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P0AGK4

- YHBY_ECOLI

UniProt

P0AGK4 - YHBY_ECOLI

Protein

RNA-binding protein YhbY

Gene

yhbY

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 2 out of 5- Experimental evidence at protein leveli
  1. Functioni

    GO - Molecular functioni

    1. RNA binding Source: UniProtKB-KW

    Keywords - Ligandi

    RNA-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:EG12794-MONOMER.
    ECOL316407:JW3147-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    RNA-binding protein YhbY
    Gene namesi
    Name:yhbY
    Ordered Locus Names:b3180, JW3147
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG12794. yhbY.

    Subcellular locationi

    Cytoplasm 1 Publication
    Note: Has been seen to comigrate with the 50S ribosomal subunit in sucrose gradients.

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 9797RNA-binding protein YhbYPRO_0000202163Add
    BLAST

    Proteomic databases

    PaxDbiP0AGK4.
    PRIDEiP0AGK4.

    Expressioni

    Gene expression databases

    GenevestigatoriP0AGK4.

    Interactioni

    Protein-protein interaction databases

    DIPiDIP-47893N.
    IntActiP0AGK4. 39 interactions.
    MINTiMINT-1224994.
    STRINGi511145.b3180.

    Structurei

    Secondary structure

    1
    97
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi5 – 1511
    Beta strandi21 – 244
    Helixi31 – 4414
    Beta strandi45 – 517
    Helixi56 – 7015
    Beta strandi73 – 786
    Beta strandi81 – 855

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1LN4X-ray1.50A3-97[»]
    ProteinModelPortaliP0AGK4.
    SMRiP0AGK4. Positions 1-96.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP0AGK4.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini1 – 9797CRMPROSITE-ProRule annotationAdd
    BLAST

    Sequence similaritiesi

    Contains 1 CRM domain.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiCOG1534.
    HOGENOMiHOG000016279.
    KOiK07574.
    OMAiRPSNEPK.
    OrthoDBiEOG6SBT94.
    PhylomeDBiP0AGK4.

    Family and domain databases

    Gene3Di3.30.110.60. 1 hit.
    InterProiIPR001890. RNA-binding_CRM.
    IPR017924. RNA-binding_YhbY.
    [Graphical view]
    PfamiPF01985. CRS1_YhbY. 1 hit.
    [Graphical view]
    ProDomiPD010559. RNA-binding_CRM. 1 hit.
    [Graphical view] [Entries sharing at least one domain]
    SMARTiSM01103. CRS1_YhbY. 1 hit.
    [Graphical view]
    SUPFAMiSSF75471. SSF75471. 1 hit.
    TIGRFAMsiTIGR00253. RNA_bind_YhbY. 1 hit.
    PROSITEiPS51295. CRM. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P0AGK4-1 [UniParc]FASTAAdd to Basket

    « Hide

    MNLSTKQKQH LKGLAHPLKP VVLLGSNGLT EGVLAEIEQA LEHHELIKVK   50
    IATEDRETKT LIVEAIVRET GACNVQVIGK TLVLYRPTKE RKISLPR 97
    Length:97
    Mass (Da):10,784
    Last modified:December 20, 2005 - v1
    Checksum:i52B4F7AD4C203382
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U01376 Genomic DNA. No translation available.
    U18997 Genomic DNA. Translation: AAA57981.1.
    U00096 Genomic DNA. Translation: AAC76212.1.
    AP009048 Genomic DNA. Translation: BAE77224.1.
    X54718 Genomic DNA. No translation available.
    PIRiF65108.
    RefSeqiNP_417647.1. NC_000913.3.
    YP_491365.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC76212; AAC76212; b3180.
    BAE77224; BAE77224; BAE77224.
    GeneIDi12932801.
    947688.
    KEGGiecj:Y75_p3100.
    eco:b3180.
    PATRICi32121778. VBIEscCol129921_3273.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U01376 Genomic DNA. No translation available.
    U18997 Genomic DNA. Translation: AAA57981.1 .
    U00096 Genomic DNA. Translation: AAC76212.1 .
    AP009048 Genomic DNA. Translation: BAE77224.1 .
    X54718 Genomic DNA. No translation available.
    PIRi F65108.
    RefSeqi NP_417647.1. NC_000913.3.
    YP_491365.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1LN4 X-ray 1.50 A 3-97 [» ]
    ProteinModelPortali P0AGK4.
    SMRi P0AGK4. Positions 1-96.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-47893N.
    IntActi P0AGK4. 39 interactions.
    MINTi MINT-1224994.
    STRINGi 511145.b3180.

    Proteomic databases

    PaxDbi P0AGK4.
    PRIDEi P0AGK4.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC76212 ; AAC76212 ; b3180 .
    BAE77224 ; BAE77224 ; BAE77224 .
    GeneIDi 12932801.
    947688.
    KEGGi ecj:Y75_p3100.
    eco:b3180.
    PATRICi 32121778. VBIEscCol129921_3273.

    Organism-specific databases

    EchoBASEi EB2646.
    EcoGenei EG12794. yhbY.

    Phylogenomic databases

    eggNOGi COG1534.
    HOGENOMi HOG000016279.
    KOi K07574.
    OMAi RPSNEPK.
    OrthoDBi EOG6SBT94.
    PhylomeDBi P0AGK4.

    Enzyme and pathway databases

    BioCyci EcoCyc:EG12794-MONOMER.
    ECOL316407:JW3147-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P0AGK4.
    PROi P0AGK4.

    Gene expression databases

    Genevestigatori P0AGK4.

    Family and domain databases

    Gene3Di 3.30.110.60. 1 hit.
    InterProi IPR001890. RNA-binding_CRM.
    IPR017924. RNA-binding_YhbY.
    [Graphical view ]
    Pfami PF01985. CRS1_YhbY. 1 hit.
    [Graphical view ]
    ProDomi PD010559. RNA-binding_CRM. 1 hit.
    [Graphical view ] [Entries sharing at least one domain ]
    SMARTi SM01103. CRS1_YhbY. 1 hit.
    [Graphical view ]
    SUPFAMi SSF75471. SSF75471. 1 hit.
    TIGRFAMsi TIGR00253. RNA_bind_YhbY. 1 hit.
    PROSITEi PS51295. CRM. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Identification and physical analysis of new genes in the argG region (69 min) of Escherichia coli chromosome."
      Wang R., Kushner S.R.
      Submitted (SEP-1993) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: K12.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    3. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
      Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
      Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    4. "The nucleotide sequence of greA, a suppressor gene that restores growth of an Escherichia coli RNA polymerase mutant at high temperature."
      Sparkowski J., Das A.
      Nucleic Acids Res. 18:6443-6443(1990) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 64-97.
    5. "The Escherichia coli GTPase CgtAE is involved in late steps of large ribosome assembly."
      Jiang M., Datta K., Walker A., Strahler J., Bagamasbad P., Andrews P.C., Maddock J.R.
      J. Bacteriol. 188:6757-6770(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION BY MASS SPECTROMETRY, SUBCELLULAR LOCATION, ASSOCIATION WITH THE 50S RIBOSOMAL SUBUNIT.
      Strain: K12 / MG1655 / ATCC 47076.
    6. "Crystal structure of E. coli YhbY: a representative of a novel class of RNA binding proteins."
      Ostheimer G.J., Barkan A., Matthews B.W.
      Structure 10:1593-1601(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) OF 5-104.

    Entry informationi

    Entry nameiYHBY_ECOLI
    AccessioniPrimary (citable) accession number: P0AGK4
    Secondary accession number(s): P42550, Q2M932
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: December 20, 2005
    Last sequence update: December 20, 2005
    Last modified: October 1, 2014
    This is version 80 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
    4. Uncharacterized protein families (UPF)
      List of uncharacterized protein family (UPF) entries

    External Data

    Dasty 3