

    Pathwayi: Antibiotic biosynthesis

    This protein is involved in Antibiotic biosynthesis.1 Publication
    View all proteins of this organism that are known to be involved in Antibiotic biosynthesis.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei14 – 141Substrate1 Publication
    Binding sitei17 – 171Substrate1 Publication
    Binding sitei21 – 211S-adenosyl-L-methionineCombined sources1 Publication
    Binding sitei46 – 461S-adenosyl-L-methionine; via carbonyl oxygenCombined sources1 Publication
    Binding sitei67 – 671S-adenosyl-L-methionineCombined sources1 Publication
    Binding sitei105 – 1051S-adenosyl-L-methionine; via carbonyl oxygenCombined sources1 Publication
    Binding sitei152 – 1521Substrate1 Publication
    Binding sitei229 – 2291Substrate1 Publication

    GO - Molecular functioni

    • protein homodimerization activity Source: UniProtKB
    • S-adenosylmethionine-dependent methyltransferase activity Source: UniProtKB

    GO - Biological processi

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

    Keywords - Molecular functioni

    Methyltransferase, Transferase

    Keywords - Biological processi

    Antibiotic biosynthesis

    Keywords - Ligandi

    S-adenosyl-L-methionine

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-16954.
    BRENDAi2.1.1.234. 6106.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    dTDP-3-amino-3,4,6-trideoxy-alpha-D-glucopyranose (EC:2.1.1.234)
    Gene namesi
    Name:desVI
    OrganismiStreptomyces venezuelae
    Taxonomic identifieri54571 [NCBI]
    Taxonomic lineageiBacteriaActinobacteriaStreptomycetalesStreptomycetaceaeStreptomyces

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 237237dTDP-3-amino-3,4,6-trideoxy-alpha-D-glucopyranosePRO_0000418452Add
    BLAST

    Interactioni

    Subunit structurei

    Homodimer.2 Publications

    GO - Molecular functioni

    • protein homodimerization activity Source: UniProtKB

    Structurei

    Secondary structure

    1
    237
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi6 – 1712Combined sources
    Helixi21 – 3515Combined sources
    Beta strandi41 – 455Combined sources
    Helixi51 – 6010Combined sources
    Beta strandi61 – 688Combined sources
    Helixi70 – 7910Combined sources
    Beta strandi84 – 874Combined sources
    Turni90 – 923Combined sources
    Beta strandi99 – 1046Combined sources
    Helixi108 – 1114Combined sources
    Helixi115 – 12713Combined sources
    Beta strandi129 – 1379Combined sources
    Turni143 – 1453Combined sources
    Beta strandi151 – 1588Combined sources
    Beta strandi161 – 17212Combined sources
    Beta strandi175 – 18612Combined sources
    Turni187 – 1893Combined sources
    Beta strandi190 – 20112Combined sources
    Helixi205 – 21410Combined sources
    Beta strandi217 – 2248Combined sources
    Turni225 – 2273Combined sources
    Beta strandi231 – 2366Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3BXOX-ray2.00A/B1-237[»]
    ProteinModelPortaliQ9ZGH6.
    SMRiQ9ZGH6. Positions 2-237.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9ZGH6.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni89 – 902S-adenosyl-L-methionine bindingCombined sources1 Publication
    Regioni145 – 1473Substrate binding1 Publication
    Regioni165 – 1695Substrate binding1 Publication

    Sequence similaritiesi

    Phylogenomic databases

    KOiK13311.

    Family and domain databases

    Gene3Di3.40.50.150. 2 hits.
    InterProiIPR029063. SAM-dependent_MTases.
    [Graphical view]
    SUPFAMiSSF53335. SSF53335. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    Q9ZGH6-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MYEVDHADVY DLFYLGRGKD YAAEASDIAD LVRSRTPEAS SLLDVACGTG
    60 70 80 90 100
    THLEHFTKEF GDTAGLELSE DMLTHARKRL PDATLHQGDM RDFRLGRKFS
    110 120 130 140 150
    AVVSMFSSVG YLKTTEELGA AVASFAEHLE PGGVVVVEPW WFPETFADGW
    160 170 180 190 200
    VSADVVRRDG RTVARVSHSV REGNATRMEV HFTVADPGKG VRHFSDVHLI
    210 220 230
    TLFHQAEYEA AFTAAGLRVE YLEGGPSGRG LFVGVPA
    Length:237
    Mass (Da):25,979
    Last modified:May 1, 1999 - v1
    Checksum:i156E67A0E7406AE8
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AF079762 Genomic DNA. Translation: AAC68678.1.
    RefSeqiWP_055641632.1. NZ_LN881739.1.

    Genome annotation databases

    KEGGiag:AAC68678.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AF079762 Genomic DNA. Translation: AAC68678.1.
    RefSeqiWP_055641632.1. NZ_LN881739.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3BXOX-ray2.00A/B1-237[»]
    ProteinModelPortaliQ9ZGH6.
    SMRiQ9ZGH6. Positions 2-237.
    ModBaseiSearch...
    MobiDBiSearch...

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    KEGGiag:AAC68678.

    Phylogenomic databases

    KOiK13311.

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-16954.
    BRENDAi2.1.1.234. 6106.

    Miscellaneous databases

    EvolutionaryTraceiQ9ZGH6.

    Family and domain databases

    Gene3Di3.40.50.150. 2 hits.
    InterProiIPR029063. SAM-dependent_MTases.
    [Graphical view]
    SUPFAMiSSF53335. SSF53335. 1 hit.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiDESVI_STRVZ
    AccessioniPrimary (citable) accession number: Q9ZGH6
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: September 5, 2012
    Last sequence update: May 1, 1999
    Last modified: March 16, 2016
    This is version 56 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.