RNJ2_BACSU
ID RNJ2_BACSU Reviewed; 555 AA.
AC O31760;
DT 15-MAY-2007, integrated into UniProtKB/Swiss-Prot.
DT 16-JUN-2009, sequence version 3.
DT 03-AUG-2022, entry version 119.
DE RecName: Full=Ribonuclease J2 {ECO:0000255|HAMAP-Rule:MF_01491};
DE Short=RNase J2 {ECO:0000255|HAMAP-Rule:MF_01491};
DE EC=3.1.-.- {ECO:0000255|HAMAP-Rule:MF_01491};
GN Name=rnjB {ECO:0000255|HAMAP-Rule:MF_01491}; Synonyms=ymfA;
GN OrderedLocusNames=BSU16780;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
RN [2]
RP SEQUENCE REVISION TO 131; 161-162 AND 200.
RX PubMed=19383706; DOI=10.1099/mic.0.027839-0;
RA Barbe V., Cruveiller S., Kunst F., Lenoble P., Meurice G., Sekowska A.,
RA Vallenet D., Wang T., Moszer I., Medigue C., Danchin A.;
RT "From a consortium sequence to a unified sequence: the Bacillus subtilis
RT 168 reference genome a decade later.";
RL Microbiology 155:1758-1775(2009).
RN [3]
RP FUNCTION, COFACTOR, SUBCELLULAR LOCATION, AND IDENTIFICATION BY MASS
RP SPECTROMETRY.
RC STRAIN=168;
RX PubMed=15831787; DOI=10.1093/nar/gki505;
RA Even S., Pellegrini O., Zig L., Labas V., Vinh J., Brechemmier-Baey D.,
RA Putzer H.;
RT "Ribonucleases J1 and J2: two novel endoribonucleases in B.subtilis with
RT functional homology to E.coli RNase E.";
RL Nucleic Acids Res. 33:2141-2152(2005).
RN [4]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=168;
RX PubMed=17229210; DOI=10.1111/j.1365-2958.2006.05499.x;
RA Britton R.A., Wen T., Schaefer L., Pellegrini O., Uicker W.C., Mathy N.,
RA Tobin C., Daou R., Szyk J., Condon C.;
RT "Maturation of the 5' end of Bacillus subtilis 16S rRNA by the essential
RT ribonuclease YkqC/RNase J1.";
RL Mol. Microbiol. 63:127-138(2007).
RN [5]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=18445592; DOI=10.1074/jbc.m801461200;
RA Deikus G., Condon C., Bechhofer D.H.;
RT "Role of Bacillus subtilis RNase J1 endonuclease and 5'-exonuclease
RT activities in trp leader RNA turnover.";
RL J. Biol. Chem. 283:17158-17167(2008).
RN [6]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=18713320; DOI=10.1111/j.1365-2958.2008.06400.x;
RA Mader U., Zig L., Kretschmer J., Homuth G., Putzer H.;
RT "mRNA processing by RNases J1 and J2 affects Bacillus subtilis gene
RT expression on a global scale.";
RL Mol. Microbiol. 70:183-196(2008).
RN [7]
RP SUBUNIT.
RC STRAIN=168;
RX PubMed=19193632; DOI=10.1074/mcp.m800546-mcp200;
RA Commichau F.M., Rothe F.M., Herzberg C., Wagner E., Hellwig D.,
RA Lehnik-Habrink M., Hammer E., Volker U., Stulke J.;
RT "Novel activities of glycolytic enzymes in Bacillus subtilis: interactions
RT with essential proteins involved in mRNA processing.";
RL Mol. Cell. Proteomics 8:1350-1360(2009).
RN [8]
RP FUNCTION, BIOPHYSICOCHEMICAL PROPERTIES, PROTEIN LEVELS, INTERACTION WITH
RP RNASE J1, AND SUBUNIT.
RC STRAIN=168;
RX PubMed=20025672; DOI=10.1111/j.1365-2958.2009.07004.x;
RA Mathy N., Hebert A., Mervelet P., Benard L., Dorleans A.,
RA Li de la Sierra-Gallay I., Noirot P., Putzer H., Condon C.;
RT "Bacillus subtilis ribonucleases J1 and J2 form a complex with altered
RT enzyme behaviour.";
RL Mol. Microbiol. 75:489-498(2010).
RN [9]
RP INTERACTION WITH RNY, AND SUBUNIT.
RC STRAIN=168;
RX PubMed=21803996; DOI=10.1128/jb.05500-11;
RA Lehnik-Habrink M., Newman J., Rothe F.M., Solovyova A.S., Rodrigues C.,
RA Herzberg C., Commichau F.M., Lewis R.J., Stulke J.;
RT "RNase Y in Bacillus subtilis: a natively disordered protein that is the
RT functional equivalent of RNase E from Escherichia coli.";
RL J. Bacteriol. 193:5431-5441(2011).
RN [10]
RP DISCUSSION OF MECHANISM, AND SUBUNIT.
RC STRAIN=168;
RX PubMed=21893285; DOI=10.1016/j.str.2011.06.017;
RA Newman J.A., Hewitt L., Rodrigues C., Solovyova A., Harwood C.R.,
RA Lewis R.J.;
RT "Unusual, dual endo- and exonuclease activity in the degradosome explained
RT by crystal structure analysis of RNase J1.";
RL Structure 19:1241-1251(2011).
RN [11]
RP FUNCTION, INTERACTION WITH RNASE J1, AND SUBUNIT.
RX PubMed=21893286; DOI=10.1016/j.str.2011.06.018;
RA Dorleans A., Li de la Sierra-Gallay I., Piton J., Zig L., Gilet L.,
RA Putzer H., Condon C.;
RT "Molecular basis for the recognition and cleavage of RNA by the
RT bifunctional 5'-3' exo/endoribonuclease RNase J.";
RL Structure 19:1252-1261(2011).
CC -!- FUNCTION: Endonucleolytically cleaves the 5'-leader sequence of certain
CC mRNAs. Endonuclease digestion by the RNase J1/J2 complex occurs at a
CC different site and in some cases more efficiently than J1 or J2 alone.
CC The exonuclease activity of the J1/J2 complex is highly processive on
CC substrates longer than 5 nucleotides, on shorter substrates is
CC distributive. Plays a role in mRNA maturation and stability. Appears to
CC have a limited effect on 16S rRNA maturation, despite its similarity to
CC RNase J1. This subunit alone has very poor 5'-3' exonuclease activity.
CC {ECO:0000269|PubMed:15831787, ECO:0000269|PubMed:17229210,
CC ECO:0000269|PubMed:18445592, ECO:0000269|PubMed:18713320,
CC ECO:0000269|PubMed:20025672, ECO:0000269|PubMed:21893286}.
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000250, ECO:0000269|PubMed:15831787,
CC ECO:0000269|PubMed:21893285};
CC Note=Binds 1 zinc ion per subunit. The inability to bind a second zinc
CC ion may explain its very poor exonuclease activity (PubMed:21893285).
CC {ECO:0000250, ECO:0000269|PubMed:15831787,
CC ECO:0000269|PubMed:21893285};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=5.96 uM for exonuclease on 30 nt RNA hybridized to 17 nt quenching
CC DNA, J2 alone {ECO:0000269|PubMed:20025672};
CC KM=0.22 uM for exonuclease on 30 nt RNA hybridized to 17 nt quenching
CC DNA, J1/J2 complex {ECO:0000269|PubMed:20025672};
CC Note=kcat is 0.58 sec (-1) for J1, 0.13 sec (-1) for J1/J2 and <0.005
CC sec (-1) for J2.;
CC -!- SUBUNIT: Unclear whether it forms homodimers or belongs to a larger
CC complex. According to (PubMed:20025672) probably does not form
CC homodimers, while (PubMed:21893285) shows homodimer formation. Both
CC reports show RNase J1 and J2 interaction, probably as a heterotetramer
CC (PubMed:19193632) shows it is a component of a possible RNA degradosome
CC complex composed of rny, rnjA, rnjB, pnp, pfkA and eno, while
CC (PubMed:20025672) finds no evidence of an RNA degradosome complex.
CC {ECO:0000269|PubMed:19193632, ECO:0000269|PubMed:20025672,
CC ECO:0000269|PubMed:21803996, ECO:0000269|PubMed:21893285,
CC ECO:0000269|PubMed:21893286}.
CC -!- INTERACTION:
CC O31760; Q45493: rnjA; NbExp=4; IntAct=EBI-6415198, EBI-6415229;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_01491,
CC ECO:0000269|PubMed:15831787}.
CC -!- DISRUPTION PHENOTYPE: Not essential. While depletion/deletion of RNase
CC J1 or J2 has no large impact on global gene expression, a double mutant
CC alters the expression of hundreds of genes (PubMed:18713320).
CC {ECO:0000269|PubMed:17229210, ECO:0000269|PubMed:18445592,
CC ECO:0000269|PubMed:18713320}.
CC -!- MISCELLANEOUS: Present in about 3000 monomers per cell in mid-log
CC phase.
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; AL009126; CAB13551.2; -; Genomic_DNA.
DR PIR; H69884; H69884.
DR RefSeq; NP_389560.2; NC_000964.3.
DR RefSeq; WP_003231875.1; NZ_JNCM01000035.1.
DR AlphaFoldDB; O31760; -.
DR SMR; O31760; -.
DR DIP; DIP-59141N; -.
DR IntAct; O31760; 4.
DR MINT; O31760; -.
DR STRING; 224308.BSU16780; -.
DR jPOST; O31760; -.
DR PaxDb; O31760; -.
DR PRIDE; O31760; -.
DR EnsemblBacteria; CAB13551; CAB13551; BSU_16780.
DR GeneID; 938463; -.
DR KEGG; bsu:BSU16780; -.
DR PATRIC; fig|224308.179.peg.1820; -.
DR eggNOG; COG0595; Bacteria.
DR InParanoid; O31760; -.
DR OMA; FKMDQFP; -.
DR PhylomeDB; O31760; -.
DR BioCyc; BSUB:BSU16780-MON; -.
DR Proteomes; UP000001570; Chromosome.
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; IDA:UniProtKB.
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; IDA:UniProtKB.
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 Pfam; PF00753; Lactamase_B; 1.
DR Pfam; PF07521; RMMBL; 1.
DR Pfam; PF17770; RNase_J_C; 1.
DR PIRSF; PIRSF004803; RnjA; 1.
DR SMART; SM00849; Lactamase_B; 1.
DR SUPFAM; SSF56281; SSF56281; 1.
DR TIGRFAMs; TIGR00649; MG423; 1.
PE 1: Evidence at protein level;
KW Cytoplasm; Endonuclease; Exonuclease; Hydrolase; Metal-binding; Nuclease;
KW Reference proteome; RNA-binding; rRNA processing; Zinc.
FT CHAIN 1..555
FT /note="Ribonuclease J2"
FT /id="PRO_0000286833"
FT BINDING 74
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01491"
FT BINDING 76
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01491"
FT BINDING 142
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01491"
FT BINDING 164
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01491"
FT BINDING 364..368
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01491"
SQ SEQUENCE 555 AA; 61175 MW; 8EA92EE42D51F282 CRC64;
MKKKNTENVR IIALGGVGEI GKNLYVIEID SDIFVVDAGL MHPENEMLGI DVVIPDISYL
IERADRVKAI FLTHGHDENI GGVFYLLNKL SVPVYGTKLT LALLREKLKQ YGHNRKTDLR
EIHSKSVITF ESTKVSFFRT IHSIPDSVGV SFKTSLGSIV CTGDFKFDQT PALNQTCDIG
EIAKIGNSGV LALLSDSANA ERPGYTPSEA AVSGEISDAL YNSQNRVIIA VFASNINRIQ
QVIHAAAQNG RKIAVAGKNL QSVLQLARKL GYIEADDELF ISVQDVKKYP KREVAIITAG
SQGEPLAALT RMANKAHKQL NIEEGDTVVI ASTPIPGQEL IYSKTVDLLA RAGAQVIFAQ
KRVHVSGHGS QEELKLMINL LKPKYLIPVN GEYRMQKAHS KIAEETGMKR SDIFLIEKGD
VVEFRGQNVK IGDKVPYGNI LIDGLGVGDI GNIVLRDRRL LSQDGILIVV ITLDKQKKHL
VSGPEIITRG FVYVRESEGL IVQATELVRS IVTEATETSN VEWSTLKQAM RDALNQFLYE
KTKRKPMIIP IIMEV
