Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
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)DescriptionActionsGraphical viewLength
    Binding sitei228Substrate1
    Metal bindingi268Magnesium1 Publication1
    Active sitei270Proton acceptor1
    Metal bindingi284Magnesium1 Publication1

    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)DescriptionActionsGraphical viewLength
    Mutagenesisi18Y → F: 600-fold decrease in catalytic efficiency. 1 Publication1
    Mutagenesisi228H → A: Loss of activity. 1 Publication1
    Mutagenesisi268E → Q: 56-fold decrease in catalytic efficiency. 1 Publication1
    Mutagenesisi270H → A: Loss of activity. 1 Publication1
    Mutagenesisi284E → Q: 137-fold decrease in catalytic efficiency. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00000685901 – 299Virginiamycin B lyaseAdd BLAST299

    Interactioni

    Subunit structurei

    Monomer.2 Publications

    Structurei

    Secondary structure

    1299
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi3 – 9Combined sources7
    Beta strandi12 – 14Combined sources3
    Beta strandi17 – 22Combined sources6
    Beta strandi24 – 26Combined sources3
    Beta strandi28 – 32Combined sources5
    Turni33 – 36Combined sources4
    Beta strandi37 – 41Combined sources5
    Beta strandi47 – 51Combined sources5
    Beta strandi53 – 55Combined sources3
    Beta strandi59 – 64Combined sources6
    Beta strandi70 – 74Combined sources5
    Turni75 – 78Combined sources4
    Beta strandi79 – 83Combined sources5
    Beta strandi89 – 93Combined sources5
    Beta strandi101 – 106Combined sources6
    Beta strandi112 – 116Combined sources5
    Turni117 – 120Combined sources4
    Beta strandi121 – 125Combined sources5
    Beta strandi131 – 135Combined sources5
    Beta strandi143 – 148Combined sources6
    Beta strandi154 – 158Combined sources5
    Turni159 – 162Combined sources4
    Beta strandi163 – 167Combined sources5
    Beta strandi173 – 177Combined sources5
    Beta strandi185 – 190Combined sources6
    Beta strandi194 – 200Combined sources7
    Turni201 – 204Combined sources4
    Beta strandi205 – 209Combined sources5
    Beta strandi215 – 219Combined sources5
    Beta strandi227 – 232Combined sources6
    Beta strandi238 – 242Combined sources5
    Turni243 – 246Combined sources4
    Beta strandi247 – 252Combined sources6
    Turni253 – 255Combined sources3
    Beta strandi256 – 261Combined sources6
    Beta strandi263 – 266Combined sources4
    Beta strandi269 – 274Combined sources6
    Beta strandi279 – 283Combined sources5
    Turni284 – 286Combined sources3
    Beta strandi287 – 293Combined sources7

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2Z2NX-ray1.65A1-299[»]
    2Z2OX-ray1.90A/B/C/D1-299[»]
    2Z2PX-ray2.80A/B1-299[»]
    ProteinModelPortaliP17978.
    SMRiP17978.
    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. 1 hit.
    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)DescriptionActionsGraphical viewLength
    Sequence conflicti267G → A in AAA98349 (PubMed:3149758).Curated1
    Sequence conflicti267G → A in AAF24088 (PubMed:10489330).Curated1

    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.
    RefSeqiWP_032489636.1. NG_048563.1.

    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.
    RefSeqiWP_032489636.1. NG_048563.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    2Z2NX-ray1.65A1-299[»]
    2Z2OX-ray1.90A/B/C/D1-299[»]
    2Z2PX-ray2.80A/B1-299[»]
    ProteinModelPortaliP17978.
    SMRiP17978.
    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. 1 hit.
    InterProiIPR011042. 6-blade_b-propeller_TolB-like.
    IPR011217. Streptogrm_lyase.
    [Graphical view]
    PIRSFiPIRSF026412. Streptogrm_lyase. 1 hit.
    ProtoNetiSearch...

    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: November 2, 2016
    This is version 71 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.