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Protein

Ribonuclease J1

Gene

rnjA

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

An RNase that has endonuclease and 5'-3' exonuclease activity, playing a role in both rRNA and mRNA stability and degradation. Endonuclease activity can cleave within 4 nucleotides of the 5'-end of a triphosphorylated RNA. Endonuclease digestion by the RNase J1/J2 complex occurs at a different site and in some cases more efficiently than J1 or J2 alone. The exonuclease activity of the J1/J2 complex is highly processive on substrates longer than 5 nucleotides, on shorter substrates is distributive. Preferentially cleaves ssRNA, possibly in AU-rich regions. The 5'-exonuclease activity acts on 5'-hydroxyl and 5'-monophosphate but not 5'-triphosphate ends; it can digest through stem-loop structures if they are not too stable. Required for maturation of 16S rRNA. Acts preferentially on 16S rRNA precursors after association of the 30S and 50S ribosomal subunits. Plays a role in the secondary pathway of 23S rRNA 5' end maturation. Probably also participates in processing of pre-scRNA (the precursor of the signal recognition particle RNA).13 Publications

Cofactori

Protein has several cofactor binding sites:

Enzyme regulationi

30S ribosomal subunit binding to Shine-Dalgarno sequences blocks exonuclease activity.1 Publication

Kineticsi

kcat is 0.58 sec (-1) for J1, 0.13 sec (-1) for J1/J2 and <0.005 sec (-1) for J2.

  1. KM=0.47 µM for exonuclease on 30 nt RNA hybridized to 17 nt quenching DNA, J1 alone1 Publication
  2. KM=0.22 µM for exonuclease on 30 nt RNA hybridized to 17 nt quenching DNA, J1/J2 complex1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi49 – 491Calcium; via carbonyl oxygen
    Metal bindingi51 – 511Calcium
    Metal bindingi74 – 741Zinc 1; via pros nitrogen; catalytic
    Metal bindingi76 – 761Zinc 1; via pros nitrogen; catalytic
    Metal bindingi78 – 781Zinc 2; catalytic
    Metal bindingi79 – 791Zinc 2; via tele nitrogen; catalytic
    Metal bindingi142 – 1421Zinc 1; via tele nitrogen; catalytic
    Metal bindingi164 – 1641Zinc 1; catalytic
    Metal bindingi164 – 1641Zinc 2; catalytic
    Active sitei195 – 1951Proton donor1 Publication
    Active sitei368 – 3681Proton acceptor1 Publication
    Metal bindingi390 – 3901Zinc 2; via tele nitrogen; catalytic
    Metal bindingi443 – 4431Calcium

    GO - Molecular functioni

    • 5'-3' exoribonuclease activity Source: UniProtKB
    • endoribonuclease activity Source: UniProtKB
    • RNA binding Source: UniProtKB-HAMAP
    • zinc ion binding Source: UniProtKB-HAMAP

    GO - Biological processi

    • mRNA processing Source: UniProtKB
    • rRNA processing Source: UniProtKB
    Complete GO annotation...

    Keywords - Molecular functioni

    Endonuclease, Exonuclease, Hydrolase, Nuclease

    Keywords - Biological processi

    mRNA processing, rRNA processing

    Keywords - Ligandi

    Calcium, Metal-binding, RNA-binding, Zinc

    Enzyme and pathway databases

    BioCyciBSUB:BSU14530-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ribonuclease J1UniRule annotation (EC:3.1.-.-UniRule annotation)
    Short name:
    RNase J1UniRule annotation
    Gene namesi
    Name:rnjAUniRule annotation
    Synonyms:ykqC
    Ordered Locus Names:BSU14530
    OrganismiBacillus subtilis (strain 168)
    Taxonomic identifieri224308 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
    Proteomesi
    • UP000001570 Componenti: Chromosome

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Disruption phenotypei

    Essential. In depletion experiments there is decreased 5'-exonuclease processing of 16S rRNA (PubMed:17512403), decreased accumulation of correctly-sized scRNA (PubMed:17576666), decreased decay of trp mRNA leader (PubMed:18445592), while correct processing of the 5' end of 23S rRNA no longer occurs in the absence of mrnC (PubMed:19880604). While depletion/deletion of RNase J1 or J2 has no large impact on global gene expression, a double mutant alters the expression of hundreds of genes (PubMed:18713320). In a more severe depletion experiment alteration of about 30% of transcripts was seen (PubMed:22412379). Later shown not to be essential in 4 strains, with a tripled doubling time. 168 trpC2 cells able to grow on minimal medium. Loss of competence for plasmid transformation, nearly complete loss of sporulation, poor growth at 30 degrees Celsius and no growth under 25 degrees Celsius. Increased sensitivity to a wide range of antibiotics. Irregularly shaped cells form clumps of spiral cells connected by long chains, with few visible septa, cell walls are altered with looser, less dense peptidoglycan. Double pnp-rnjA or rnjA-rny mutants could not be isolated (PubMed:23504012).9 Publications

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi45 – 451D → A: Slight decrease in endonuclease and 10-fold decrease in 5'-exonuclease activity; when associated with A-337. 1 Publication
    Mutagenesisi76 – 761H → A: Loss of endo- and 5'-exonuclease activity. 2 Publications
    Mutagenesisi78 – 792DH → KA: Severe loss of endo- and 5'-exonuclease activity. 1 Publication
    Mutagenesisi337 – 3371N → A: Slight decrease in endonuclease and 10-fold decrease in 5'-exonuclease activity; when associated with A-45. 1 Publication
    Mutagenesisi366 – 3661S → L: 30% endonuclease and 10% 5'-exonuclease activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 555555Ribonuclease J1PRO_0000215268Add
    BLAST

    Proteomic databases

    PaxDbiQ45493.

    Interactioni

    Subunit structurei

    Unclear whether it forms homodimers or belongs to a larger complex. According to (PubMed:20025672) probably does not form homodimers, while (PubMed:21893285) shows homodimer formation. Both reports show RNase J1 and J2 interaction, probably as a heterotetramer (PubMed:19193632) shows it is a component of a possible RNA degradosome complex composed of rny, rnjA, rnjB, pnp, pfkA and eno, while (PubMed:20025672) finds no evidence of an RNA degradosome complex.6 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    rnyO317742EBI-6415229,EBI-6415578

    Protein-protein interaction databases

    DIPiDIP-46392N.
    IntActiQ45493. 3 interactions.
    MINTiMINT-8365355.
    STRINGi224308.Bsubs1_010100008056.

    Structurei

    Secondary structure

    1
    555
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi8 – 2114Combined sources
    Beta strandi24 – 296Combined sources
    Beta strandi32 – 387Combined sources
    Beta strandi51 – 555Combined sources
    Helixi58 – 614Combined sources
    Turni62 – 665Combined sources
    Beta strandi67 – 737Combined sources
    Helixi77 – 804Combined sources
    Helixi83 – 875Combined sources
    Beta strandi94 – 963Combined sources
    Helixi98 – 11114Combined sources
    Turni113 – 1164Combined sources
    Beta strandi119 – 1213Combined sources
    Beta strandi128 – 1303Combined sources
    Beta strandi133 – 1419Combined sources
    Beta strandi143 – 15412Combined sources
    Beta strandi157 – 1615Combined sources
    Beta strandi172 – 1743Combined sources
    Helixi178 – 1869Combined sources
    Beta strandi189 – 1957Combined sources
    Turni197 – 2004Combined sources
    Helixi208 – 22114Combined sources
    Beta strandi226 – 2294Combined sources
    Helixi235 – 24612Combined sources
    Turni247 – 2493Combined sources
    Beta strandi251 – 2566Combined sources
    Helixi257 – 26711Combined sources
    Helixi268 – 2703Combined sources
    Helixi276 – 2783Combined sources
    Helixi282 – 2843Combined sources
    Turni285 – 2873Combined sources
    Helixi290 – 2923Combined sources
    Beta strandi293 – 2975Combined sources
    Helixi307 – 3126Combined sources
    Beta strandi326 – 3294Combined sources
    Helixi338 – 35013Combined sources
    Beta strandi354 – 3563Combined sources
    Beta strandi358 – 3614Combined sources
    Helixi371 – 38010Combined sources
    Beta strandi383 – 3919Combined sources
    Helixi393 – 40513Combined sources
    Helixi410 – 4123Combined sources
    Beta strandi421 – 4255Combined sources
    Beta strandi428 – 4314Combined sources
    Beta strandi439 – 4435Combined sources
    Helixi452 – 46413Combined sources
    Beta strandi466 – 4738Combined sources
    Beta strandi475 – 4773Combined sources
    Beta strandi480 – 49213Combined sources
    Helixi494 – 4974Combined sources
    Helixi500 – 51617Combined sources
    Helixi523 – 54220Combined sources
    Beta strandi547 – 5548Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3ZQ4X-ray3.00A/C/D/E1-555[»]
    ProteinModelPortaliQ45493.
    SMRiQ45493. Positions 5-554.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ45493.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni364 – 3685Substrate bindingUniRule annotation
    Regioni450 – 555106Required for endo- and 5'-exonuclease activity and dimerizationAdd
    BLAST

    Domaini

    The C-terminal domain (residues 450-555) are required for nuclease activity and dimerization.1 Publication

    Sequence similaritiesi

    Belongs to the metallo-beta-lactamase superfamily. RNA-metabolizing metallo-beta-lactamase-like family. Bacterial RNase J subfamily.UniRule annotation

    Phylogenomic databases

    eggNOGiENOG4105CN5. Bacteria.
    COG0595. LUCA.
    HOGENOMiHOG000280201.
    InParanoidiQ45493.
    KOiK12574.
    OMAiKIHTSGH.
    PhylomeDBiQ45493.

    Family and domain databases

    Gene3Di3.60.15.10. 1 hit.
    HAMAPiMF_01491. RNase_J_bact. 1 hit.
    InterProiIPR001279. Metallo-B-lactamas.
    IPR011108. RMMBL.
    IPR004613. RNase_J.
    IPR030854. RNase_J_bac.
    IPR001587. RNase_J_CS.
    [Graphical view]
    PANTHERiPTHR11203:SF22. PTHR11203:SF22. 1 hit.
    PfamiPF00753. Lactamase_B. 1 hit.
    PF07521. RMMBL. 1 hit.
    [Graphical view]
    PIRSFiPIRSF004803. RnjA. 1 hit.
    SMARTiSM00849. Lactamase_B. 1 hit.
    [Graphical view]
    SUPFAMiSSF56281. SSF56281. 1 hit.
    TIGRFAMsiTIGR00649. MG423. 1 hit.
    PROSITEiPS01292. UPF0036. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q45493-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MKFVKNDQTA VFALGGLGEI GKNTYAVQFQ DEIVLIDAGI KFPEDELLGI
    60 70 80 90 100
    DYVIPDYTYL VKNEDKIKGL FITHGHEDHI GGIPYLLRQV NIPVYGGKLA
    110 120 130 140 150
    IGLLRNKLEE HGLLRQTKLN IIGEDDIVKF RKTAVSFFRT THSIPDSYGI
    160 170 180 190 200
    VVKTPPGNIV HTGDFKFDFT PVGEPANLTK MAEIGKEGVL CLLSDSTNSE
    210 220 230 240 250
    NPEFTMSERR VGESIHDIFR KVDGRIIFAT FASNIHRLQQ VIEAAVQNGR
    260 270 280 290 300
    KVAVFGRSME SAIEIGQTLG YINCPKNTFI EHNEINRMPA NKVTILCTGS
    310 320 330 340 350
    QGEPMAALSR IANGTHRQIS INPGDTVVFS SSPIPGNTIS VSRTINQLYR
    360 370 380 390 400
    AGAEVIHGPL NDIHTSGHGG QEEQKLMLRL IKPKFFMPIH GEYRMQKMHV
    410 420 430 440 450
    KLATDCGIPE ENCFIMDNGE VLALKGDEAS VAGKIPSGSV YIDGSGIGDI
    460 470 480 490 500
    GNIVLRDRRI LSEEGLVIVV VSIDMDDFKI SAGPDLISRG FVYMRESGDL
    510 520 530 540 550
    INDAQELISN HLQKVMERKT TQWSEIKNEI TDTLAPFLYE KTKRRPMILP

    IIMEV
    Length:555
    Mass (Da):61,517
    Last modified:November 1, 1996 - v1
    Checksum:i48091B448B8431C9
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AF012285 Genomic DNA. Translation: AAC24928.1.
    AL009126 Genomic DNA. Translation: CAB13326.1.
    PIRiB69862.
    RefSeqiNP_389336.1. NC_000964.3.
    WP_003245660.1. NZ_JNCM01000035.1.

    Genome annotation databases

    EnsemblBacteriaiCAB13326; CAB13326; BSU14530.
    GeneIDi939483.
    KEGGibsu:BSU14530.
    PATRICi18974695. VBIBacSub10457_1539.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AF012285 Genomic DNA. Translation: AAC24928.1.
    AL009126 Genomic DNA. Translation: CAB13326.1.
    PIRiB69862.
    RefSeqiNP_389336.1. NC_000964.3.
    WP_003245660.1. NZ_JNCM01000035.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3ZQ4X-ray3.00A/C/D/E1-555[»]
    ProteinModelPortaliQ45493.
    SMRiQ45493. Positions 5-554.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    DIPiDIP-46392N.
    IntActiQ45493. 3 interactions.
    MINTiMINT-8365355.
    STRINGi224308.Bsubs1_010100008056.

    Proteomic databases

    PaxDbiQ45493.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiCAB13326; CAB13326; BSU14530.
    GeneIDi939483.
    KEGGibsu:BSU14530.
    PATRICi18974695. VBIBacSub10457_1539.

    Phylogenomic databases

    eggNOGiENOG4105CN5. Bacteria.
    COG0595. LUCA.
    HOGENOMiHOG000280201.
    InParanoidiQ45493.
    KOiK12574.
    OMAiKIHTSGH.
    PhylomeDBiQ45493.

    Enzyme and pathway databases

    BioCyciBSUB:BSU14530-MONOMER.

    Miscellaneous databases

    EvolutionaryTraceiQ45493.

    Family and domain databases

    Gene3Di3.60.15.10. 1 hit.
    HAMAPiMF_01491. RNase_J_bact. 1 hit.
    InterProiIPR001279. Metallo-B-lactamas.
    IPR011108. RMMBL.
    IPR004613. RNase_J.
    IPR030854. RNase_J_bac.
    IPR001587. RNase_J_CS.
    [Graphical view]
    PANTHERiPTHR11203:SF22. PTHR11203:SF22. 1 hit.
    PfamiPF00753. Lactamase_B. 1 hit.
    PF07521. RMMBL. 1 hit.
    [Graphical view]
    PIRSFiPIRSF004803. RnjA. 1 hit.
    SMARTiSM00849. Lactamase_B. 1 hit.
    [Graphical view]
    SUPFAMiSSF56281. SSF56281. 1 hit.
    TIGRFAMsiTIGR00649. MG423. 1 hit.
    PROSITEiPS01292. UPF0036. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiRNJ1_BACSU
    AccessioniPrimary (citable) accession number: Q45493
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1997
    Last sequence update: November 1, 1996
    Last modified: September 7, 2016
    This is version 110 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Present in about 2500 monomers per cell in mid-log phase.

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Bacillus subtilis
      Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
    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

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.