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Protein

Devancosaminyl-vancomycin vancosaminetransferase

Gene

gtfD

Organism
Amycolatopsis orientalis (Nocardia orientalis)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the attachment of L-vancosamine to a monoglucosylated heptapeptide intermediate during the final stage of glycopeptide antibiotic vancomycin biosynthesis.2 Publications

Catalytic activityi

dTDP-beta-L-vancosamine + devancosaminyl-vancomycin = dTDP + vancomycin.1 Publication

Kineticsi

kcat is 67.6 min (-1).

  1. KM=16.3 µM for devancoaminyl-vancomycin1 Publication
  2. KM=2.0 mM for UDP-L-epivancosamine1 Publication

    Pathwayi: vancomycin biosynthesis

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

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei13beta-D-glucose1 Publication1
    Binding sitei76Devancoaminyl-vancomycin; via carbonyl oxygen1 Publication1
    Binding sitei80Devancoaminyl-vancomycin1 Publication1
    Binding sitei103beta-D-glucose1 Publication1
    Binding sitei246dTDP1 Publication1

    GO - Molecular functioni

    • transferase activity, transferring hexosyl groups Source: UniProtKB

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Glycosyltransferase, Transferase

    Keywords - Biological processi

    Antibiotic biosynthesis

    Enzyme and pathway databases

    BioCyciMetaCyc:MONOMER-18443.
    BRENDAi2.4.1.322. 315.
    UniPathwayiUPA00162.

    Protein family/group databases

    CAZyiGT1. Glycosyltransferase Family 1.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Devancosaminyl-vancomycin vancosaminetransferase (EC:2.4.1.322)
    Alternative name(s):
    Devancosamine-vancomycin TDP-vancosaminyltransferase
    Glycosyltransferase GtfD
    Gene namesi
    Name:gtfD
    OrganismiAmycolatopsis orientalis (Nocardia orientalis)
    Taxonomic identifieri31958 [NCBI]
    Taxonomic lineageiBacteriaActinobacteriaPseudonocardialesPseudonocardiaceaeAmycolatopsis

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi10T → A: Strongly decreased activity. 1 Publication1
    Mutagenesisi13D → A: Abolishes catalytic activity. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00004304391 – 408Devancosaminyl-vancomycin vancosaminetransferaseAdd BLAST408

    Structurei

    Secondary structure

    1408
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi2 – 9Combined sources8
    Helixi11 – 26Combined sources16
    Beta strandi30 – 35Combined sources6
    Helixi37 – 39Combined sources3
    Helixi40 – 46Combined sources7
    Beta strandi50 – 52Combined sources3
    Helixi57 – 59Combined sources3
    Helixi70 – 91Combined sources22
    Turni92 – 94Combined sources3
    Beta strandi96 – 102Combined sources7
    Helixi104 – 117Combined sources14
    Beta strandi121 – 127Combined sources7
    Helixi128 – 130Combined sources3
    Beta strandi134 – 136Combined sources3
    Helixi151 – 176Combined sources26
    Helixi185 – 188Combined sources4
    Turni200 – 202Combined sources3
    Helixi227 – 234Combined sources8
    Beta strandi235 – 237Combined sources3
    Beta strandi240 – 242Combined sources3
    Helixi250 – 265Combined sources16
    Beta strandi270 – 273Combined sources4
    Turni275 – 278Combined sources4
    Beta strandi288 – 293Combined sources6
    Helixi296 – 299Combined sources4
    Helixi300 – 302Combined sources3
    Beta strandi303 – 308Combined sources6
    Helixi312 – 321Combined sources10
    Beta strandi325 – 327Combined sources3
    Helixi334 – 343Combined sources10
    Beta strandi346 – 349Combined sources4
    Beta strandi351 – 353Combined sources3
    Helixi357 – 367Combined sources11
    Helixi370 – 379Combined sources10
    Turni380 – 382Combined sources3
    Helixi387 – 400Combined sources14

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1RRVX-ray2.00A/B1-408[»]
    ProteinModelPortaliQ9AFC7.
    SMRiQ9AFC7.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9AFC7.

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni10 – 12dTDP binding1 Publication3
    Regioni293 – 296dTDP binding1 Publication4
    Regioni309 – 314dTDP binding1 Publication6

    Sequence similaritiesi

    Belongs to the glycosyltransferase 28 family.Curated

    Phylogenomic databases

    KOiK16443.

    Family and domain databases

    InterProiIPR004276. GlycoTrans_28_N.
    IPR002213. UDP_glucos_trans.
    [Graphical view]
    PANTHERiPTHR11926. PTHR11926. 1 hit.
    PfamiPF03033. Glyco_transf_28. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q9AFC7-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MRVLLSVCGT RGDVEIGVAL ADRLKALGVQ TRMCAPPAAE ERLAEVGVPH
    60 70 80 90 100
    VPVGLPQHMM LQEGMPPPPP EEEQRLAAMT VEMQFDAVPG AAEGCAAVVA
    110 120 130 140 150
    VGDLAAATGV RSVAEKLGLP FFYSVPSPVY LASPHLPPAY DEPTTPGVTD
    160 170 180 190 200
    IRVLWEERAA RFADRYGPTL NRRRAEIGLP PVEDVFGYGH GERPCWPADP
    210 220 230 240 250
    VLAPLQPDVD AVQTGAWLLS DERPLPPELE AFLAAGSPPV HIGFGSSSGR
    260 270 280 290 300
    GIADAAKVAV EAIRAQGRRV ILSRGWTELV LPDDRDDCFA IDEVNFQALF
    310 320 330 340 350
    RRVAAVIHHG SAGTEHVATR AGVPQLVIPR NTDQPYFAGR VAALGIGVAH
    360 370 380 390 400
    DGPTPTFESL SAALTTVLAP ETRARAEAVA GMVLTDGAAA AADLVLAAVG

    REKPAVPA
    Length:408
    Mass (Da):42,881
    Last modified:June 1, 2001 - v1
    Checksum:i1233D71CD99D1FBD
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AF351621 Genomic DNA. Translation: AAK31352.1.

    Genome annotation databases

    KEGGiag:AAK31352.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AF351621 Genomic DNA. Translation: AAK31352.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1RRVX-ray2.00A/B1-408[»]
    ProteinModelPortaliQ9AFC7.
    SMRiQ9AFC7.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein family/group databases

    CAZyiGT1. Glycosyltransferase Family 1.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    KEGGiag:AAK31352.

    Phylogenomic databases

    KOiK16443.

    Enzyme and pathway databases

    UniPathwayiUPA00162.
    BioCyciMetaCyc:MONOMER-18443.
    BRENDAi2.4.1.322. 315.

    Miscellaneous databases

    EvolutionaryTraceiQ9AFC7.

    Family and domain databases

    InterProiIPR004276. GlycoTrans_28_N.
    IPR002213. UDP_glucos_trans.
    [Graphical view]
    PANTHERiPTHR11926. PTHR11926. 1 hit.
    PfamiPF03033. Glyco_transf_28. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiGTFD_AMYOR
    AccessioniPrimary (citable) accession number: Q9AFC7
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 2014
    Last sequence update: June 1, 2001
    Last modified: November 30, 2016
    This is version 54 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    In A.orientalis different glycosyltransferases are involved in biosynthesis of the vancomycin group of antibiotics. GtfA (AC P96558), GtfB (AC P96559) and GtfC (AC P96560) are involved in biosynthesis of antibiotic chloroeremomycin, while GtfD and GtfE (AC G4V4R9) are involved in biosynthesis of vancomycin.

    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.