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Protein

N-glycosidase YbiA

Gene

ybiA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: -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

    Keywordsi

    Molecular functionGlycosidase, Hydrolase

    Enzyme and pathway databases

    BioCyciEcoCyc:EG11579-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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    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)DescriptionActionsGraphical viewLength
    Mutagenesisi48E → A: Loss of enzymatic activity. 1 Publication1
    Mutagenesisi89W → A: Large decrease in enzymatic activity. 1 Publication1
    Mutagenesisi130D → A: Loss of enzymatic activity. 1 Publication1
    Mutagenesisi133W → A: Loss of enzymatic activity. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001687241 – 160N-glycosidase YbiAAdd BLAST160

    Proteomic databases

    PaxDbiP30176
    PRIDEiP30176

    Interactioni

    Protein-protein interaction databases

    BioGridi4259963, 15 interactors
    DIPiDIP-11424N
    IntActiP30176, 15 interactors
    STRINGi316385.ECDH10B_0866

    Structurei

    Secondary structure

    1160
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi7 – 10Combined sources4
    Beta strandi13 – 19Combined sources7
    Helixi25 – 27Combined sources3
    Beta strandi37 – 39Combined sources3
    Beta strandi42 – 46Combined sources5
    Helixi47 – 55Combined sources9
    Helixi59 – 67Combined sources9
    Helixi71 – 78Combined sources8
    Beta strandi81 – 83Combined sources3
    Helixi89 – 106Combined sources18
    Helixi109 – 117Combined sources9
    Turni118 – 120Combined sources3
    Beta strandi121 – 125Combined sources5
    Beta strandi132 – 134Combined sources3
    Turni136 – 139Combined sources4
    Helixi144 – 160Combined sources17

    3D structure databases

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

    Miscellaneous databases

    EvolutionaryTraceiP30176

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the YbiA family.Curated

    Phylogenomic databases

    eggNOGiENOG4108UV1 Bacteria
    COG3236 LUCA
    HOGENOMiHOG000270609
    InParanoidiP30176
    KOiK09935
    OMAiAEHFMMA
    PhylomeDBiP30176

    Family and domain databases

    CDDicd15457 NADAR, 1 hit
    Gene3Di1.10.357.40, 1 hit
    InterProiView protein in InterPro
    IPR012816 NADAR
    IPR037238 YbiA-like_sf
    PfamiView protein in Pfam
    PF08719 DUF1768, 1 hit
    SUPFAMiSSF143990 SSF143990, 1 hit
    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
    WP_001145126.1, NZ_LN832404.1

    Genome annotation databases

    EnsemblBacteriaiAAC73885; AAC73885; b0798
    BAA35458; BAA35458; BAA35458
    GeneIDi945426
    KEGGiecj:JW0783
    eco:b0798
    PATRICifig|511145.12.peg.825

    Similar proteinsi

    Entry informationi

    Entry nameiRIBX_ECOLI
    AccessioniPrimary (citable) accession number: P30176
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: April 1, 1993
    Last sequence update: April 1, 1993
    Last modified: March 28, 2018
    This is version 127 of the entry and version 1 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome
    UniProt is an ELIXIR core data resource
    Main funding by: National Institutes of Health