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Entry version 115 (07 Apr 2021)
Sequence version 3 (16 Jun 2009)
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Protein

Ribonuclease J2

Gene

rnjB

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score:

Annotation score:5 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

Endonucleolytically cleaves the 5'-leader sequence of certain mRNAs. 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. Plays a role in mRNA maturation and stability. Appears to have a limited effect on 16S rRNA maturation, despite its similarity to RNase J1. This subunit alone has very poor 5'-3' exonuclease activity.6 Publications

Miscellaneous

Present in about 3000 monomers per cell in mid-log phase.

<p>This subsection of the 'Function' section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

Zn2+By similarity2 PublicationsNote: Binds 1 zinc ion per subunit. The inability to bind a second zinc ion may explain its very poor exonuclease activity (PubMed:21893285).By similarity2 Publications

<p>This subsection of the 'Function' section describes biophysical and chemical properties, such as maximal absorption, kinetic parameters, pH dependence, redox potentials and temperature dependence.<p><a href='/help/biophysicochemical_properties' target='_top'>More...</a></p>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=5.96 µM for exonuclease on 30 nt RNA hybridized to 17 nt quenching DNA, J2 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)DescriptionActionsGraphical viewLength
    <p>This subsection of the <a href="http://www.uniprot.org/help/function%5Fsection">Function</a> section indicates at which position the protein binds a given metal ion. The nature of the metal is indicated in the 'Description' field.<p><a href='/help/metal' target='_top'>More...</a></p>Metal bindingi74Zinc; catalyticUniRule annotation1
    Metal bindingi76Zinc; catalyticUniRule annotation1
    Metal bindingi142Zinc; catalyticUniRule annotation1
    Metal bindingi164Zinc; catalyticUniRule annotation1

    <p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

    GO - Biological processi

    <p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

    Molecular functionEndonuclease, Exonuclease, Hydrolase, Nuclease, RNA-binding
    Biological processrRNA processing
    LigandMetal-binding, Zinc

    Enzyme and pathway databases

    BioCyc Collection of Pathway/Genome Databases

    More...
    BioCyci
    BSUB:BSU16780-MONOMER

    <p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
    Recommended name:
    Ribonuclease J2UniRule annotation (EC:3.1.-.-UniRule annotation)
    Short name:
    RNase J2UniRule annotation
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
    Name:rnjBUniRule annotation
    Synonyms:ymfA
    Ordered Locus Names:BSU16780
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiBacillus subtilis (strain 168)
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri224308 [NCBI]
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
    <p>This subsection of the <a href="http://www.uniprot.org/help/names%5Fand%5Ftaxonomy%5Fsection">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
    • UP000001570 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes%5Fmanual">proteome</a> can consist of several components.<br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome

    <p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

    Keywords - Cellular componenti

    Cytoplasm

    <p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

    <p>This subsection of the 'Pathology and Biotech' section describes the in vivo effects caused by ablation of the gene (or one or more transcripts) coding for the protein described in the entry. This includes gene knockout and knockdown, provided experiments have been performed in the context of a whole organism or a specific tissue, and not at the single-cell level.<p><a href='/help/disruption_phenotype' target='_top'>More...</a></p>Disruption phenotypei

    Not essential. 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).3 Publications

    <p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the 'PTM / Processing' section describes the extent of a polypeptide chain in the mature protein following processing or proteolytic cleavage.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00002868331 – 555Ribonuclease J2Add BLAST555

    Proteomic databases

    jPOST - Japan Proteome Standard Repository/Database

    More...
    jPOSTi
    O31760

    PaxDb, a database of protein abundance averages across all three domains of life

    More...
    PaxDbi
    O31760

    PRoteomics IDEntifications database

    More...
    PRIDEi
    O31760

    <p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

    <p>This subsection of the <a href="http://www.uniprot.org/help/interaction%5Fsection">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function%5Fsection">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>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.

    5 Publications

    <p>This subsection of the '<a href="http://www.uniprot.org/help/interaction%5Fsection">Interaction</a>' section provides information about binary protein-protein interactions. The data presented in this section are a quality-filtered subset of binary interactions automatically derived from the <a href="https://www.ebi.ac.uk/intact/">IntAct database</a>. It is updated at every <a href="http://www.uniprot.org/help/synchronization">UniProt release</a>.<p><a href='/help/binary_interactions' target='_top'>More...</a></p>Binary interactionsi

    Protein-protein interaction databases

    Database of interacting proteins

    More...
    DIPi
    DIP-59141N

    Protein interaction database and analysis system

    More...
    IntActi
    O31760, 4 interactors

    Molecular INTeraction database

    More...
    MINTi
    O31760

    STRING: functional protein association networks

    More...
    STRINGi
    224308.BSU16780

    <p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

    3D structure databases

    SWISS-MODEL Repository - a database of annotated 3D protein structure models

    More...
    SMRi
    O31760

    Database of comparative protein structure models

    More...
    ModBasei
    Search...

    <p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    <p>This subsection of the 'Family and Domains' section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni364 – 368Substrate bindingUniRule annotation5

    <p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

    Phylogenomic databases

    evolutionary genealogy of genes: Non-supervised Orthologous Groups

    More...
    eggNOGi
    COG0595, Bacteria

    InParanoid: Eukaryotic Ortholog Groups

    More...
    InParanoidi
    O31760

    Identification of Orthologs from Complete Genome Data

    More...
    OMAi
    DFKMDQF

    Database for complete collections of gene phylogenies

    More...
    PhylomeDBi
    O31760

    Family and domain databases

    Gene3D Structural and Functional Annotation of Protein Families

    More...
    Gene3Di
    3.40.50.10710, 1 hit
    3.60.15.10, 1 hit

    HAMAP database of protein families

    More...
    HAMAPi
    MF_01491, RNase_J_bact, 1 hit

    Integrated resource of protein families, domains and functional sites

    More...
    InterProi
    View protein in InterPro
    IPR001279, Metallo-B-lactamas
    IPR036866, RibonucZ/Hydroxyglut_hydro
    IPR011108, RMMBL
    IPR004613, RNase_J
    IPR042173, RNase_J_2
    IPR030854, RNase_J_bac
    IPR041636, RNase_J_C

    Pfam protein domain database

    More...
    Pfami
    View protein in Pfam
    PF00753, Lactamase_B, 1 hit
    PF07521, RMMBL, 1 hit
    PF17770, RNase_J_C, 1 hit

    PIRSF; a whole-protein classification database

    More...
    PIRSFi
    PIRSF004803, RnjA, 1 hit

    Simple Modular Architecture Research Tool; a protein domain database

    More...
    SMARTi
    View protein in SMART
    SM00849, Lactamase_B, 1 hit

    Superfamily database of structural and functional annotation

    More...
    SUPFAMi
    SSF56281, SSF56281, 1 hit

    TIGRFAMs; a protein family database

    More...
    TIGRFAMsi
    TIGR00649, MG423, 1 hit

    <p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence%5Flength">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

    <p>This subsection of the <a href="http://www.uniprot.org/help/sequences%5Fsection">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

    O31760-1 [UniParc]FASTAAdd to basket
    « Hide
            10         20         30         40         50
    MKKKNTENVR IIALGGVGEI GKNLYVIEID SDIFVVDAGL MHPENEMLGI
    60 70 80 90 100
    DVVIPDISYL IERADRVKAI FLTHGHDENI GGVFYLLNKL SVPVYGTKLT
    110 120 130 140 150
    LALLREKLKQ YGHNRKTDLR EIHSKSVITF ESTKVSFFRT IHSIPDSVGV
    160 170 180 190 200
    SFKTSLGSIV CTGDFKFDQT PALNQTCDIG EIAKIGNSGV LALLSDSANA
    210 220 230 240 250
    ERPGYTPSEA AVSGEISDAL YNSQNRVIIA VFASNINRIQ QVIHAAAQNG
    260 270 280 290 300
    RKIAVAGKNL QSVLQLARKL GYIEADDELF ISVQDVKKYP KREVAIITAG
    310 320 330 340 350
    SQGEPLAALT RMANKAHKQL NIEEGDTVVI ASTPIPGQEL IYSKTVDLLA
    360 370 380 390 400
    RAGAQVIFAQ KRVHVSGHGS QEELKLMINL LKPKYLIPVN GEYRMQKAHS
    410 420 430 440 450
    KIAEETGMKR SDIFLIEKGD VVEFRGQNVK IGDKVPYGNI LIDGLGVGDI
    460 470 480 490 500
    GNIVLRDRRL LSQDGILIVV ITLDKQKKHL VSGPEIITRG FVYVRESEGL
    510 520 530 540 550
    IVQATELVRS IVTEATETSN VEWSTLKQAM RDALNQFLYE KTKRKPMIIP

    IIMEV
    Length:555
    Mass (Da):61,175
    Last modified:June 16, 2009 - v3
    <p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i8EA92EE42D51F282
    GO

    Sequence databases

    Select the link destinations:

    EMBL nucleotide sequence database

    More...
    EMBLi

    GenBank nucleotide sequence database

    More...
    GenBanki

    DNA Data Bank of Japan; a nucleotide sequence database

    More...
    DDBJi
    Links Updated
    AL009126 Genomic DNA Translation: CAB13551.2

    Protein sequence database of the Protein Information Resource

    More...
    PIRi
    H69884

    NCBI Reference Sequences

    More...
    RefSeqi
    NP_389560.2, NC_000964.3
    WP_003231875.1, NZ_JNCM01000035.1

    Genome annotation databases

    Ensembl bacterial and archaeal genome annotation project

    More...
    EnsemblBacteriai
    CAB13551; CAB13551; BSU_16780

    Database of genes from NCBI RefSeq genomes

    More...
    GeneIDi
    938463

    KEGG: Kyoto Encyclopedia of Genes and Genomes

    More...
    KEGGi
    bsu:BSU16780

    Pathosystems Resource Integration Center (PATRIC)

    More...
    PATRICi
    fig|224308.179.peg.1820

    <p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

    <p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AL009126 Genomic DNA Translation: CAB13551.2
    PIRiH69884
    RefSeqiNP_389560.2, NC_000964.3
    WP_003231875.1, NZ_JNCM01000035.1

    3D structure databases

    SMRiO31760
    ModBaseiSearch...

    Protein-protein interaction databases

    DIPiDIP-59141N
    IntActiO31760, 4 interactors
    MINTiO31760
    STRINGi224308.BSU16780

    Proteomic databases

    jPOSTiO31760
    PaxDbiO31760
    PRIDEiO31760

    Genome annotation databases

    EnsemblBacteriaiCAB13551; CAB13551; BSU_16780
    GeneIDi938463
    KEGGibsu:BSU16780
    PATRICifig|224308.179.peg.1820

    Phylogenomic databases

    eggNOGiCOG0595, Bacteria
    InParanoidiO31760
    OMAiDFKMDQF
    PhylomeDBiO31760

    Enzyme and pathway databases

    BioCyciBSUB:BSU16780-MONOMER

    Family and domain databases

    Gene3Di3.40.50.10710, 1 hit
    3.60.15.10, 1 hit
    HAMAPiMF_01491, RNase_J_bact, 1 hit
    InterProiView protein in InterPro
    IPR001279, Metallo-B-lactamas
    IPR036866, RibonucZ/Hydroxyglut_hydro
    IPR011108, RMMBL
    IPR004613, RNase_J
    IPR042173, RNase_J_2
    IPR030854, RNase_J_bac
    IPR041636, RNase_J_C
    PfamiView protein in Pfam
    PF00753, Lactamase_B, 1 hit
    PF07521, RMMBL, 1 hit
    PF17770, RNase_J_C, 1 hit
    PIRSFiPIRSF004803, RnjA, 1 hit
    SMARTiView protein in SMART
    SM00849, Lactamase_B, 1 hit
    SUPFAMiSSF56281, SSF56281, 1 hit
    TIGRFAMsiTIGR00649, MG423, 1 hit

    ProtoNet; Automatic hierarchical classification of proteins

    More...
    ProtoNeti
    Search...

    MobiDB: a database of protein disorder and mobility annotations

    More...
    MobiDBi
    Search...

    <p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

    <p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiRNJ2_BACSU
    <p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: O31760
    <p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical%5Fand%5Fisoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 15, 2007
    Last sequence update: June 16, 2009
    Last modified: April 7, 2021
    This is version 115 of the entry and version 3 of the sequence. See complete history.
    <p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    <p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

    Keywords - Technical termi

    Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families
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