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Protein

Exoribonuclease 2

Gene

rnb

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

Functioni

Involved in mRNA degradation. Hydrolyzes single-stranded polyribonucleotides processively in the 3' to 5' direction (PubMed:11948193). RNases 2 and R (rnr) contribute to rRNA degradation during starvation, while RNase R and PNPase (pnp) are the major contributors to quality control of rRNA during steady state growth (PubMed:21135037). This RNase is required to decrease expression of RNase PH (rnp) at 42 degrees Celsius during starvation, which in turn represses rRNA degradation (PubMed:28625967).3 Publications

Miscellaneous

In K12 strains that are derived from W1485 (including MG1655 and W3110) the rph gene has a frameshift that leads to loss of its ribonuclease PH activity. In strain K12 / MG1655(Seq)* the wild-type Rph protein has been restored (PubMed:28625967).1 Publication

Catalytic activityi

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

Cofactori

Mg2+1 Publication

Activity regulationi

Stimulated by the presence of a monovalent cation (PubMed:11948193).1 Publication

Kineticsi

    1. Vmax=109800 nmol/min/mg enzyme with Poly(A) as substrate1 Publication
    2. Vmax=160 nmol/min/mg enzyme with 23S rRNA as substrate1 Publication
    3. Vmax=30 nmol/min/mg enzyme with 16S rRNA as substrate1 Publication
    4. 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

    • 3'-5' exonuclease activity Source: EcoCyc
    • exoribonuclease II activity Source: UniProtKB-UniRule
    • RNA binding Source: UniProtKB-KW

    GO - Biological processi

    Keywordsi

    Molecular functionExonuclease, Hydrolase, Nuclease, RNA-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:EG11620-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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG11620 rnb

    Subcellular locationi

    GO - Cellular componenti

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Disruption phenotypei

    In the presence of wild-type RNase PH (rph) 80-90% reduction in viability in stationary phase (96 hours of growth) at 31 and 42 degrees Celsius or when cells are rapidly starved at 42 degrees Celsius; if rph is also absent there is no visible phenotype under these 3 growth conditions (PubMed:28625967). Its absence leads to extensive degradation of rRNA (PubMed:28625967).1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001663801 – 644Exoribonuclease 2Add BLAST644

    Proteomic databases

    PaxDbiP30850
    PRIDEiP30850

    Interactioni

    Binary interactionsi

    Protein-protein interaction databases

    BioGridi4263341, 45 interactors
    DIPiDIP-10724N
    IntActiP30850, 10 interactors
    STRINGi316385.ECDH10B_1403

    Structurei

    Secondary structure

    1644
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details

    3D structure databases

    ProteinModelPortaliP30850
    SMRiP30850
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP30850

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini561 – 643S1 motifAdd BLAST83

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiENOG4108IEC Bacteria
    COG4776 LUCA
    HOGENOMiHOG000271427
    InParanoidiP30850
    KOiK01147
    OMAiCFTNYLP
    PhylomeDBiP30850

    Family and domain databases

    HAMAPiMF_01036 RNase_II, 1 hit
    InterProiView protein in InterPro
    IPR011129 CSD
    IPR012340 NA-bd_OB-fold
    IPR013223 RNase_B_OB_dom
    IPR011804 RNase_II
    IPR022966 RNase_II/R_CS
    IPR004476 RNase_II/RNase_R
    IPR003029 S1_domain
    PfamiView protein in Pfam
    PF08206 OB_RNB, 1 hit
    PF00575 S1, 1 hit
    SMARTiView protein in SMART
    SM00357 CSP, 1 hit
    SUPFAMiSSF50249 SSF50249, 4 hits
    TIGRFAMsiTIGR00358 3_prime_RNase, 1 hit
    TIGR02062 RNase_B, 1 hit
    PROSITEiView protein in PROSITE
    PS01175 RIBONUCLEASE_II, 1 hit

    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)DescriptionActionsGraphical viewLength
    Sequence conflicti384I → N in CAA48112 (PubMed:8497196).Curated1
    Sequence conflicti399C → G in CAA48112 (PubMed:8497196).Curated1
    Sequence conflicti513A → R in CAA48112 (PubMed:8497196).Curated1

    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
    WP_000484984.1, NZ_LN832404.1

    Genome annotation databases

    EnsemblBacteriaiAAC74368; AAC74368; b1286
    BAA14840; BAA14840; BAA14840
    GeneIDi945864
    KEGGiecj:JW1279
    eco:b1286
    PATRICifig|1411691.4.peg.993

    Similar proteinsi

    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
    PIRiA64877
    RefSeqiNP_415802.1, NC_000913.3
    WP_000484984.1, NZ_LN832404.1

    3D structure databases

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

    Protein-protein interaction databases

    BioGridi4263341, 45 interactors
    DIPiDIP-10724N
    IntActiP30850, 10 interactors
    STRINGi316385.ECDH10B_1403

    Proteomic databases

    PaxDbiP30850
    PRIDEiP30850

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC74368; AAC74368; b1286
    BAA14840; BAA14840; BAA14840
    GeneIDi945864
    KEGGiecj:JW1279
    eco:b1286
    PATRICifig|1411691.4.peg.993

    Organism-specific databases

    EchoBASEiEB1577
    EcoGeneiEG11620 rnb

    Phylogenomic databases

    eggNOGiENOG4108IEC Bacteria
    COG4776 LUCA
    HOGENOMiHOG000271427
    InParanoidiP30850
    KOiK01147
    OMAiCFTNYLP
    PhylomeDBiP30850

    Enzyme and pathway databases

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

    Miscellaneous databases

    EvolutionaryTraceiP30850
    PROiPR:P30850

    Family and domain databases

    HAMAPiMF_01036 RNase_II, 1 hit
    InterProiView protein in InterPro
    IPR011129 CSD
    IPR012340 NA-bd_OB-fold
    IPR013223 RNase_B_OB_dom
    IPR011804 RNase_II
    IPR022966 RNase_II/R_CS
    IPR004476 RNase_II/RNase_R
    IPR003029 S1_domain
    PfamiView protein in Pfam
    PF08206 OB_RNB, 1 hit
    PF00575 S1, 1 hit
    SMARTiView protein in SMART
    SM00357 CSP, 1 hit
    SUPFAMiSSF50249 SSF50249, 4 hits
    TIGRFAMsiTIGR00358 3_prime_RNase, 1 hit
    TIGR02062 RNase_B, 1 hit
    PROSITEiView protein in PROSITE
    PS01175 RIBONUCLEASE_II, 1 hit
    ProtoNetiSearch...

    Entry informationi

    Entry nameiRNB_ECOLI
    AccessioniPrimary (citable) accession number: P30850
    Secondary accession number(s): P78280
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 1, 1993
    Last sequence update: November 1, 1997
    Last modified: October 10, 2018
    This is version 163 of the entry and version 3 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

    Documents

    1. SIMILARITY comments
      Index of protein domains and families
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
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