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Protein

N-glycosidase YbiA

Gene

ybiA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the hydrolysis of the N-glycosidic bond in the first two intermediates of riboflavin biosynthesis, which are highly reactive metabolites, yielding relatively innocuous products. Thus, can divert a surplus of harmful intermediates into relatively harmless products and pre-empt the damage these intermediates would otherwise do. Helps maintain flavin levels. May act on other substrates in vivo. Has no activity against GTP, nucleoside monophosphates or ADP-ribose (PubMed:25431972). Is Required for swarming motility (PubMed:17122336).2 Publications

Catalytic activityi

2,5-diamino-6-hydroxy-4-(5-phospho-D-ribosylamino)pyrimidine + H2O = 2,5,6-triamino-4-hydroxypyrimidine + ribose-5-phosphate.1 Publication
5-amino-6-(5-phospho-D-ribosylamino)uracil + H2O = 5,6-diaminouracil + ribose-5-phosphate.1 Publication

Kineticsi

kcat is 0.006 sec(-1) with 2,5-diamino-6-hydroxy-4-(5-phospho-D-ribosylamino)pyrimidine as substrate. kcat is 0.80 sec(-1) with 5-amino-6-(5-phospho-D-ribosylamino)uracil as substrate.1 Publication

  1. KM=4.04 mM for 2,5-diamino-6-hydroxy-4-(5-phospho-D-ribosylamino)pyrimidine1 Publication
  2. KM=5.84 mM for 5-amino-6-(5-phospho-D-ribosylamino)uracil1 Publication

    GO - Molecular functioni

    • hydrolase activity, hydrolyzing N-glycosyl compounds Source: UniProtKB

    GO - Biological processi

    • carbohydrate derivative metabolic process Source: UniProtKB
    • RNA modification Source: GO_Central
    Complete GO annotation...

    Keywords - Molecular functioni

    Glycosidase, Hydrolase

    Enzyme and pathway databases

    BioCyciEcoCyc:EG11579-MONOMER.
    ECOL316407:JW0783-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    N-glycosidase YbiA1 Publication (EC:3.2.2.-1 Publication)
    Alternative name(s):
    Riboflavin biosynthesis intermediates N-glycosidase1 Publication
    Gene namesi
    Name:ybiA
    Ordered Locus Names:b0798, JW0783
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG11579. ybiA.

    Pathology & Biotechi

    Disruption phenotypei

    Strongly represses cell swarming but no effect on cell swimming (PubMed:17122336). Cells lacking this gene show significantly reduced FAD and FMN levels (both by 13%) (PubMed:25431972).2 Publications

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi48 – 481E → A: Loss of enzymatic activity. 1 Publication
    Mutagenesisi89 – 891W → A: Large decrease in enzymatic activity. 1 Publication
    Mutagenesisi130 – 1301D → A: Loss of enzymatic activity. 1 Publication
    Mutagenesisi133 – 1331W → A: Loss of enzymatic activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 160160N-glycosidase YbiAPRO_0000168724Add
    BLAST

    Proteomic databases

    PaxDbiP30176.
    PRIDEiP30176.

    Interactioni

    Protein-protein interaction databases

    BioGridi4259963. 13 interactions.
    DIPiDIP-11424N.
    IntActiP30176. 15 interactions.
    STRINGi511145.b0798.

    Structurei

    Secondary structure

    1
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi7 – 104Combined sources
    Beta strandi13 – 197Combined sources
    Helixi25 – 273Combined sources
    Beta strandi37 – 393Combined sources
    Beta strandi42 – 465Combined sources
    Helixi47 – 559Combined sources
    Helixi59 – 679Combined sources
    Helixi71 – 788Combined sources
    Beta strandi81 – 833Combined sources
    Helixi89 – 10618Combined sources
    Helixi109 – 1179Combined sources
    Turni118 – 1203Combined sources
    Beta strandi121 – 1255Combined sources
    Beta strandi132 – 1343Combined sources
    Turni136 – 1394Combined sources
    Helixi144 – 16017Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2B3WNMR-A1-160[»]
    ProteinModelPortaliP30176.
    SMRiP30176. Positions 1-160.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP30176.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the YbiA family.Curated

    Phylogenomic databases

    eggNOGiENOG4108UV1. Bacteria.
    COG3236. LUCA.
    HOGENOMiHOG000270609.
    InParanoidiP30176.
    KOiK09935.
    OMAiNFSPHGF.
    PhylomeDBiP30176.

    Family and domain databases

    CDDicd15457. NADAR. 1 hit.
    InterProiIPR012816. NADAR.
    [Graphical view]
    PfamiPF08719. DUF1768. 1 hit.
    [Graphical view]
    TIGRFAMsiTIGR02464. ribofla_fusion. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P30176-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MPVRAQRIQH VMQDTIINFY STSDDYGDFS NFAAWPIKVD GKTWPTSEHY
    60 70 80 90 100
    FQAQKFLDEK YREEIRRVSS PMVAARMGRD RSKPLRKNWE SVKEQVMRKA
    110 120 130 140 150
    LRAKFEQHAE LRALLLATAP AKLVEHTEND AYWGDGGHGK GKNRLGYLLM
    160
    ELREQLAIEK
    Length:160
    Mass (Da):18,669
    Last modified:April 1, 1993 - v1
    Checksum:i28D6DA5C6748653C
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    L02123 Genomic DNA. Translation: AAA53654.1.
    U00096 Genomic DNA. Translation: AAC73885.1.
    AP009048 Genomic DNA. Translation: BAA35458.1.
    PIRiF64816.
    RefSeqiNP_415319.1. NC_000913.3.

    Genome annotation databases

    EnsemblBacteriaiAAC73885; AAC73885; b0798.
    BAA35458; BAA35458; BAA35458.
    GeneIDi945426.
    KEGGiecj:JW0783.
    eco:b0798.
    PATRICi32116799. VBIEscCol129921_0825.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    L02123 Genomic DNA. Translation: AAA53654.1.
    U00096 Genomic DNA. Translation: AAC73885.1.
    AP009048 Genomic DNA. Translation: BAA35458.1.
    PIRiF64816.
    RefSeqiNP_415319.1. NC_000913.3.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2B3WNMR-A1-160[»]
    ProteinModelPortaliP30176.
    SMRiP30176. Positions 1-160.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4259963. 13 interactions.
    DIPiDIP-11424N.
    IntActiP30176. 15 interactions.
    STRINGi511145.b0798.

    Proteomic databases

    PaxDbiP30176.
    PRIDEiP30176.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC73885; AAC73885; b0798.
    BAA35458; BAA35458; BAA35458.
    GeneIDi945426.
    KEGGiecj:JW0783.
    eco:b0798.
    PATRICi32116799. VBIEscCol129921_0825.

    Organism-specific databases

    EchoBASEiEB1539.
    EcoGeneiEG11579. ybiA.

    Phylogenomic databases

    eggNOGiENOG4108UV1. Bacteria.
    COG3236. LUCA.
    HOGENOMiHOG000270609.
    InParanoidiP30176.
    KOiK09935.
    OMAiNFSPHGF.
    PhylomeDBiP30176.

    Enzyme and pathway databases

    BioCyciEcoCyc:EG11579-MONOMER.
    ECOL316407:JW0783-MONOMER.

    Miscellaneous databases

    EvolutionaryTraceiP30176.
    PROiP30176.

    Family and domain databases

    CDDicd15457. NADAR. 1 hit.
    InterProiIPR012816. NADAR.
    [Graphical view]
    PfamiPF08719. DUF1768. 1 hit.
    [Graphical view]
    TIGRFAMsiTIGR02464. ribofla_fusion. 1 hit.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiRIBX_ECOLI
    AccessioniPrimary (citable) accession number: P30176
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 1, 1993
    Last sequence update: April 1, 1993
    Last modified: September 7, 2016
    This is version 117 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, Complete proteome, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    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.