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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)DescriptionActionsGraphical viewLength
    Binding sitei14Substrate1 Publication1
    Binding sitei17Substrate1 Publication1
    Binding sitei21S-adenosyl-L-methionineCombined sources1 Publication1
    Binding sitei46S-adenosyl-L-methionine; via carbonyl oxygenCombined sources1 Publication1
    Binding sitei67S-adenosyl-L-methionineCombined sources1 Publication1
    Binding sitei105S-adenosyl-L-methionine; via carbonyl oxygenCombined sources1 Publication1
    Binding sitei152Substrate1 Publication1
    Binding sitei229Substrate1 Publication1

    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)DescriptionActionsGraphical viewLength
    ChainiPRO_00004184521 – 237dTDP-3-amino-3,4,6-trideoxy-alpha-D-glucopyranoseAdd BLAST237

    Interactioni

    Subunit structurei

    Homodimer.2 Publications

    GO - Molecular functioni

    • protein homodimerization activity Source: UniProtKB

    Structurei

    Secondary structure

    1237
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi6 – 17Combined sources12
    Helixi21 – 35Combined sources15
    Beta strandi41 – 45Combined sources5
    Helixi51 – 60Combined sources10
    Beta strandi61 – 68Combined sources8
    Helixi70 – 79Combined sources10
    Beta strandi84 – 87Combined sources4
    Turni90 – 92Combined sources3
    Beta strandi99 – 104Combined sources6
    Helixi108 – 111Combined sources4
    Helixi115 – 127Combined sources13
    Beta strandi129 – 137Combined sources9
    Turni143 – 145Combined sources3
    Beta strandi151 – 158Combined sources8
    Beta strandi161 – 172Combined sources12
    Beta strandi175 – 186Combined sources12
    Turni187 – 189Combined sources3
    Beta strandi190 – 201Combined sources12
    Helixi205 – 214Combined sources10
    Beta strandi217 – 224Combined sources8
    Turni225 – 227Combined sources3
    Beta strandi231 – 236Combined sources6

    3D structure databases

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

    Miscellaneous databases

    EvolutionaryTraceiQ9ZGH6.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni89 – 90S-adenosyl-L-methionine bindingCombined sources1 Publication2
    Regioni145 – 147Substrate binding1 Publication3
    Regioni165 – 169Substrate binding1 Publication5

    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
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    3BXOX-ray2.00A/B1-237[»]
    ProteinModelPortaliQ9ZGH6.
    SMRiQ9ZGH6.
    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: November 2, 2016
    This is version 58 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.