RNJ_HELP8
ID RNJ_HELP8 Reviewed; 691 AA.
AC B9XZG7;
DT 03-SEP-2014, integrated into UniProtKB/Swiss-Prot.
DT 14-APR-2009, sequence version 1.
DT 03-AUG-2022, entry version 42.
DE RecName: Full=Ribonuclease J {ECO:0000255|HAMAP-Rule:MF_01491};
DE EC=3.1.-.- {ECO:0000255|HAMAP-Rule:MF_01491};
GN Name=rnaJ; ORFNames=HPB128_16g80;
OS Helicobacter pylori (strain B128).
OC Bacteria; Proteobacteria; Epsilonproteobacteria; Campylobacterales;
OC Helicobacteraceae; Helicobacter.
OX NCBI_TaxID=544406;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=B128;
RX PubMed=19123947; DOI=10.1186/1471-2164-10-3;
RA McClain M.S., Shaffer C.L., Israel D.A., Peek R.M. Jr., Cover T.L.;
RT "Genome sequence analysis of Helicobacter pylori strains associated with
RT gastric ulceration and gastric cancer.";
RL BMC Genomics 10:3-3(2009).
RN [2]
RP FUNCTION AS AN RNASE, INTERACTION WITH RHPA, SUBUNIT, SUBCELLULAR LOCATION,
RP DOMAIN, AND DISRUPTION PHENOTYPE.
RC STRAIN=B128;
RX PubMed=23093592; DOI=10.1093/nar/gks945;
RA Redko Y., Aubert S., Stachowicz A., Lenormand P., Namane A., Darfeuille F.,
RA Thibonnier M., De Reuse H.;
RT "A minimal bacterial RNase J-based degradosome is associated with
RT translating ribosomes.";
RL Nucleic Acids Res. 41:288-301(2013).
CC -!- FUNCTION: An RNase that has 5'-3' exonuclease and possibly
CC endoonuclease activity. Degrades 5'-monophosphorylated ssRNA and dsRNA,
CC considerably more active on ssRNA. Association with RhpA significantly
CC increases the dsRNase activity. Stimulates ATPase activity of RNA
CC helicase RhpA. Involved in stabilization of mRNA but apparently not
CC rRNA. {ECO:0000269|PubMed:23093592}.
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01491};
CC Note=Binds up to 2 Zn(2+) ions per subunit. It is not clear if Zn(2+)
CC or Mg(2+) is physiologically important. {ECO:0000255|HAMAP-
CC Rule:MF_01491};
CC -!- SUBUNIT: Homodimer (By similarity). Interacts with RNA helicase RphA,
CC might be a member of a minimal RNA degradosome complex. {ECO:0000250,
CC ECO:0000269|PubMed:23093592}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_01491,
CC ECO:0000269|PubMed:23093592}. Note=The RNaseJ-RhpA complex co-localizes
CC with 70S ribosomes and polysomes; remains associated with ribosomes in
CC the absence of RhpA.
CC -!- DOMAIN: The first 132 residues are not conserved outside of
CC Helicobacter. Important for protein stability; a depletion mutant
CC expressing this truncated protein accumulates more ureI mRNA than a
CC depletion mutant able to express low levels of wild-type protein. The
CC trunated protein still stimulates ATPase activity of RNA helicase RhpA.
CC {ECO:0000269|PubMed:23093592}.
CC -!- DISRUPTION PHENOTYPE: Essential, it cannot be disrupted. Depletion
CC experiments show only slightly retarded growth with an increase in
CC levels of at least 1 mRNA (ureI). RhpA remains associated with the
CC ribosomes and polysomes. {ECO:0000269|PubMed:23093592}.
CC -!- SIMILARITY: Belongs to the metallo-beta-lactamase superfamily. RNA-
CC metabolizing metallo-beta-lactamase-like family. Bacterial RNase J
CC subfamily. {ECO:0000255|HAMAP-Rule:MF_01491}.
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DR EMBL; ABSY01000006; EEC24876.1; -; Genomic_DNA.
DR RefSeq; WP_000131608.1; NZ_CP024951.1.
DR AlphaFoldDB; B9XZG7; -.
DR SMR; B9XZG7; -.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0004534; F:5'-3' exoribonuclease activity; IEA:UniProtKB-UniRule.
DR GO; GO:0004521; F:endoribonuclease activity; IEA:UniProtKB-UniRule.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-UniRule.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0006397; P:mRNA processing; IEA:UniProtKB-KW.
DR GO; GO:0006364; P:rRNA processing; IEA:UniProtKB-UniRule.
DR Gene3D; 3.40.50.10710; -; 1.
DR Gene3D; 3.60.15.10; -; 1.
DR HAMAP; MF_01491; RNase_J_bact; 1.
DR InterPro; IPR001279; Metallo-B-lactamas.
DR InterPro; IPR036866; RibonucZ/Hydroxyglut_hydro.
DR InterPro; IPR011108; RMMBL.
DR InterPro; IPR004613; RNase_J.
DR InterPro; IPR042173; RNase_J_2.
DR InterPro; IPR030854; RNase_J_bac.
DR InterPro; IPR041636; RNase_J_C.
DR InterPro; IPR001587; RNase_J_CS.
DR Pfam; PF00753; Lactamase_B; 1.
DR Pfam; PF07521; RMMBL; 1.
DR Pfam; PF17770; RNase_J_C; 1.
DR SMART; SM00849; Lactamase_B; 1.
DR SUPFAM; SSF56281; SSF56281; 1.
DR TIGRFAMs; TIGR00649; MG423; 1.
DR PROSITE; PS01292; UPF0036; 1.
PE 1: Evidence at protein level;
KW Cytoplasm; Endonuclease; Exonuclease; Hydrolase; Metal-binding;
KW mRNA processing; Nuclease; RNA-binding; Zinc.
FT CHAIN 1..691
FT /note="Ribonuclease J"
FT /id="PRO_0000430113"
FT REGION 1..132
FT /note="Loss of region decreases protein stability, still
FT able to interact with RhpA, but has decreased RNase
FT activity even on ssRNA"
FT REGION 1..89
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..16
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 17..56
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 57..79
FT /note="Basic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 208
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01491"
FT BINDING 210
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01491"
FT BINDING 212
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01491"
FT BINDING 213
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01491"
FT BINDING 277
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01491"
FT BINDING 299
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01491"
FT BINDING 299
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01491"
FT BINDING 500..504
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01491"
FT BINDING 526
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01491"
SQ SEQUENCE 691 AA; 77608 MW; 3FDAE97031793208 CRC64;
MTDNNHYENN ESNENSSENS KVDEARAGAF ERFTNRKKRF RENAQKNGES SHHEAPSHHK
KEHRPNKKPN NHHKQKHAKT RNYAKEELDS NKVEGVTEIL HVNERGTLGF HKELKKGVET
NNKIQVEHLN PHYKMNLNSK ASVKITPLGG LGEIGGNMMV IETPKSAIVI DAGMSFPKEG
LFGVDILIPD FSYLHQIKDK IAGIIITHAH EDHIGATPYL FKELQFPLYG TPLSLGLIGS
KFDEHGLKKY RSYFKIVEKR CPISVGEFII EWIHITHSII DSSALAIQTK AGTIIHTGDF
KIDHTPVDNL PTDLYRLAHY GEKGVMLLLS DSTNSHKSGT TPSESTIAPA FDTLFKEAQG
RVIMSTFSSN IHRVYQAIQY GIKYNRKIAV IGRSMEKNLD IARELGYIHL PYQSFIEANE
VAKYPDNEVL IVTTGSQGET MSALYRMATD EHRHISIKPN DLVIISAKAI PGNEASVSAV
LNFLIKKEAK VAYQEFDNIH VSGHAAQEEQ KLMLRLIKPK FFLPVHGEYN HVARHKQTAI
SCGVPEKNIY LMEDGDQVEV GPAFIKKVGT IKSGKSYVDN QSNLSIDTSI VQQREEVASA
GVFAATIFVN KNKQALLESS QFSSLGLVGF KDEKHLIKEI QGGLEMLLKS SNAEILNNPK
KLEDHTRNFI RKALFKKFRK YPAIICHAHS F
