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Protein

Virginiamycin B lyase

Gene

vgb

Organism
Staphylococcus aureus
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Inactivates the type B streptogramin antibiotics by linearizing the lactone ring at the ester linkage, generating a free phenylglycine carboxylate and converting the threonyl moiety into 2-amino-butenoic acid.1 Publication

Cofactori

Mg2+1 Publication

Kineticsi

  1. KM=8 µM for quinupristin2 Publications
  2. KM=19 µM for pristinamycin IA2 Publications
  3. KM=0.19 mM for magnesium2 Publications

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei228 – 2281Substrate
    Metal bindingi268 – 2681Magnesium1 Publication
    Active sitei270 – 2701Proton acceptor
    Metal bindingi284 – 2841Magnesium1 Publication

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Lyase

    Keywords - Biological processi

    Antibiotic resistance

    Keywords - Ligandi

    Magnesium, Metal-binding

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Virginiamycin B lyase (EC:4.2.99.-)
    Alternative name(s):
    Streptogramin B lyase
    Gene namesi
    Name:vgb
    Synonyms:vgh
    Encoded oniPlasmid pIP6302 Publications
    Plasmid pIP5242 Publications
    OrganismiStaphylococcus aureus
    Taxonomic identifieri1280 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesStaphylococcaceaeStaphylococcus

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi18 – 181Y → F: 600-fold decrease in catalytic efficiency. 1 Publication
    Mutagenesisi228 – 2281H → A: Loss of activity. 1 Publication
    Mutagenesisi268 – 2681E → Q: 56-fold decrease in catalytic efficiency. 1 Publication
    Mutagenesisi270 – 2701H → A: Loss of activity. 1 Publication
    Mutagenesisi284 – 2841E → Q: 137-fold decrease in catalytic efficiency. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 299299Virginiamycin B lyasePRO_0000068590Add
    BLAST

    Interactioni

    Subunit structurei

    Monomer.2 Publications

    Structurei

    Secondary structure

    1
    299
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi3 – 97Combined sources
    Beta strandi12 – 143Combined sources
    Beta strandi17 – 226Combined sources
    Beta strandi24 – 263Combined sources
    Beta strandi28 – 325Combined sources
    Turni33 – 364Combined sources
    Beta strandi37 – 415Combined sources
    Beta strandi47 – 515Combined sources
    Beta strandi53 – 553Combined sources
    Beta strandi59 – 646Combined sources
    Beta strandi70 – 745Combined sources
    Turni75 – 784Combined sources
    Beta strandi79 – 835Combined sources
    Beta strandi89 – 935Combined sources
    Beta strandi101 – 1066Combined sources
    Beta strandi112 – 1165Combined sources
    Turni117 – 1204Combined sources
    Beta strandi121 – 1255Combined sources
    Beta strandi131 – 1355Combined sources
    Beta strandi143 – 1486Combined sources
    Beta strandi154 – 1585Combined sources
    Turni159 – 1624Combined sources
    Beta strandi163 – 1675Combined sources
    Beta strandi173 – 1775Combined sources
    Beta strandi185 – 1906Combined sources
    Beta strandi194 – 2007Combined sources
    Turni201 – 2044Combined sources
    Beta strandi205 – 2095Combined sources
    Beta strandi215 – 2195Combined sources
    Beta strandi227 – 2326Combined sources
    Beta strandi238 – 2425Combined sources
    Turni243 – 2464Combined sources
    Beta strandi247 – 2526Combined sources
    Turni253 – 2553Combined sources
    Beta strandi256 – 2616Combined sources
    Beta strandi263 – 2664Combined sources
    Beta strandi269 – 2746Combined sources
    Beta strandi279 – 2835Combined sources
    Turni284 – 2863Combined sources
    Beta strandi287 – 2937Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2Z2NX-ray1.65A1-299[»]
    2Z2OX-ray1.90A/B/C/D1-299[»]
    2Z2PX-ray2.80A/B1-299[»]
    ProteinModelPortaliP17978.
    SMRiP17978. Positions 1-299.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP17978.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the Vgb family.Curated

    Phylogenomic databases

    KOiK18235.

    Family and domain databases

    Gene3Di2.120.10.30. 2 hits.
    HAMAPiMF_01282. VirginiamycinB_lyase.
    InterProiIPR011042. 6-blade_b-propeller_TolB-like.
    IPR011217. Streptogrm_lyase.
    [Graphical view]
    PIRSFiPIRSF026412. Streptogrm_lyase. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P17978-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MEFKLQELNL TNQDTGPYGI TVSDKGKVWI TQHKANMISC INLDGKITEY
    60 70 80 90 100
    PLPTPDAKVM CLTISSDGEV WFTENAANKI GRITKKGIIK EYTLPNPDSA
    110 120 130 140 150
    PYGITEGPNG DIWFTEMNGN RIGRITDDGK IREYELPNKG SYPSFITLGS
    160 170 180 190 200
    DNALWFTENQ NNAIGRITES GDITEFKIPT PASGPVGITK GNDDALWFVE
    210 220 230 240 250
    IIGNKIGRIT PLGEITEFKI PTPNARPHAI TAGAGIDLWF TEWGANKIGR
    260 270 280 290
    LTSNNIIEEY PIQIKSGEPH GICFDGETIW FAMECDKIGK LTLIKDNME
    Length:299
    Mass (Da):33,058
    Last modified:November 1, 1990 - v1
    Checksum:iD2D35588C38FC0E3
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti267 – 2671G → A in AAA98349 (PubMed:3149758).Curated
    Sequence conflicti267 – 2671G → A in AAF24088 (PubMed:10489330).Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M36022 Genomic DNA. Translation: AAA98259.1.
    M20129 Genomic DNA. Translation: AAA98349.1.
    AF117258 Genomic DNA. Translation: AAF24088.1.
    PIRiS27668. PN0638.

    Genome annotation databases

    KEGGiag:AAA98349.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    M36022 Genomic DNA. Translation: AAA98259.1.
    M20129 Genomic DNA. Translation: AAA98349.1.
    AF117258 Genomic DNA. Translation: AAF24088.1.
    PIRiS27668. PN0638.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2Z2NX-ray1.65A1-299[»]
    2Z2OX-ray1.90A/B/C/D1-299[»]
    2Z2PX-ray2.80A/B1-299[»]
    ProteinModelPortaliP17978.
    SMRiP17978. Positions 1-299.
    ModBaseiSearch...
    MobiDBiSearch...

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    KEGGiag:AAA98349.

    Phylogenomic databases

    KOiK18235.

    Miscellaneous databases

    EvolutionaryTraceiP17978.

    Family and domain databases

    Gene3Di2.120.10.30. 2 hits.
    HAMAPiMF_01282. VirginiamycinB_lyase.
    InterProiIPR011042. 6-blade_b-propeller_TolB-like.
    IPR011217. Streptogrm_lyase.
    [Graphical view]
    PIRSFiPIRSF026412. Streptogrm_lyase. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    1. "Nucleotide sequence of a staphylococcal plasmid gene, vgb, encoding a hydrolase inactivating the B components of virginiamycin-like antibiotics."
      Allignet J., Loncle V., Mazodier P., El Solh N.
      Plasmid 20:271-275(1988) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Plasmid: pIP630
    2. "Comparative analysis of staphylococcal plasmids carrying three streptogramin-resistance genes: vat-vgb-vga."
      Allignet J., El Solh N.
      Plasmid 42:134-138(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: BM3093.
      Plasmid: pIP630
    3. "Vgb from Staphylococcus aureus inactivates streptogramin B antibiotics by an elimination mechanism not hydrolysis."
      Mukhtar T.A., Koteva K.P., Hughes D.W., Wright G.D.
      Biochemistry 40:8877-8886(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION AS A LYASE, REACTION MECHANISM, SUBSTRATE SPECIFICITY, SUBUNIT, COFACTOR, BIOPHYSICOCHEMICAL PROPERTIES.
      Strain: BM3002.
      Plasmid: pIP524
    4. "Structural basis for streptogramin B resistance in Staphylococcus aureus by virginiamycin B lyase."
      Korczynska M., Mukhtar T.A., Wright G.D., Berghuis A.M.
      Proc. Natl. Acad. Sci. U.S.A. 104:10388-10393(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS) OF WILD-TYPE AND MUTANT ALA-270 IN COMPLEX WITH QUINUPRISTIN AND MAGNESIUM, CATALYTIC MECHANISM, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF TYR-18; HIS-228; GLU-268; HIS-270 AND GLU-284.
      Strain: BM3002.
      Plasmid: pIP524

    Entry informationi

    Entry nameiVGB_STAAU
    AccessioniPrimary (citable) accession number: P17978
    Secondary accession number(s): Q53744
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1990
    Last sequence update: November 1, 1990
    Last modified: May 11, 2016
    This is version 69 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Has unequivocally been shown (PubMed:11467949) to cleave the ester bond of streptogramin B antibiotics by an elimination reaction and not by hydrolysis, therefore is a lyase and not a hydrolase. The olefinic dehydrobutyrine thus generated in the N-terminal position has a Z stereochemistry.1 Publication

    Keywords - Technical termi

    3D-structure, Plasmid

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. 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.