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mRNA endoribonuclease toxin LS (EC 3.1.-.-) (RNase LS) (Toxin LS)

 RNLA_ECOLI              Reviewed;         357 AA.
P52129; P76604; Q2MAE1;
01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
01-NOV-1997, sequence version 2.
22-NOV-2017, entry version 109.
RecName: Full=mRNA endoribonuclease toxin LS;
EC=3.1.-.-;
AltName: Full=RNase LS {ECO:0000303|PubMed:17895580};
AltName: Full=Toxin LS;
Name=rnlA; Synonyms=std, yfjN; OrderedLocusNames=b2630, JW2611;
Escherichia coli (strain K12).
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
Enterobacteriaceae; Escherichia.
NCBI_TaxID=83333;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / MG1655 / ATCC 47076;
PubMed=9278503; DOI=10.1126/science.277.5331.1453;
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J.,
Mau B., Shao Y.;
"The complete genome sequence of Escherichia coli K-12.";
Science 277:1453-1462(1997).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=16738553; DOI=10.1038/msb4100049;
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
"Highly accurate genome sequences of Escherichia coli K-12 strains
MG1655 and W3110.";
Mol. Syst. Biol. 2:E1-E5(2006).
[3]
IDENTIFICATION, DISRUPTION PHENOTYPE, AND MUTAGENESIS OF
188-GLU--ASP-196.
STRAIN=K12;
PubMed=15677746; DOI=10.1534/genetics.104.033290;
Otsuka Y., Yonesaki T.;
"A novel endoribonuclease, RNase LS, in Escherichia coli.";
Genetics 169:13-20(2005).
[4]
FUNCTION AS AN ENDORIBONUCLEASE, AND SUBCELLULAR LOCATION.
STRAIN=K12;
PubMed=17895580; DOI=10.1266/ggs.82.291;
Otsuka Y., Koga M., Iwamoto A., Yonesaki T.;
"A role of RnlA in the RNase LS activity from Escherichia coli.";
Genes Genet. Syst. 82:291-299(2007).
[5]
FUNCTION, AND DISRUPTION PHENOTYPE.
STRAIN=K12;
PubMed=19019153; DOI=10.1111/j.1365-2958.2008.06504.x;
Iwamoto A., Lemire S., Yonesaki T.;
"Post-transcriptional control of Crp-cAMP by RNase LS in Escherichia
coli.";
Mol. Microbiol. 70:1570-1578(2008).
[6]
INDUCTION.
STRAIN=K12;
PubMed=20421606; DOI=10.1534/genetics.110.114462;
Otsuka Y., Miki K., Koga M., Katayama N., Morimoto W., Takahashi Y.,
Yonesaki T.;
"IscR regulates RNase LS activity by repressing rnlA transcription.";
Genetics 185:823-830(2010).
[7]
FUNCTION AS A TOXIN, FUNCTION AS A MRNA ENDORIBONUCLEASE, AND
INTERACTION WITH RNLB.
STRAIN=K12;
PubMed=20980243; DOI=10.1534/genetics.110.121798;
Koga M., Otsuka Y., Lemire S., Yonesaki T.;
"Escherichia coli rnlA and rnlB compose a novel toxin-antitoxin
system.";
Genetics 187:123-130(2011).
[8]
FUNCTION AS A TOXIN, FUNCTION AS AN MRNA ENDORIBONUCLEASE, AND
INTERACTION WITH ENTEROBACTERIA PHAGE T4 ANTITOXIN DMD.
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=22403819; DOI=10.1111/j.1365-2958.2012.07975.x;
Otsuka Y., Yonesaki T.;
"Dmd of bacteriophage T4 functions as an antitoxin against Escherichia
coli LsoA and RnlA toxins.";
Mol. Microbiol. 83:669-681(2012).
[9]
X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS), FUNCTION, SUBUNIT, DOMAIN, AND
MUTAGENESIS OF 327-VAL--VAL-357.
STRAIN=K12;
PubMed=24112600; DOI=10.1111/mmi.12409;
Wei Y., Gao Z.Q., Otsuka Y., Naka K., Yonesaki T., Zhang H.,
Dong Y.H.;
"Structure-function studies of Escherichia coli RnlA reveal a novel
toxin structure involved in bacteriophage resistance.";
Mol. Microbiol. 90:956-965(2013).
-!- FUNCTION: Toxic component of a type II toxin-antitoxin (TA) module
(PubMed:20980243, PubMed:24112600). A stable (half-life 27.6
minutes) endoribonuclease that in the absence of cognate antitoxin
RnlB causes generalized RNA degradation. Degrades late
enterobacteria phage T4 mRNAs, protecting the host against T4
reproduction. Activity is inhibited by cognate antitoxin RnlB and
by enterobacteria phage T4 protein Dmd (PubMed:20980243,
PubMed:22403819). Targets cyaA mRNA (PubMed:19019153).
{ECO:0000269|PubMed:17895580, ECO:0000269|PubMed:19019153,
ECO:0000269|PubMed:20980243, ECO:0000269|PubMed:22403819,
ECO:0000269|PubMed:24112600}.
-!- SUBUNIT: Forms homodimer in solution (PubMed:24112600). Forms a
complex with cognate antitoxin RnlB (PubMed:20980243) and with
enterobacteria phage T4 antitoxin Dmd (PubMed:22403819).
{ECO:0000269|PubMed:20980243, ECO:0000269|PubMed:22403819}.
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:17895580}.
Note=May associate with ribosomes, it sediments in a P100 fraction
(pellet of a 100,000 x g centrifugation).
{ECO:0000305|PubMed:17895580}.
-!- INDUCTION: Repressed by IscR. rnlA-rnlB forms an operon, the
downstream rnlB also has its own promoter.
{ECO:0000269|PubMed:20421606}.
-!- DOMAIN: Composed of 3 domains, the NTD (N-terminal domain,
residues 1-90), NRD (N-repeated domain, residues 91-197) and DBD
(Dmd-binding domain, residues 198-357). The DBD is responsible for
dimerization, growth inhibition upon overexpression and
recognition of T4 antitoxin Dmd (via residues 327-357) and
antitoxin RnlB and subcellular location (PubMed:24112600).
{ECO:0000269|PubMed:24112600}.
-!- DISRUPTION PHENOTYPE: Not essential, slightly smaller colonies on
minimal agar plates at 30 degrees Celsius. Strongly reduces RNase
LS activity, restores growth of an enterobacteria phage T4 dmd
mutant. Altered mRNA half-life for some cellular transcripts,
including an increased half-life for an internal fragment of 23S
rRNA. Allele rnlA2 is due to a premature stop codon at residue 33
(PubMed:15677746). Sensitive to high concentrations of NaCl,
sensitivity is eliminated in a crp or cyaA deletion mutant.
Increased levels of Crp and thus increased levels of cAMP.
{ECO:0000269|PubMed:15677746, ECO:0000269|PubMed:19019153}.
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EMBL; U36840; AAA79799.1; -; Genomic_DNA.
EMBL; U00096; AAC75678.1; -; Genomic_DNA.
EMBL; AP009048; BAE76765.1; -; Genomic_DNA.
PIR; H65041; H65041.
RefSeq; NP_417119.1; NC_000913.3.
RefSeq; WP_000155570.1; NZ_LN832404.1.
PDB; 4I8O; X-ray; 2.10 A; A/B=1-357.
PDBsum; 4I8O; -.
ProteinModelPortal; P52129; -.
SMR; P52129; -.
BioGrid; 4259437; 32.
DIP; DIP-12079N; -.
IntAct; P52129; 2.
MINT; MINT-1290895; -.
STRING; 316385.ECDH10B_2796; -.
PaxDb; P52129; -.
PRIDE; P52129; -.
EnsemblBacteria; AAC75678; AAC75678; b2630.
EnsemblBacteria; BAE76765; BAE76765; BAE76765.
GeneID; 947107; -.
KEGG; ecj:JW2611; -.
KEGG; eco:b2630; -.
PATRIC; fig|1411691.4.peg.4109; -.
EchoBASE; EB2992; -.
EcoGene; EG13200; rnlA.
eggNOG; ENOG4106K8T; Bacteria.
eggNOG; ENOG410YAX4; LUCA.
HOGENOM; HOG000012167; -.
BioCyc; EcoCyc:G7365-MONOMER; -.
BioCyc; MetaCyc:G7365-MONOMER; -.
PRO; PR:P52129; -.
Proteomes; UP000000318; Chromosome.
Proteomes; UP000000625; Chromosome.
GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
GO; GO:0004521; F:endoribonuclease activity; IDA:EcoCyc.
GO; GO:0090729; F:toxin activity; IEA:UniProtKB-KW.
GO; GO:0051607; P:defense response to virus; IEA:UniProtKB-KW.
GO; GO:0006402; P:mRNA catabolic process; IMP:EcoCyc.
InterPro; IPR031845; RnlA_toxin.
Pfam; PF15935; RnlA_toxin; 1.
1: Evidence at protein level;
3D-structure; Antiviral defense; Complete proteome; Cytoplasm;
Endonuclease; Hydrolase; Nuclease; Reference proteome.
CHAIN 1 357 mRNA endoribonuclease toxin LS.
/FTId=PRO_0000169279.
MUTAGEN 188 196 EKVLIRQED->KKVLIRQEN: In rnlA5; strongly
reduces RNase LS activity.
{ECO:0000269|PubMed:15677746}.
MUTAGEN 327 357 Missing: No longer interacts with T4
phage antitoxin Dmd.
{ECO:0000269|PubMed:24112600}.
STRAND 7 9 {ECO:0000244|PDB:4I8O}.
HELIX 13 15 {ECO:0000244|PDB:4I8O}.
HELIX 16 26 {ECO:0000244|PDB:4I8O}.
STRAND 30 35 {ECO:0000244|PDB:4I8O}.
STRAND 43 49 {ECO:0000244|PDB:4I8O}.
STRAND 56 62 {ECO:0000244|PDB:4I8O}.
STRAND 68 71 {ECO:0000244|PDB:4I8O}.
STRAND 73 76 {ECO:0000244|PDB:4I8O}.
HELIX 78 90 {ECO:0000244|PDB:4I8O}.
HELIX 94 97 {ECO:0000244|PDB:4I8O}.
STRAND 100 104 {ECO:0000244|PDB:4I8O}.
HELIX 109 119 {ECO:0000244|PDB:4I8O}.
STRAND 126 132 {ECO:0000244|PDB:4I8O}.
STRAND 134 143 {ECO:0000244|PDB:4I8O}.
TURN 144 147 {ECO:0000244|PDB:4I8O}.
STRAND 148 155 {ECO:0000244|PDB:4I8O}.
TURN 156 159 {ECO:0000244|PDB:4I8O}.
STRAND 160 165 {ECO:0000244|PDB:4I8O}.
HELIX 169 178 {ECO:0000244|PDB:4I8O}.
HELIX 179 181 {ECO:0000244|PDB:4I8O}.
HELIX 184 192 {ECO:0000244|PDB:4I8O}.
HELIX 199 201 {ECO:0000244|PDB:4I8O}.
HELIX 204 215 {ECO:0000244|PDB:4I8O}.
HELIX 216 221 {ECO:0000244|PDB:4I8O}.
HELIX 224 238 {ECO:0000244|PDB:4I8O}.
HELIX 247 250 {ECO:0000244|PDB:4I8O}.
HELIX 251 266 {ECO:0000244|PDB:4I8O}.
TURN 267 269 {ECO:0000244|PDB:4I8O}.
TURN 274 276 {ECO:0000244|PDB:4I8O}.
HELIX 279 281 {ECO:0000244|PDB:4I8O}.
STRAND 286 288 {ECO:0000244|PDB:4I8O}.
HELIX 293 296 {ECO:0000244|PDB:4I8O}.
HELIX 301 322 {ECO:0000244|PDB:4I8O}.
HELIX 336 355 {ECO:0000244|PDB:4I8O}.
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


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