RNJ_PYRAB
ID RNJ_PYRAB Reviewed; 451 AA.
AC Q9V076; G8ZI82;
DT 09-JUL-2014, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 105.
DE RecName: Full=Ribonuclease J {ECO:0000255|HAMAP-Rule:MF_01492};
DE Short=RNase J {ECO:0000255|HAMAP-Rule:MF_01492};
DE EC=3.1.-.- {ECO:0000255|HAMAP-Rule:MF_01492};
DE AltName: Full=Pab-RNase J;
GN Name=rnj {ECO:0000255|HAMAP-Rule:MF_01492}; OrderedLocusNames=PYRAB09150;
GN ORFNames=PAB1751;
OS Pyrococcus abyssi (strain GE5 / Orsay).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Pyrococcus.
OX NCBI_TaxID=272844;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=GE5 / Orsay;
RX PubMed=12622808; DOI=10.1046/j.1365-2958.2003.03381.x;
RA Cohen G.N., Barbe V., Flament D., Galperin M., Heilig R., Lecompte O.,
RA Poch O., Prieur D., Querellou J., Ripp R., Thierry J.-C., Van der Oost J.,
RA Weissenbach J., Zivanovic Y., Forterre P.;
RT "An integrated analysis of the genome of the hyperthermophilic archaeon
RT Pyrococcus abyssi.";
RL Mol. Microbiol. 47:1495-1512(2003).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=GE5 / Orsay;
RX PubMed=22057919; DOI=10.1007/s00284-011-0035-x;
RA Gao J., Wang J.;
RT "Re-annotation of two hyperthermophilic archaea Pyrococcus abyssi GE5 and
RT Pyrococcus furiosus DSM 3638.";
RL Curr. Microbiol. 64:118-129(2012).
RN [3]
RP FUNCTION, COFACTOR, ACTIVITY REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, AND
RP MUTAGENESIS OF 47-HIS--LEU-60; HIS-86; GLU-209; 298-ARG--LEU-307; HIS-388
RP AND HIS-410.
RX PubMed=20375016; DOI=10.1074/jbc.m109.095117;
RA Clouet-d'Orval B., Rinaldi D., Quentin Y., Carpousis A.J.;
RT "Euryarchaeal beta-CASP proteins with homology to bacterial RNase J have
RT 5'- to 3'-exoribonuclease activity.";
RL J. Biol. Chem. 285:17574-17583(2010).
CC -!- FUNCTION: A highly processive 5'-3' exoribonuclease; no evidence has
CC been seen for endonuclease activity. Prefers 5'-phosphate or 5'-
CC hydroxyl ends; 5'-triphosphate substrates are very poorly degraded,
CC does not degrade circular RNA. Does not degrade pre-tRNA(Trp)
CC suggesting it is inhibited by strong secondary structures. Also
CC degrades ssNDA but not dsDNA. {ECO:0000269|PubMed:20375016}.
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01492};
CC Note=Binds 2 Zn(2+) ions per subunit. It is not clear if Zn(2+) or
CC Mg(2+) is physiologically important. {ECO:0000255|HAMAP-Rule:MF_01492};
CC -!- ACTIVITY REGULATION: Inhibited by 1,10-phenanthroline.
CC {ECO:0000269|PubMed:20375016}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is 6-8. {ECO:0000269|PubMed:20375016};
CC Temperature dependence:
CC Optimum temperature is 95 degrees Celsius.
CC {ECO:0000269|PubMed:20375016};
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_01492}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_01492}.
CC -!- MISCELLANEOUS: Mutagenesis of His-410 to Val in the T.kodakaraensis
CC homolog (AC Q5JH57) reduces exoribonuclease activity to 1%.
CC -!- SIMILARITY: Belongs to the metallo-beta-lactamase superfamily. RNA-
CC metabolizing metallo-beta-lactamase-like family. Archaeal RNase J
CC subfamily. {ECO:0000255|HAMAP-Rule:MF_01492}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CCE70323.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AJ248285; CAB49829.1; -; Genomic_DNA.
DR EMBL; HE613800; CCE70323.1; ALT_INIT; Genomic_DNA.
DR PIR; D75139; D75139.
DR AlphaFoldDB; Q9V076; -.
DR SMR; Q9V076; -.
DR STRING; 272844.PAB1751; -.
DR EnsemblBacteria; CAB49829; CAB49829; PAB1751.
DR KEGG; pab:PAB1751; -.
DR PATRIC; fig|272844.11.peg.969; -.
DR eggNOG; arCOG00546; Archaea.
DR HOGENOM; CLU_008727_4_1_2; -.
DR OMA; KNTCVFE; -.
DR PhylomeDB; Q9V076; -.
DR BRENDA; 3.1.13.B1; 5242.
DR Proteomes; UP000000810; Chromosome.
DR Proteomes; UP000009139; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0004534; F:5'-3' exoribonuclease activity; IDA:UniProtKB.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0008270; F:zinc ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0006401; P:RNA catabolic process; IDA:UniProtKB.
DR Gene3D; 3.40.50.10710; -; 1.
DR Gene3D; 3.60.15.10; -; 1.
DR HAMAP; MF_01492; RNase_J_arch; 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; IPR030879; RNase_J_arc.
DR InterPro; IPR001587; RNase_J_CS.
DR Pfam; PF00753; Lactamase_B; 1.
DR Pfam; PF07521; RMMBL; 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; Exonuclease; Hydrolase; Metal-binding; Nuclease; RNA-binding;
KW Zinc.
FT CHAIN 1..451
FT /note="Ribonuclease J"
FT /id="PRO_0000429576"
FT BINDING 84
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_01492"
FT BINDING 86
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_01492"
FT BINDING 88
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_01492"
FT BINDING 89
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_01492"
FT BINDING 155
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_01492"
FT BINDING 177
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_01492"
FT BINDING 177
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_01492"
FT BINDING 384..388
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01492"
FT BINDING 410
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_01492"
FT MUTAGEN 47..60
FT /note="Missing: 25% exoribonuclease activity."
FT /evidence="ECO:0000269|PubMed:20375016"
FT MUTAGEN 86
FT /note="H->A: 5% exoribonuclease activity."
FT /evidence="ECO:0000269|PubMed:20375016"
FT MUTAGEN 209
FT /note="E->A: 5% exoribonuclease activity."
FT /evidence="ECO:0000269|PubMed:20375016"
FT MUTAGEN 298..307
FT /note="Missing: 8% exoribonuclease activity."
FT /evidence="ECO:0000269|PubMed:20375016"
FT MUTAGEN 388
FT /note="H->A: 1% exoribonuclease activity."
FT /evidence="ECO:0000269|PubMed:20375016"
FT MUTAGEN 410
FT /note="H->A: Wild-type."
FT /evidence="ECO:0000269|PubMed:20375016"
SQ SEQUENCE 451 AA; 50517 MW; AA689437804BC24E CRC64;
MWEEINMIKI YTLGGYEEVG KNMTAVEYNG EVVIVDMGIR LDRVLIHEDV EFQKMSSKDL
RKLGAIPDDR PIRNKKVVAI ALSHGHLDHI GAVGKLAPHY PDVPIYGTPY TIRLAKSEIK
GEEYFEVTNP LYETNYGEIV QVSENLAIEF VQITHSIPQS SIVVIHTPEG AVVYACDYKF
DNNHPYGERP DYKRLKELGK EGVKVLIAES TRVAEETKTP SEAVAKMLLE DFFLYEGMEA
DGLIATTFAS HIARLQELIE IANKMGRQAI FIGRSLAKYT GIAKQLGLIK MKGSRVLRSP
NAVSKVLKEV SQARENYLLI VTGHQGEPGA ILTRMANGEL YDIGPRDTVV FSAGVIPNPL
NVAQRYALET KLRMKGVRMI KNLHVSGHAS KEDHRYLIRM LNPEYIVPAH GEFRMLTHYA
ELAEEEGYMI GKEVFISRNG HVVEIPGSLE G
