B9XZG7 · RNJ_HELP8

Function

function

An RNase that has 5'-3' exoribonuclease and endoribonuclease activity (PubMed:23093592, PubMed:38057323).
Degrades 5'-monophosphorylated ssRNA and dsRNA, considerably more active on ssRNA (PubMed:23093592).
Association with RhpA significantly increases the dsRNase activity (PubMed:23093592).
Degrades RNA substrate with hairpin structures at both ends with low activity, but presence of RhpA significantly increases the activity on this substrate (PubMed:38057323).
Stimulates ATPase activity of RNA helicase RhpA (PubMed:23093592).
Involved in stabilization of mRNA but apparently not rRNA (PubMed:23093592).

Cofactor

Zn2+ (UniProtKB | Rhea| CHEBI:29105 )

Note: Binds up to 2 Zn2+ ions per subunit. It is not clear if Zn2+ or Mg2+ is physiologically important.

Activity regulation

Catalytic activity is regulated by the balance between homodimers and homotetramers, with homotetramers being the active forms of this enzyme. Acetylation allosterically regulates the homooligomerization state and hence the catalytic activity.

Features

Showing features for binding site.

TypeIDPosition(s)Description
Binding site208Zn2+ 1 (UniProtKB | ChEBI); catalytic
Binding site210Zn2+ 1 (UniProtKB | ChEBI); catalytic
Binding site212Zn2+ 2 (UniProtKB | ChEBI); catalytic
Binding site213Zn2+ 2 (UniProtKB | ChEBI); catalytic
Binding site277Zn2+ 1 (UniProtKB | ChEBI); catalytic
Binding site299Zn2+ 1 (UniProtKB | ChEBI); catalytic
Binding site299Zn2+ 2 (UniProtKB | ChEBI); catalytic
Binding site500-504substrate
Binding site526Zn2+ 2 (UniProtKB | ChEBI); catalytic

GO annotations

AspectTerm
Cellular Componentcytoplasm
Molecular Function5'-3' RNA exonuclease activity
Molecular Functionidentical protein binding
Molecular Functionprotein homodimerization activity
Molecular FunctionRNA binding
Molecular FunctionRNA endonuclease activity
Molecular Functionzinc ion binding
Biological ProcessmRNA processing
Biological Processprotein homotetramerization
Biological Processregulation of cell growth
Biological ProcessrRNA processing

Keywords

Enzyme and pathway databases

Names & Taxonomy

Protein names

  • Recommended name
    Ribonuclease J
  • EC number
  • Short names
    RNase J

Gene names

    • Name
      rnj
    • ORF names
      HPB128_16g80

Organism names

Accessions

  • Primary accession
    B9XZG7

Subcellular Location

Cytoplasm
Note: The RNaseJ-RhpA complex co-localizes with 70S ribosomes and polysomes; remains associated with ribosomes in the absence of RhpA.

Keywords

Phenotypes & Variants

Disruption phenotype

Essential, it cannot be disrupted. Depletion experiments show only slightly retarded growth with an increase in levels of at least 1 mRNA (ureI). RhpA remains associated with the ribosomes and polysomes.

Features

Showing features for mutagenesis.

TypeIDPosition(s)Description
Mutagenesis134Altered cell morphology and significant cell lysis and cellular debris.
Mutagenesis140Altered cell morphology, but no significant cell lysis.
Mutagenesis299Loss of catalytic activity.
Mutagenesis323No effect on cell morphology.
Mutagenesis337Altered cell morphology and significant cell lysis and cellular debris.
Mutagenesis397Coccoid cell morphology without any cells in a typical helical form. Significant cell lysis and cellular debris.
Mutagenesis511Altered cell morphology and significant cell lysis and cellular debris.
Mutagenesis547No effect on cell morphology.
Mutagenesis595No effect on homooligomerization.
Mutagenesis596No effect on homooligomerization.
Mutagenesis611No effect on homooligomerization.
Mutagenesis618Significantly decreased homooligomerization.
Mutagenesis634No effect on homooligomerization. Slight effect on cell morphology.
Mutagenesis649Loss of acetylation and positive charge. Loss of homodimerization. Exists solely as a homotetramer in vitro. No effect on protein folding as secondary structures remain as in wild-type. Significantly increased exoribonuclease activity. No effect on endoribonuclease activity on RNA substrate with hairpin structures at both ends in the presence or absence of RhpA. No effect on cell morphology.
Mutagenesis649Acetylated mimic with no positive charge. Has a significant increase in homotetramerization over homodimerization compared to wild-type. Decreased exoribonuclease activity. Significantly decreased endoribonuclease activity on RNA substrate with hairpin structures at both ends in the presence or absence of RhpA.
Mutagenesis649Non-acetylated mimic with a positive charge. No effect on homooligomerization as forms both homodimers and homotetramers as wild-type. Significantly decreased exoribonuclease activity. Has significant endoribonuclease activity on RNA substrate with hairpin structures at both ends in the presence of RhpA, but not in its absence.
Mutagenesis654Significantly decreased homooligomerization.
Mutagenesis660Significantly decreased homooligomerization.
Mutagenesis663Significantly decreased homooligomerization.

PTM/Processing

Features

Showing features for chain, modified residue.

TypeIDPosition(s)Description
ChainPRO_00004301131-691Ribonuclease J
Modified residue134N6-acetyllysine
Modified residue140N6-acetyllysine
Modified residue323N6-acetyllysine
Modified residue337N6-acetyllysine
Modified residue397N6-acetyllysine
Modified residue511N6-acetyllysine
Modified residue547N6-acetyllysine
Modified residue634N6-acetyllysine
Modified residue649N6-acetyllysine

Post-translational modification

Acetylated on nine lysine residues. Some of the residues are acetylated by multiple different mechanisms. RimL is partially responsible for the acetylation of Lys-323, Lys-397 and Lys-649. HPB8_1270 homolog is partially responsible for the acetylation of Lys-323, Lys-397, Lys-511 and Lys-649. Acetyl-phosphate-mediated non-enzymatic acetylation pathway takes part in the acetylation of Lys-134, Lys-323, Lys-397, Lys-511 and Lys-649. Acetylation of the remaining residues Lys-140, Lys-337, Lys-547 and Lys-634 occurs by a yet undetermined mechanism. Acetylation on a number of these residues is important for growth regulation and proper cell morphology.

Keywords

Interaction

Subunit

Homodimer (PubMed:38057323).
Homotetramer; dimer of homodimers (PubMed:38057323).
Interacts with RNA helicase RphA, might be a member of a minimal RNA degradosome complex (PubMed:23093592).

Family & Domains

Features

Showing features for compositional bias, region.

TypeIDPosition(s)Description
Compositional bias1-16Polar residues
Region1-89Disordered
Region1-132Loss of region decreases protein stability, still able to interact with RhpA, but has decreased RNase activity even on ssRNA
Compositional bias17-56Basic and acidic residues
Compositional bias57-79Basic residues

Domain

The first 132 residues are not conserved outside of Helicobacter. Important for protein stability; a depletion mutant expressing this truncated protein accumulates more ureI mRNA than a depletion mutant able to express low levels of wild-type protein. The truncated protein still stimulates ATPase activity of RNA helicase RhpA (PubMed:23093592).
The C-terminal domain is required for homooligomerization (PubMed:38057323).

Sequence similarities

Family and domain databases

Sequence

  • Sequence status
    Complete
  • Length
    691
  • Mass (Da)
    77,608
  • Last updated
    2009-04-14 v1
  • Checksum
    3FDAE97031793208
MTDNNHYENNESNENSSENSKVDEARAGAFERFTNRKKRFRENAQKNGESSHHEAPSHHKKEHRPNKKPNNHHKQKHAKTRNYAKEELDSNKVEGVTEILHVNERGTLGFHKELKKGVETNNKIQVEHLNPHYKMNLNSKASVKITPLGGLGEIGGNMMVIETPKSAIVIDAGMSFPKEGLFGVDILIPDFSYLHQIKDKIAGIIITHAHEDHIGATPYLFKELQFPLYGTPLSLGLIGSKFDEHGLKKYRSYFKIVEKRCPISVGEFIIEWIHITHSIIDSSALAIQTKAGTIIHTGDFKIDHTPVDNLPTDLYRLAHYGEKGVMLLLSDSTNSHKSGTTPSESTIAPAFDTLFKEAQGRVIMSTFSSNIHRVYQAIQYGIKYNRKIAVIGRSMEKNLDIARELGYIHLPYQSFIEANEVAKYPDNEVLIVTTGSQGETMSALYRMATDEHRHISIKPNDLVIISAKAIPGNEASVSAVLNFLIKKEAKVAYQEFDNIHVSGHAAQEEQKLMLRLIKPKFFLPVHGEYNHVARHKQTAISCGVPEKNIYLMEDGDQVEVGPAFIKKVGTIKSGKSYVDNQSNLSIDTSIVQQREEVASAGVFAATIFVNKNKQALLESSQFSSLGLVGFKDEKHLIKEIQGGLEMLLKSSNAEILNNPKKLEDHTRNFIRKALFKKFRKYPAIICHAHSF

Features

Showing features for compositional bias.

TypeIDPosition(s)Description
Compositional bias1-16Polar residues
Compositional bias17-56Basic and acidic residues
Compositional bias57-79Basic residues

Keywords

Sequence databases

Nucleotide SequenceProtein SequenceMolecule TypeStatus
ABSY01000006
EMBL· GenBank· DDBJ
EEC24876.1
EMBL· GenBank· DDBJ
Genomic DNA

Similar Proteins

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