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P30850

- RNB_ECOLI

UniProt

P30850 - RNB_ECOLI

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Protein
Exoribonuclease 2
Gene
rnb, b1286, JW1279
Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

Involved in mRNA degradation. Hydrolyzes single-stranded polyribonucleotides processively in the 3' to 5' direction.1 Publication

Catalytic activityi

Exonucleolytic cleavage in the 3'- to 5'-direction to yield nucleoside 5'-phosphates.UniRule annotation

Cofactori

Magnesium.1 Publication

Enzyme regulationi

Stimulated by the presence of a monovalent cation.1 Publication

Kineticsi

    Vmax=109800 nmol/min/mg enzyme with Poly(A) as substrate1 Publication

    Vmax=160 nmol/min/mg enzyme with 23S rRNA as substrate

    Vmax=30 nmol/min/mg enzyme with 16S rRNA as substrate

    Vmax=20 nmol/min/mg enzyme with 5S rRNA as substrate

    pH dependencei

    Optimum pH is 7.5-9.5.

    Temperature dependencei

    Optimum temperature is 50 degrees Celsius.

    GO - Molecular functioni

    1. 3'-5' exonuclease activity Source: EcoCyc
    2. RNA binding Source: UniProtKB-KW
    3. exoribonuclease II activity Source: UniProtKB-HAMAP
    4. protein binding Source: IntAct
    Complete GO annotation...

    GO - Biological processi

    1. mRNA catabolic process Source: UniProtKB-HAMAP
    2. nucleic acid phosphodiester bond hydrolysis Source: GOC
    3. tRNA catabolic process Source: EcoCyc
    Complete GO annotation...

    Keywords - Molecular functioni

    Exonuclease, Hydrolase, Nuclease

    Keywords - Ligandi

    RNA-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:EG11620-MONOMER.
    ECOL316407:JW1279-MONOMER.
    MetaCyc:EG11620-MONOMER.
    BRENDAi3.1.13.1. 2026.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Exoribonuclease 2 (EC:3.1.13.1)
    Alternative name(s):
    Exoribonuclease II
    Short name:
    RNase II
    Short name:
    Ribonuclease II
    Gene namesi
    Name:rnb
    Ordered Locus Names:b1286, JW1279
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG11620. rnb.

    Subcellular locationi

    Cytoplasm UniRule annotation

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell
    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 644644Exoribonuclease 2UniRule annotation
    PRO_0000166380Add
    BLAST

    Proteomic databases

    PaxDbiP30850.
    PRIDEiP30850.

    Expressioni

    Gene expression databases

    GenevestigatoriP30850.

    Interactioni

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    rpsEP0A7W12EBI-557325,EBI-543949

    Protein-protein interaction databases

    DIPiDIP-10724N.
    IntActiP30850. 10 interactions.
    MINTiMINT-1248196.
    STRINGi511145.b1286.

    Structurei

    Secondary structure

    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi6 – 1712
    Beta strandi21 – 277
    Beta strandi30 – 323
    Beta strandi34 – 374
    Beta strandi39 – 413
    Beta strandi43 – 464
    Helixi48 – 514
    Beta strandi59 – 657
    Beta strandi68 – 703
    Beta strandi72 – 809
    Beta strandi84 – 9310
    Beta strandi96 – 1038
    Beta strandi110 – 1145
    Beta strandi127 – 1348
    Helixi136 – 1383
    Beta strandi144 – 1529
    Helixi159 – 1679
    Beta strandi198 – 2014
    Beta strandi210 – 2145
    Beta strandi218 – 2203
    Beta strandi222 – 2298
    Helixi231 – 2333
    Helixi240 – 2489
    Beta strandi252 – 2543
    Beta strandi257 – 2593
    Helixi264 – 2674
    Turni268 – 2703
    Beta strandi278 – 28811
    Beta strandi300 – 3067
    Beta strandi310 – 3123
    Helixi313 – 3197
    Helixi331 – 35424
    Beta strandi364 – 3685
    Beta strandi374 – 3796
    Helixi384 – 40724
    Beta strandi413 – 4164
    Turni421 – 4233
    Helixi424 – 43411
    Helixi440 – 4434
    Helixi446 – 45712
    Beta strandi459 – 4624
    Helixi463 – 4686
    Helixi469 – 4713
    Beta strandi476 – 4805
    Turni485 – 4884
    Beta strandi489 – 4913
    Turni498 – 5003
    Helixi502 – 51413
    Helixi527 – 55428
    Helixi555 – 5573
    Beta strandi564 – 5729
    Beta strandi575 – 5806
    Turni581 – 5833
    Beta strandi586 – 5905
    Helixi591 – 5933
    Helixi598 – 6003
    Beta strandi601 – 6044
    Turni605 – 6084
    Beta strandi609 – 6124
    Beta strandi615 – 6195
    Beta strandi623 – 63210
    Turni633 – 6364
    Beta strandi637 – 6426

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2ID0X-ray2.35A/B/C/D1-644[»]
    2IX0X-ray2.44A6-644[»]
    2IX1X-ray2.74A6-644[»]
    ProteinModelPortaliP30850.

    Miscellaneous databases

    EvolutionaryTraceiP30850.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini561 – 64383S1 motif
    Add
    BLAST

    Sequence similaritiesi

    Contains 1 S1 motif domain.

    Phylogenomic databases

    eggNOGiCOG4776.
    HOGENOMiHOG000271427.
    KOiK01147.
    OMAiEASIFTG.
    OrthoDBiEOG6Q5NRD.
    PhylomeDBiP30850.

    Family and domain databases

    HAMAPiMF_01036. RNase_II.
    InterProiIPR011129. Cold_shock_prot.
    IPR012340. NA-bd_OB-fold.
    IPR003029. Rbsml_prot_S1_RNA-bd_dom.
    IPR022967. RNA-binding_domain_S1.
    IPR013223. RNase_B_OB_dom.
    IPR011804. RNase_II.
    IPR022966. RNase_II/R_CS.
    IPR004476. RNase_II/RNase_R.
    [Graphical view]
    PfamiPF08206. OB_RNB. 1 hit.
    PF00575. S1. 1 hit.
    [Graphical view]
    SMARTiSM00357. CSP. 1 hit.
    SM00316. S1. 1 hit.
    [Graphical view]
    SUPFAMiSSF50249. SSF50249. 4 hits.
    TIGRFAMsiTIGR00358. 3_prime_RNase. 1 hit.
    TIGR02062. RNase_B. 1 hit.
    PROSITEiPS01175. RIBONUCLEASE_II. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P30850-1 [UniParc]FASTAAdd to Basket

    « Hide

    MFQDNPLLAQ LKQQLHSQTP RAEGVVKATE KGFGFLEVDA QKSYFIPPPQ    50
    MKKVMHGDRI IAVIHSEKER ESAEPEELVE PFLTRFVGKV QGKNDRLAIV 100
    PDHPLLKDAI PCRAARGLNH EFKEGDWAVA EMRRHPLKGD RSFYAELTQY 150
    ITFGDDHFVP WWVTLARHNL EKEAPDGVAT EMLDEGLVRE DLTALDFVTI 200
    DSASTEDMDD ALFAKALPDD KLQLIVAIAD PTAWIAEGSK LDKAAKIRAF 250
    TNYLPGFNIP MLPRELSDDL CSLRANEVRP VLACRMTLSA DGTIEDNIEF 300
    FAATIESKAK LVYDQVSDWL ENTGDWQPES EAIAEQVRLL AQICQRRGEW 350
    RHNHALVFKD RPDYRFILGE KGEVLDIVAE PRRIANRIVE EAMIAANICA 400
    ARVLRDKLGF GIYNVHMGFD PANADALAAL LKTHGLHVDA EEVLTLDGFC 450
    KLRRELDAQP TGFLDSRIRR FQSFAEISTE PGPHFGLGLE AYATWTSPIR 500
    KYGDMINHRL LKAVIKGETA TRPQDEITVQ MAERRRLNRM AERDVGDWLY 550
    ARFLKDKAGT DTRFAAEIVD ISRGGMRVRL VDNGAIAFIP APFLHAVRDE 600
    LVCSQENGTV QIKGETVYKV TDVIDVTIAE VRMETRSIIA RPVA 644
    Length:644
    Mass (Da):72,491
    Last modified:November 1, 1997 - v3
    Checksum:i36B16712CDF14394
    GO

    Sequence conflict

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti384 – 3841I → N in CAA48112. 1 Publication
    Sequence conflicti399 – 3991C → G in CAA48112. 1 Publication
    Sequence conflicti513 – 5131A → R in CAA48112. 1 Publication

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X67913 Genomic DNA. Translation: CAA48112.1.
    U00096 Genomic DNA. Translation: AAC74368.1.
    AP009048 Genomic DNA. Translation: BAA14840.1.
    PIRiA64877.
    RefSeqiNP_415802.1. NC_000913.3.
    YP_489554.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC74368; AAC74368; b1286.
    BAA14840; BAA14840; BAA14840.
    GeneIDi12934347.
    945864.
    KEGGiecj:Y75_p1261.
    eco:b1286.
    PATRICi32117840. VBIEscCol129921_1340.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X67913 Genomic DNA. Translation: CAA48112.1 .
    U00096 Genomic DNA. Translation: AAC74368.1 .
    AP009048 Genomic DNA. Translation: BAA14840.1 .
    PIRi A64877.
    RefSeqi NP_415802.1. NC_000913.3.
    YP_489554.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2ID0 X-ray 2.35 A/B/C/D 1-644 [» ]
    2IX0 X-ray 2.44 A 6-644 [» ]
    2IX1 X-ray 2.74 A 6-644 [» ]
    ProteinModelPortali P30850.
    ModBasei Search...

    Protein-protein interaction databases

    DIPi DIP-10724N.
    IntActi P30850. 10 interactions.
    MINTi MINT-1248196.
    STRINGi 511145.b1286.

    Proteomic databases

    PaxDbi P30850.
    PRIDEi P30850.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC74368 ; AAC74368 ; b1286 .
    BAA14840 ; BAA14840 ; BAA14840 .
    GeneIDi 12934347.
    945864.
    KEGGi ecj:Y75_p1261.
    eco:b1286.
    PATRICi 32117840. VBIEscCol129921_1340.

    Organism-specific databases

    EchoBASEi EB1577.
    EcoGenei EG11620. rnb.

    Phylogenomic databases

    eggNOGi COG4776.
    HOGENOMi HOG000271427.
    KOi K01147.
    OMAi EASIFTG.
    OrthoDBi EOG6Q5NRD.
    PhylomeDBi P30850.

    Enzyme and pathway databases

    BioCyci EcoCyc:EG11620-MONOMER.
    ECOL316407:JW1279-MONOMER.
    MetaCyc:EG11620-MONOMER.
    BRENDAi 3.1.13.1. 2026.

    Miscellaneous databases

    EvolutionaryTracei P30850.
    PROi P30850.

    Gene expression databases

    Genevestigatori P30850.

    Family and domain databases

    HAMAPi MF_01036. RNase_II.
    InterProi IPR011129. Cold_shock_prot.
    IPR012340. NA-bd_OB-fold.
    IPR003029. Rbsml_prot_S1_RNA-bd_dom.
    IPR022967. RNA-binding_domain_S1.
    IPR013223. RNase_B_OB_dom.
    IPR011804. RNase_II.
    IPR022966. RNase_II/R_CS.
    IPR004476. RNase_II/RNase_R.
    [Graphical view ]
    Pfami PF08206. OB_RNB. 1 hit.
    PF00575. S1. 1 hit.
    [Graphical view ]
    SMARTi SM00357. CSP. 1 hit.
    SM00316. S1. 1 hit.
    [Graphical view ]
    SUPFAMi SSF50249. SSF50249. 4 hits.
    TIGRFAMsi TIGR00358. 3_prime_RNase. 1 hit.
    TIGR02062. RNase_B. 1 hit.
    PROSITEi PS01175. RIBONUCLEASE_II. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    « Hide 'large scale' publications
    1. "DNA sequencing and expression of the gene rnb encoding Escherichia coli ribonuclease II."
      Zilhao R., Camelo L., Arraiano C.M.
      Mol. Microbiol. 8:43-51(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: K12.
    2. Zilhao R.
      Submitted (OCT-1994) to the EMBL/GenBank/DDBJ databases
      Cited for: SEQUENCE REVISION.
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    5. "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.
    6. "Purification and characterization of the Escherichia coli exoribonuclease RNase R. Comparison with RNase II."
      Cheng Z.F., Deutscher M.P.
      J. Biol. Chem. 277:21624-21629(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, COFACTOR, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES.

    Entry informationi

    Entry nameiRNB_ECOLI
    AccessioniPrimary (citable) accession number: P30850
    Secondary accession number(s): P78280
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 1, 1993
    Last sequence update: November 1, 1997
    Last modified: June 11, 2014
    This is version 131 of the entry and version 3 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

    External Data

    Dasty 3

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