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P30850

- RNB_ECOLI

UniProt

P30850 - RNB_ECOLI

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Protein

Exoribonuclease 2

Gene

rnb

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.

Cofactori

Mg2+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 substrate1 Publication

    Vmax=30 nmol/min/mg enzyme with 16S rRNA as substrate1 Publication

    Vmax=20 nmol/min/mg enzyme with 5S rRNA as substrate1 Publication

    pH dependencei

    Optimum pH is 7.5-9.5.1 Publication

    Temperature dependencei

    Optimum temperature is 50 degrees Celsius.1 Publication

    GO - Molecular functioni

    1. 3'-5' exonuclease activity Source: EcoCyc
    2. exoribonuclease II activity Source: UniProtKB-HAMAP
    3. RNA binding Source: UniProtKB-KW

    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

    GO - Cellular componenti

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

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 644644Exoribonuclease 2PRO_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

    1
    644
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi6 – 1712Combined sources
    Beta strandi21 – 277Combined sources
    Beta strandi30 – 323Combined sources
    Beta strandi34 – 374Combined sources
    Beta strandi39 – 413Combined sources
    Beta strandi43 – 464Combined sources
    Helixi48 – 514Combined sources
    Beta strandi59 – 657Combined sources
    Beta strandi68 – 703Combined sources
    Beta strandi72 – 809Combined sources
    Beta strandi84 – 9310Combined sources
    Beta strandi96 – 1038Combined sources
    Beta strandi110 – 1145Combined sources
    Beta strandi127 – 1348Combined sources
    Helixi136 – 1383Combined sources
    Beta strandi144 – 1529Combined sources
    Helixi159 – 1679Combined sources
    Beta strandi198 – 2014Combined sources
    Beta strandi210 – 2145Combined sources
    Beta strandi218 – 2203Combined sources
    Beta strandi222 – 2298Combined sources
    Helixi231 – 2333Combined sources
    Helixi240 – 2489Combined sources
    Beta strandi252 – 2543Combined sources
    Beta strandi257 – 2593Combined sources
    Helixi264 – 2674Combined sources
    Turni268 – 2703Combined sources
    Beta strandi278 – 28811Combined sources
    Beta strandi300 – 3067Combined sources
    Beta strandi310 – 3123Combined sources
    Helixi313 – 3197Combined sources
    Helixi331 – 35424Combined sources
    Beta strandi364 – 3685Combined sources
    Beta strandi374 – 3796Combined sources
    Helixi384 – 40724Combined sources
    Beta strandi413 – 4164Combined sources
    Turni421 – 4233Combined sources
    Helixi424 – 43411Combined sources
    Helixi440 – 4434Combined sources
    Helixi446 – 45712Combined sources
    Beta strandi459 – 4624Combined sources
    Helixi463 – 4686Combined sources
    Helixi469 – 4713Combined sources
    Beta strandi476 – 4805Combined sources
    Turni485 – 4884Combined sources
    Beta strandi489 – 4913Combined sources
    Turni498 – 5003Combined sources
    Helixi502 – 51413Combined sources
    Helixi527 – 55428Combined sources
    Helixi555 – 5573Combined sources
    Beta strandi564 – 5729Combined sources
    Beta strandi575 – 5806Combined sources
    Turni581 – 5833Combined sources
    Beta strandi586 – 5905Combined sources
    Helixi591 – 5933Combined sources
    Helixi598 – 6003Combined sources
    Beta strandi601 – 6044Combined sources
    Turni605 – 6084Combined sources
    Beta strandi609 – 6124Combined sources
    Beta strandi615 – 6195Combined sources
    Beta strandi623 – 63210Combined sources
    Turni633 – 6364Combined sources
    Beta strandi637 – 6426Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2ID0X-ray2.35A/B/C/D1-644[»]
    2IX0X-ray2.44A6-644[»]
    2IX1X-ray2.74A6-644[»]
    ProteinModelPortaliP30850.
    SMRiP30850. Positions 5-644.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP30850.

    Family & Domainsi

    Domains and Repeats

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

    Sequence similaritiesi

    Contains 1 S1 motif domain.Curated

    Phylogenomic databases

    eggNOGiCOG4776.
    HOGENOMiHOG000271427.
    InParanoidiP30850.
    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.
    IPR013223. RNase_B_OB_dom.
    IPR011804. RNase_II.
    IPR022966. RNase_II/R_CS.
    IPR004476. RNase_II/RNase_R.
    IPR022967. S1_dom.
    [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

            10         20         30         40         50
    MFQDNPLLAQ LKQQLHSQTP RAEGVVKATE KGFGFLEVDA QKSYFIPPPQ
    60 70 80 90 100
    MKKVMHGDRI IAVIHSEKER ESAEPEELVE PFLTRFVGKV QGKNDRLAIV
    110 120 130 140 150
    PDHPLLKDAI PCRAARGLNH EFKEGDWAVA EMRRHPLKGD RSFYAELTQY
    160 170 180 190 200
    ITFGDDHFVP WWVTLARHNL EKEAPDGVAT EMLDEGLVRE DLTALDFVTI
    210 220 230 240 250
    DSASTEDMDD ALFAKALPDD KLQLIVAIAD PTAWIAEGSK LDKAAKIRAF
    260 270 280 290 300
    TNYLPGFNIP MLPRELSDDL CSLRANEVRP VLACRMTLSA DGTIEDNIEF
    310 320 330 340 350
    FAATIESKAK LVYDQVSDWL ENTGDWQPES EAIAEQVRLL AQICQRRGEW
    360 370 380 390 400
    RHNHALVFKD RPDYRFILGE KGEVLDIVAE PRRIANRIVE EAMIAANICA
    410 420 430 440 450
    ARVLRDKLGF GIYNVHMGFD PANADALAAL LKTHGLHVDA EEVLTLDGFC
    460 470 480 490 500
    KLRRELDAQP TGFLDSRIRR FQSFAEISTE PGPHFGLGLE AYATWTSPIR
    510 520 530 540 550
    KYGDMINHRL LKAVIKGETA TRPQDEITVQ MAERRRLNRM AERDVGDWLY
    560 570 580 590 600
    ARFLKDKAGT DTRFAAEIVD ISRGGMRVRL VDNGAIAFIP APFLHAVRDE
    610 620 630 640
    LVCSQENGTV QIKGETVYKV TDVIDVTIAE VRMETRSIIA RPVA
    Length:644
    Mass (Da):72,491
    Last modified:November 1, 1997 - v3
    Checksum:i36B16712CDF14394
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti384 – 3841I → N in CAA48112. (PubMed:8497196)Curated
    Sequence conflicti399 – 3991C → G in CAA48112. (PubMed:8497196)Curated
    Sequence conflicti513 – 5131A → R in CAA48112. (PubMed:8497196)Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    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:
    EMBLi
    GenBanki
    DDBJi
    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:
    PDBei
    RCSB PDBi
    PDBji
    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.
    SMRi P30850. Positions 5-644.
    ModBasei Search...
    MobiDBi 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.
    InParanoidi P30850.
    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.
    IPR013223. RNase_B_OB_dom.
    IPR011804. RNase_II.
    IPR022966. RNase_II/R_CS.
    IPR004476. RNase_II/RNase_R.
    IPR022967. S1_dom.
    [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: November 26, 2014
    This is version 134 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