RNLA_ECOLI
ID RNLA_ECOLI Reviewed; 357 AA.
AC P52129; P76604; Q2MAE1;
DT 01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 2.
DT 03-AUG-2022, entry version 131.
DE RecName: Full=mRNA endoribonuclease toxin LS;
DE EC=3.1.-.-;
DE AltName: Full=RNase LS {ECO:0000303|PubMed:17895580};
DE AltName: Full=Toxin LS;
GN Name=rnlA; Synonyms=std, yfjN; OrderedLocusNames=b2630, JW2611;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [3]
RP IDENTIFICATION, DISRUPTION PHENOTYPE, AND MUTAGENESIS OF 188-GLU--ASP-196.
RC STRAIN=K12;
RX PubMed=15677746; DOI=10.1534/genetics.104.033290;
RA Otsuka Y., Yonesaki T.;
RT "A novel endoribonuclease, RNase LS, in Escherichia coli.";
RL Genetics 169:13-20(2005).
RN [4]
RP FUNCTION AS AN ENDORIBONUCLEASE, AND SUBCELLULAR LOCATION.
RC STRAIN=K12;
RX PubMed=17895580; DOI=10.1266/ggs.82.291;
RA Otsuka Y., Koga M., Iwamoto A., Yonesaki T.;
RT "A role of RnlA in the RNase LS activity from Escherichia coli.";
RL Genes Genet. Syst. 82:291-299(2007).
RN [5]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=K12;
RX PubMed=19019153; DOI=10.1111/j.1365-2958.2008.06504.x;
RA Iwamoto A., Lemire S., Yonesaki T.;
RT "Post-transcriptional control of Crp-cAMP by RNase LS in Escherichia
RT coli.";
RL Mol. Microbiol. 70:1570-1578(2008).
RN [6]
RP INDUCTION.
RC STRAIN=K12;
RX PubMed=20421606; DOI=10.1534/genetics.110.114462;
RA Otsuka Y., Miki K., Koga M., Katayama N., Morimoto W., Takahashi Y.,
RA Yonesaki T.;
RT "IscR regulates RNase LS activity by repressing rnlA transcription.";
RL Genetics 185:823-830(2010).
RN [7]
RP FUNCTION AS A TOXIN, FUNCTION AS A MRNA ENDORIBONUCLEASE, AND INTERACTION
RP WITH RNLB.
RC STRAIN=K12;
RX PubMed=20980243; DOI=10.1534/genetics.110.121798;
RA Koga M., Otsuka Y., Lemire S., Yonesaki T.;
RT "Escherichia coli rnlA and rnlB compose a novel toxin-antitoxin system.";
RL Genetics 187:123-130(2011).
RN [8]
RP FUNCTION AS A TOXIN, FUNCTION AS AN MRNA ENDORIBONUCLEASE, AND INTERACTION
RP WITH ENTEROBACTERIA PHAGE T4 ANTITOXIN DMD.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=22403819; DOI=10.1111/j.1365-2958.2012.07975.x;
RA Otsuka Y., Yonesaki T.;
RT "Dmd of bacteriophage T4 functions as an antitoxin against Escherichia coli
RT LsoA and RnlA toxins.";
RL Mol. Microbiol. 83:669-681(2012).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS), FUNCTION, SUBUNIT, DOMAIN, AND
RP MUTAGENESIS OF 327-VAL--VAL-357.
RC STRAIN=K12;
RX PubMed=24112600; DOI=10.1111/mmi.12409;
RA Wei Y., Gao Z.Q., Otsuka Y., Naka K., Yonesaki T., Zhang H., Dong Y.H.;
RT "Structure-function studies of Escherichia coli RnlA reveal a novel toxin
RT structure involved in bacteriophage resistance.";
RL Mol. Microbiol. 90:956-965(2013).
CC -!- FUNCTION: Toxic component of a type II toxin-antitoxin (TA) system
CC (PubMed:20980243, PubMed:24112600). A stable (half-life 27.6 minutes)
CC endoribonuclease that in the absence of cognate antitoxin RnlB causes
CC generalized RNA degradation. Degrades late enterobacteria phage T4
CC mRNAs, protecting the host against T4 reproduction. Activity is
CC inhibited by cognate antitoxin RnlB and by enterobacteria phage T4
CC protein Dmd (PubMed:20980243, PubMed:22403819). Targets cyaA mRNA
CC (PubMed:19019153). {ECO:0000269|PubMed:17895580,
CC ECO:0000269|PubMed:19019153, ECO:0000269|PubMed:20980243,
CC ECO:0000269|PubMed:22403819, ECO:0000269|PubMed:24112600}.
CC -!- SUBUNIT: Forms homodimer in solution (PubMed:24112600). Forms a complex
CC with cognate antitoxin RnlB (PubMed:20980243) and with enterobacteria
CC phage T4 antitoxin Dmd (PubMed:22403819). {ECO:0000269|PubMed:20980243,
CC ECO:0000269|PubMed:22403819}.
CC -!- INTERACTION:
CC P52129; P52130: rnlB; NbExp=2; IntAct=EBI-560462, EBI-21183386;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:17895580}. Note=May
CC associate with ribosomes, it sediments in a P100 fraction (pellet of a
CC 100,000 x g centrifugation). {ECO:0000305|PubMed:17895580}.
CC -!- INDUCTION: Repressed by IscR. rnlA-rnlB forms an operon, the downstream
CC rnlB also has its own promoter. {ECO:0000269|PubMed:20421606}.
CC -!- DOMAIN: Composed of 3 domains, the NTD (N-terminal domain, residues 1-
CC 90), NRD (N-repeated domain, residues 91-197) and DBD (Dmd-binding
CC domain, residues 198-357). The DBD is responsible for dimerization,
CC growth inhibition upon overexpression and recognition of T4 antitoxin
CC Dmd (via residues 327-357) and antitoxin RnlB and subcellular location
CC (PubMed:24112600). {ECO:0000269|PubMed:24112600}.
CC -!- DISRUPTION PHENOTYPE: Not essential, slightly smaller colonies on
CC minimal agar plates at 30 degrees Celsius. Strongly reduces RNase LS
CC activity, restores growth of an enterobacteria phage T4 dmd mutant.
CC Altered mRNA half-life for some cellular transcripts, including an
CC increased half-life for an internal fragment of 23S rRNA. Allele rnlA2
CC is due to a premature stop codon at residue 33 (PubMed:15677746).
CC Sensitive to high concentrations of NaCl, sensitivity is eliminated in
CC a crp or cyaA deletion mutant. Increased levels of Crp and thus
CC increased levels of cAMP. {ECO:0000269|PubMed:15677746,
CC ECO:0000269|PubMed:19019153}.
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DR EMBL; U36840; AAA79799.1; -; Genomic_DNA.
DR EMBL; U00096; AAC75678.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE76765.1; -; Genomic_DNA.
DR PIR; H65041; H65041.
DR RefSeq; NP_417119.1; NC_000913.3.
DR RefSeq; WP_000155570.1; NZ_LN832404.1.
DR PDB; 4I8O; X-ray; 2.10 A; A/B=1-357.
DR PDB; 6Y2P; X-ray; 2.64 A; A/B=1-357.
DR PDB; 6Y2Q; X-ray; 2.99 A; A/B=1-357.
DR PDB; 6Y2R; X-ray; 3.89 A; A/B=2-357.
DR PDB; 6Y2S; X-ray; 3.79 A; A/B=2-357.
DR PDB; 7AEX; X-ray; 1.95 A; A=92-357.
DR PDBsum; 4I8O; -.
DR PDBsum; 6Y2P; -.
DR PDBsum; 6Y2Q; -.
DR PDBsum; 6Y2R; -.
DR PDBsum; 6Y2S; -.
DR PDBsum; 7AEX; -.
DR AlphaFoldDB; P52129; -.
DR SASBDB; P52129; -.
DR SMR; P52129; -.
DR BioGRID; 4259437; 32.
DR ComplexPortal; CPX-4115; RnlAB toxin-antitoxin complex.
DR DIP; DIP-12079N; -.
DR IntAct; P52129; 3.
DR STRING; 511145.b2630; -.
DR jPOST; P52129; -.
DR PaxDb; P52129; -.
DR PRIDE; P52129; -.
DR EnsemblBacteria; AAC75678; AAC75678; b2630.
DR EnsemblBacteria; BAE76765; BAE76765; BAE76765.
DR GeneID; 947107; -.
DR KEGG; ecj:JW2611; -.
DR KEGG; eco:b2630; -.
DR PATRIC; fig|1411691.4.peg.4109; -.
DR EchoBASE; EB2992; -.
DR eggNOG; ENOG502ZABA; Bacteria.
DR HOGENOM; CLU_065781_0_0_6; -.
DR OMA; CYRAFIF; -.
DR BioCyc; EcoCyc:G7365-MON; -.
DR BioCyc; MetaCyc:G7365-MON; -.
DR PRO; PR:P52129; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0110001; C:toxin-antitoxin complex; IPI:ComplexPortal.
DR GO; GO:0004521; F:endoribonuclease activity; IDA:EcoCyc.
DR GO; GO:0051607; P:defense response to virus; IEA:UniProtKB-KW.
DR GO; GO:0006402; P:mRNA catabolic process; IMP:EcoCyc.
DR GO; GO:0040008; P:regulation of growth; IC:ComplexPortal.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; IC:ComplexPortal.
DR GO; GO:0044010; P:single-species biofilm formation; IC:ComplexPortal.
DR InterPro; IPR043994; RnlA/LsoA-toxin_DBD.
DR InterPro; IPR045837; RnlA_toxin_N.
DR InterPro; IPR031845; RnlA_toxin_NRD.
DR Pfam; PF19034; RnlA-toxin_DBD; 1.
DR Pfam; PF15935; RnlA_toxin; 1.
DR Pfam; PF19417; RnlA_toxin_N; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Antiviral defense; Cytoplasm; Endonuclease; Hydrolase;
KW Nuclease; Reference proteome; Toxin-antitoxin system.
FT CHAIN 1..357
FT /note="mRNA endoribonuclease toxin LS"
FT /id="PRO_0000169279"
FT MUTAGEN 188..196
FT /note="EKVLIRQED->KKVLIRQEN: In rnlA5; strongly reduces
FT RNase LS activity."
FT /evidence="ECO:0000269|PubMed:15677746"
FT MUTAGEN 327..357
FT /note="Missing: No longer interacts with T4 phage antitoxin
FT Dmd."
FT /evidence="ECO:0000269|PubMed:24112600"
FT STRAND 7..9
FT /evidence="ECO:0007829|PDB:4I8O"
FT HELIX 13..15
FT /evidence="ECO:0007829|PDB:4I8O"
FT HELIX 16..26
FT /evidence="ECO:0007829|PDB:4I8O"
FT STRAND 30..35
FT /evidence="ECO:0007829|PDB:4I8O"
FT STRAND 38..41
FT /evidence="ECO:0007829|PDB:6Y2P"
FT STRAND 43..49
FT /evidence="ECO:0007829|PDB:4I8O"
FT STRAND 56..62
FT /evidence="ECO:0007829|PDB:4I8O"
FT STRAND 68..71
FT /evidence="ECO:0007829|PDB:4I8O"
FT STRAND 73..76
FT /evidence="ECO:0007829|PDB:4I8O"
FT HELIX 78..90
FT /evidence="ECO:0007829|PDB:4I8O"
FT HELIX 94..97
FT /evidence="ECO:0007829|PDB:7AEX"
FT STRAND 100..106
FT /evidence="ECO:0007829|PDB:7AEX"
FT HELIX 109..120
FT /evidence="ECO:0007829|PDB:7AEX"
FT STRAND 125..132
FT /evidence="ECO:0007829|PDB:7AEX"
FT STRAND 134..143
FT /evidence="ECO:0007829|PDB:7AEX"
FT TURN 144..147
FT /evidence="ECO:0007829|PDB:7AEX"
FT STRAND 148..155
FT /evidence="ECO:0007829|PDB:7AEX"
FT TURN 156..159
FT /evidence="ECO:0007829|PDB:7AEX"
FT STRAND 160..165
FT /evidence="ECO:0007829|PDB:7AEX"
FT HELIX 169..178
FT /evidence="ECO:0007829|PDB:7AEX"
FT HELIX 179..181
FT /evidence="ECO:0007829|PDB:7AEX"
FT HELIX 184..192
FT /evidence="ECO:0007829|PDB:7AEX"
FT HELIX 199..201
FT /evidence="ECO:0007829|PDB:7AEX"
FT HELIX 204..215
FT /evidence="ECO:0007829|PDB:7AEX"
FT HELIX 216..221
FT /evidence="ECO:0007829|PDB:7AEX"
FT HELIX 224..238
FT /evidence="ECO:0007829|PDB:7AEX"
FT HELIX 247..250
FT /evidence="ECO:0007829|PDB:7AEX"
FT HELIX 251..267
FT /evidence="ECO:0007829|PDB:7AEX"
FT TURN 274..276
FT /evidence="ECO:0007829|PDB:7AEX"
FT HELIX 277..281
FT /evidence="ECO:0007829|PDB:7AEX"
FT STRAND 286..288
FT /evidence="ECO:0007829|PDB:4I8O"
FT HELIX 293..296
FT /evidence="ECO:0007829|PDB:7AEX"
FT HELIX 301..322
FT /evidence="ECO:0007829|PDB:7AEX"
FT HELIX 325..328
FT /evidence="ECO:0007829|PDB:7AEX"
FT HELIX 330..332
FT /evidence="ECO:0007829|PDB:7AEX"
FT HELIX 337..355
FT /evidence="ECO:0007829|PDB:7AEX"
SQ SEQUENCE 357 AA; 40061 MW; 78FB0506AC9AE45A CRC64;
MTIRSYKNLN LVRANIETES RQFIENKNYS IQSIGPMPGS RAGLRVVFTR PGVNLATVDI
FYNGDGSTTI QYLTGANRSL GQELADHLFE TINPAEFEQV NMVLQGFVET SVLPVLELSA
DESHIEFREH SRNAHTVVWK IISTSYQDEL TVSLHITTGK LQIQGRPLSC YRVFTFNLAA
LLDLQGLEKV LIRQEDGKAN IVQQEVARTY LQTVMADAYP HLHVTAEKLL VSGLCVKLAA
PDLPDYCMLL YPELRTIEGV LKSKMSGLGM PVQQPAGFGT YFDKPAAHYI LKPQFAATLR
PEQINIISTA YTFFNVERHS LFHMETVVDA SRMISDMARL MGKATRAWGI IKDLYIV
