B9XZG7 · RNJ_HELP8
- ProteinRibonuclease J
- Genernj
- StatusUniProtKB reviewed (Swiss-Prot)
- Amino acids691 (go to sequence)
- Protein existenceEvidence at protein level
- Annotation score5/5
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).
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
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.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Binding site | 208 | Zn2+ 1 (UniProtKB | ChEBI); catalytic | ||||
Sequence: H | ||||||
Binding site | 210 | Zn2+ 1 (UniProtKB | ChEBI); catalytic | ||||
Sequence: H | ||||||
Binding site | 212 | Zn2+ 2 (UniProtKB | ChEBI); catalytic | ||||
Sequence: D | ||||||
Binding site | 213 | Zn2+ 2 (UniProtKB | ChEBI); catalytic | ||||
Sequence: H | ||||||
Binding site | 277 | Zn2+ 1 (UniProtKB | ChEBI); catalytic | ||||
Sequence: H | ||||||
Binding site | 299 | Zn2+ 1 (UniProtKB | ChEBI); catalytic | ||||
Sequence: D | ||||||
Binding site | 299 | Zn2+ 2 (UniProtKB | ChEBI); catalytic | ||||
Sequence: D | ||||||
Binding site | 500-504 | substrate | ||||
Sequence: HVSGH | ||||||
Binding site | 526 | Zn2+ 2 (UniProtKB | ChEBI); catalytic | ||||
Sequence: H |
GO annotations
Aspect | Term | |
---|---|---|
Cellular Component | cytoplasm | |
Molecular Function | 5'-3' RNA exonuclease activity | |
Molecular Function | identical protein binding | |
Molecular Function | protein homodimerization activity | |
Molecular Function | RNA binding | |
Molecular Function | RNA endonuclease activity | |
Molecular Function | zinc ion binding | |
Biological Process | mRNA processing | |
Biological Process | protein homotetramerization | |
Biological Process | regulation of cell growth | |
Biological Process | rRNA processing |
Keywords
- Molecular function
- Biological process
- Ligand
Enzyme and pathway databases
Names & Taxonomy
Protein names
- Recommended nameRibonuclease J
- EC number
- Short namesRNase J
Gene names
Organism names
- Strain
- Taxonomic lineageBacteria > Campylobacterota > Epsilonproteobacteria > Campylobacterales > Helicobacteraceae > Helicobacter
Accessions
- Primary accessionB9XZG7
Subcellular Location
UniProt Annotation
GO Annotation
Note: The RNaseJ-RhpA complex co-localizes with 70S ribosomes and polysomes; remains associated with ribosomes in the absence of RhpA.
Keywords
- Cellular component
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.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Mutagenesis | 134 | Altered cell morphology and significant cell lysis and cellular debris. | ||||
Sequence: K → A | ||||||
Mutagenesis | 140 | Altered cell morphology, but no significant cell lysis. | ||||
Sequence: K → A | ||||||
Mutagenesis | 299 | Loss of catalytic activity. | ||||
Sequence: D → A | ||||||
Mutagenesis | 323 | No effect on cell morphology. | ||||
Sequence: K → A | ||||||
Mutagenesis | 337 | Altered cell morphology and significant cell lysis and cellular debris. | ||||
Sequence: K → A | ||||||
Mutagenesis | 397 | Coccoid cell morphology without any cells in a typical helical form. Significant cell lysis and cellular debris. | ||||
Sequence: K → A | ||||||
Mutagenesis | 511 | Altered cell morphology and significant cell lysis and cellular debris. | ||||
Sequence: K → A | ||||||
Mutagenesis | 547 | No effect on cell morphology. | ||||
Sequence: K → A | ||||||
Mutagenesis | 595 | No effect on homooligomerization. | ||||
Sequence: E → A | ||||||
Mutagenesis | 596 | No effect on homooligomerization. | ||||
Sequence: E → A | ||||||
Mutagenesis | 611 | No effect on homooligomerization. | ||||
Sequence: K → A | ||||||
Mutagenesis | 618 | Significantly decreased homooligomerization. | ||||
Sequence: E → A | ||||||
Mutagenesis | 634 | No effect on homooligomerization. Slight effect on cell morphology. | ||||
Sequence: K → A | ||||||
Mutagenesis | 649 | Loss 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. | ||||
Sequence: K → A | ||||||
Mutagenesis | 649 | Acetylated 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. | ||||
Sequence: K → Q | ||||||
Mutagenesis | 649 | Non-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. | ||||
Sequence: K → R | ||||||
Mutagenesis | 654 | Significantly decreased homooligomerization. | ||||
Sequence: E → A | ||||||
Mutagenesis | 660 | Significantly decreased homooligomerization. | ||||
Sequence: K → A | ||||||
Mutagenesis | 663 | Significantly decreased homooligomerization. | ||||
Sequence: E → A |
PTM/Processing
Features
Showing features for chain, modified residue.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Chain | PRO_0000430113 | 1-691 | Ribonuclease J | |||
Sequence: MTDNNHYENNESNENSSENSKVDEARAGAFERFTNRKKRFRENAQKNGESSHHEAPSHHKKEHRPNKKPNNHHKQKHAKTRNYAKEELDSNKVEGVTEILHVNERGTLGFHKELKKGVETNNKIQVEHLNPHYKMNLNSKASVKITPLGGLGEIGGNMMVIETPKSAIVIDAGMSFPKEGLFGVDILIPDFSYLHQIKDKIAGIIITHAHEDHIGATPYLFKELQFPLYGTPLSLGLIGSKFDEHGLKKYRSYFKIVEKRCPISVGEFIIEWIHITHSIIDSSALAIQTKAGTIIHTGDFKIDHTPVDNLPTDLYRLAHYGEKGVMLLLSDSTNSHKSGTTPSESTIAPAFDTLFKEAQGRVIMSTFSSNIHRVYQAIQYGIKYNRKIAVIGRSMEKNLDIARELGYIHLPYQSFIEANEVAKYPDNEVLIVTTGSQGETMSALYRMATDEHRHISIKPNDLVIISAKAIPGNEASVSAVLNFLIKKEAKVAYQEFDNIHVSGHAAQEEQKLMLRLIKPKFFLPVHGEYNHVARHKQTAISCGVPEKNIYLMEDGDQVEVGPAFIKKVGTIKSGKSYVDNQSNLSIDTSIVQQREEVASAGVFAATIFVNKNKQALLESSQFSSLGLVGFKDEKHLIKEIQGGLEMLLKSSNAEILNNPKKLEDHTRNFIRKALFKKFRKYPAIICHAHSF | ||||||
Modified residue | 134 | N6-acetyllysine | ||||
Sequence: K | ||||||
Modified residue | 140 | N6-acetyllysine | ||||
Sequence: K | ||||||
Modified residue | 323 | N6-acetyllysine | ||||
Sequence: K | ||||||
Modified residue | 337 | N6-acetyllysine | ||||
Sequence: K | ||||||
Modified residue | 397 | N6-acetyllysine | ||||
Sequence: K | ||||||
Modified residue | 511 | N6-acetyllysine | ||||
Sequence: K | ||||||
Modified residue | 547 | N6-acetyllysine | ||||
Sequence: K | ||||||
Modified residue | 634 | N6-acetyllysine | ||||
Sequence: K | ||||||
Modified residue | 649 | N6-acetyllysine | ||||
Sequence: K |
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
- PTM
Structure
Family & Domains
Features
Showing features for compositional bias, region.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Compositional bias | 1-16 | Polar residues | ||||
Sequence: MTDNNHYENNESNENS | ||||||
Region | 1-89 | Disordered | ||||
Sequence: MTDNNHYENNESNENSSENSKVDEARAGAFERFTNRKKRFRENAQKNGESSHHEAPSHHKKEHRPNKKPNNHHKQKHAKTRNYAKEELD | ||||||
Region | 1-132 | Loss of region decreases protein stability, still able to interact with RhpA, but has decreased RNase activity even on ssRNA | ||||
Sequence: MTDNNHYENNESNENSSENSKVDEARAGAFERFTNRKKRFRENAQKNGESSHHEAPSHHKKEHRPNKKPNNHHKQKHAKTRNYAKEELDSNKVEGVTEILHVNERGTLGFHKELKKGVETNNKIQVEHLNPH | ||||||
Compositional bias | 17-56 | Basic and acidic residues | ||||
Sequence: SENSKVDEARAGAFERFTNRKKRFRENAQKNGESSHHEAP | ||||||
Compositional bias | 57-79 | Basic residues | ||||
Sequence: SHHKKEHRPNKKPNNHHKQKHAK |
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).
The C-terminal domain is required for homooligomerization (PubMed:38057323).
Sequence similarities
Belongs to the metallo-beta-lactamase superfamily. RNA-metabolizing metallo-beta-lactamase-like family. Bacterial RNase J subfamily.
Family and domain databases
Sequence
- Sequence statusComplete
- Length691
- Mass (Da)77,608
- Last updated2009-04-14 v1
- Checksum3FDAE97031793208
Features
Showing features for compositional bias.
Type | ID | Position(s) | Description | |||
---|---|---|---|---|---|---|
Compositional bias | 1-16 | Polar residues | ||||
Sequence: MTDNNHYENNESNENS | ||||||
Compositional bias | 17-56 | Basic and acidic residues | ||||
Sequence: SENSKVDEARAGAFERFTNRKKRFRENAQKNGESSHHEAP | ||||||
Compositional bias | 57-79 | Basic residues | ||||
Sequence: SHHKKEHRPNKKPNNHHKQKHAK |
Keywords
- Technical term