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Ribonuclease E (RNase E) (EC 3.1.26.12)

 RNE_ECOLI               Reviewed;        1061 AA.
P21513; P77591;
01-MAY-1991, integrated into UniProtKB/Swiss-Prot.
29-AUG-2003, sequence version 6.
25-OCT-2017, entry version 174.
RecName: Full=Ribonuclease E {ECO:0000255|HAMAP-Rule:MF_00970};
Short=RNase E {ECO:0000255|HAMAP-Rule:MF_00970};
EC=3.1.26.12 {ECO:0000255|HAMAP-Rule:MF_00970};
Name=rne {ECO:0000255|HAMAP-Rule:MF_00970}; Synonyms=ams, hmp1;
OrderedLocusNames=b1084, JW1071;
Escherichia coli (strain K12).
Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
Enterobacteriaceae; Escherichia.
NCBI_TaxID=83333;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
PubMed=8905232; DOI=10.1093/dnares/3.3.137;
Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A.,
Ikemoto K., Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K.,
Kimura S., Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K.,
Mori H., Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N.,
Sampei G., Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y.,
Yano M., Horiuchi T.;
"A 718-kb DNA sequence of the Escherichia coli K-12 genome
corresponding to the 12.7-28.0 min region on the linkage map.";
DNA Res. 3:137-155(1996).
[2]
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).
[3]
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).
[4]
NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-1025.
STRAIN=K12;
PubMed=1447789; DOI=10.1016/0022-2836(92)90489-7;
Casaregola S., Jacq A., Laoudj D., McGurk G., Margarson S.,
Tempete M., Norris V., Holland I.B.;
"Cloning and analysis of the entire Escherichia coli ams gene. ams is
identical to hmp1 and encodes a 114 kDa protein that migrates as a 180
kDa protein.";
J. Mol. Biol. 228:30-40(1992).
[5]
NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-844.
STRAIN=K12;
PubMed=1704367;
Claverie-Martin F., Diaz-Torres M., Yancey S.D., Kushner S.R.;
"Analysis of the altered mRNA stability (ams) gene from Escherichia
coli. Nucleotide sequence, transcriptional analysis, and homology of
its product to MRP3, a mitochondrial ribosomal protein from Neurospora
crassa.";
J. Biol. Chem. 266:2843-2851(1991).
[6]
PARTIAL NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PROTEIN SEQUENCE OF
1-27.
STRAIN=K12;
PubMed=2011493; DOI=10.1093/nar/19.1.125;
Chauhan A.K., Miczak A., Taraseviciene L., Apirion D.;
"Sequencing and expression of the rne gene of Escherichia coli.";
Nucleic Acids Res. 19:125-129(1991).
[7]
NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 844-1061, AND CHARACTERIZATION.
STRAIN=K12;
PubMed=8415644; DOI=10.1073/pnas.90.19.9006;
Cormack R.S., Genereaux J.L., Mackie G.A.;
"RNase E activity is conferred by a single polypeptide:
overexpression, purification, and properties of the ams/rne/hmp1 gene
product.";
Proc. Natl. Acad. Sci. U.S.A. 90:9006-9010(1993).
[8]
FUNCTION IN 5S RRNA MATURATION.
PubMed=6339234; DOI=10.1111/j.1432-1033.1983.tb07238.x;
Roy M.K., Singh B., Ray B.K., Apirion D.;
"Maturation of 5-S rRNA: ribonuclease E cleavages and their dependence
on precursor sequences.";
Eur. J. Biochem. 131:119-127(1983).
[9]
FUNCTION IN PROCESSING OF DICF-RNA.
PubMed=1691299; DOI=10.1016/0022-2836(90)90325-G;
Faubladier M., Cam K., Bouche J.P.;
"Escherichia coli cell division inhibitor DicF-RNA of the dicB operon.
Evidence for its generation in vivo by transcription termination and
by RNase III and RNase E-dependent processing.";
J. Mol. Biol. 212:461-471(1990).
[10]
FUNCTION.
PubMed=1708438; DOI=10.1111/j.1365-2958.1990.tb00574.x;
Mudd E.A., Krisch H.M., Higgins C.F.;
"RNase E, an endoribonuclease, has a general role in the chemical
decay of Escherichia coli mRNA: evidence that rne and ams are the same
genetic locus.";
Mol. Microbiol. 4:2127-2135(1990).
[11]
FUNCTION, INTERACTION WITH RHLB; PNPASE AND ENOLASE, AND DOMAIN.
PubMed=9732274; DOI=10.1101/gad.12.17.2770;
Vanzo N.F., Li Y.S., Py B., Blum E., Higgins C.F., Raynal L.C.,
Krisch H.M., Carpousis A.J.;
"Ribonuclease E organizes the protein interactions in the Escherichia
coli RNA degradosome.";
Genes Dev. 12:2770-2781(1998).
[12]
FUNCTION IN 16S RRNA MATURATION.
STRAIN=K12;
PubMed=10329633; DOI=10.1093/emboj/18.10.2878;
Li Z., Pandit S., Deutscher M.P.;
"RNase G (CafA protein) and RNase E are both required for the 5'
maturation of 16S ribosomal RNA.";
EMBO J. 18:2878-2885(1999).
[13]
SUBUNIT, AND SUBCELLULAR LOCATION.
PubMed=11134527; DOI=10.1073/pnas.98.1.63;
Liou G.G., Jane W.N., Cohen S.N., Lin N.S., Lin-Chao S.;
"RNA degradosomes exist in vivo in Escherichia coli as multicomponent
complexes associated with the cytoplasmic membrane via the N-terminal
region of ribonuclease E.";
Proc. Natl. Acad. Sci. U.S.A. 98:63-68(2001).
[14]
FUNCTION IN CLEAVAGE OF POLY(A).
PubMed=11328869; DOI=10.1093/nar/29.9.1864;
Walsh A.P., Tock M.R., Mallen M.H., Kaberdin V.R., Gabain Av A.,
McDowall K.J.;
"Cleavage of poly(A) tails on the 3'-end of RNA by ribonuclease E of
Escherichia coli.";
Nucleic Acids Res. 29:1864-1871(2001).
[15]
FUNCTION IN TRNA MATURATION.
STRAIN=K12;
PubMed=11871663; DOI=10.1017/S1355838202014929;
Li Z., Deutscher M.P.;
"RNase E plays an essential role in the maturation of Escherichia coli
tRNA precursors.";
RNA 8:97-109(2002).
[16]
INTERACTION WITH DEAD.
STRAIN=CF881;
PubMed=15554978; DOI=10.1111/j.1365-2958.2004.04360.x;
Prud'homme-Genereux A., Beran R.K., Iost I., Ramey C.S., Mackie G.A.,
Simons R.W.;
"Physical and functional interactions among RNase E, polynucleotide
phosphorylase and the cold-shock protein, CsdA: evidence for a 'cold
shock degradosome'.";
Mol. Microbiol. 54:1409-1421(2004).
[17]
CATALYTIC ACTIVITY, RNA-BINDING, SUBUNIT, ZINC-BINDING, COFACTOR,
IDENTIFICATION BY MASS SPECTROMETRY, AND MUTAGENESIS OF CYS-404 AND
CYS-407.
PubMed=15779893; DOI=10.1021/bi0478244;
Callaghan A.J., Redko Y., Murphy L.M., Grossmann J.G., Yates D.,
Garman E., Ilag L.L., Robinson C.V., Symmons M.F., McDowall K.J.,
Luisi B.F.;
"'Zn-link': a metal-sharing interface that organizes the quaternary
structure and catalytic site of the endoribonuclease, RNase E.";
Biochemistry 44:4667-4675(2005).
[18]
INTERACTION WITH RHLB; PNPASE AND ENOLASE.
PubMed=18337249; DOI=10.1074/jbc.M709118200;
Taghbalout A., Rothfield L.;
"RNaseE and RNA helicase B play central roles in the cytoskeletal
organization of the RNA degradosome.";
J. Biol. Chem. 283:13850-13855(2008).
[19]
CATALYTIC ACTIVITY, FUNCTION, AND MUTAGENESIS OF THR-170.
PubMed=19889093; DOI=10.1111/j.1365-2958.2009.06935.x;
Kime L., Jourdan S.S., Stead J.A., Hidalgo-Sastre A., McDowall K.J.;
"Rapid cleavage of RNA by RNase E in the absence of 5' monophosphate
stimulation.";
Mol. Microbiol. 76:590-604(2010).
[20]
ENZYME REGULATION, AND SUBCELLULAR LOCATION.
PubMed=22509045; DOI=10.1073/pnas.1120181109;
Murashko O.N., Kaberdin V.R., Lin-Chao S.;
"Membrane binding of Escherichia coli RNase E catalytic domain
stabilizes protein structure and increases RNA substrate affinity.";
Proc. Natl. Acad. Sci. U.S.A. 109:7019-7024(2012).
[21] {ECO:0000244|PDB:1SLJ, ECO:0000244|PDB:1SMX, ECO:0000244|PDB:1SN8}
X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) OF 35-125, STRUCTURE BY NMR OF
35-125, SUBUNIT, RNA-BINDING, DOMAIN, AND MUTAGENESIS OF GLY-66.
PubMed=15312761; DOI=10.1016/j.jmb.2004.05.061;
Schubert M., Edge R.E., Lario P., Cook M.A., Strynadka N.C.,
Mackie G.A., McIntosh L.P.;
"Structural characterization of the RNase E S1 domain and
identification of its oligonucleotide-binding and dimerization
interfaces.";
J. Mol. Biol. 341:37-54(2004).
[22] {ECO:0000244|PDB:2BX2, ECO:0000244|PDB:2C0B, ECO:0000244|PDB:2C4R}
X-RAY CRYSTALLOGRAPHY (2.85 ANGSTROMS) OF 1-510 IN COMPLEXES WITH RNA;
ZINC AND MAGNESIUM IONS, FUNCTION, CATALYTIC ACTIVITY, COFACTOR,
SUBUNIT, AND MUTAGENESIS OF PHE-57; PHE-67; LYS-112; THR-170; ASP-303;
ASN-305; ASP-346 AND ARG-373.
PubMed=16237448; DOI=10.1038/nature04084;
Callaghan A.J., Marcaida M.J., Stead J.A., McDowall K.J., Scott W.G.,
Luisi B.F.;
"Structure of Escherichia coli RNase E catalytic domain and
implications for RNA turnover.";
Nature 437:1187-1191(2005).
[23] {ECO:0000244|PDB:2FYM}
X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) OF 833-850 IN COMPLEX WITH ENO,
AND SUBUNIT.
PubMed=16516921; DOI=10.1016/j.jmb.2006.02.012;
Chandran V., Luisi B.F.;
"Recognition of enolase in the Escherichia coli RNA degradosome.";
J. Mol. Biol. 358:8-15(2006).
[24] {ECO:0000244|PDB:2VMK, ECO:0000244|PDB:2VRT}
X-RAY CRYSTALLOGRAPHY (3.30 ANGSTROMS) OF 1-515 IN COMPLEX WITH RNA
AND ZINC IONS, AND SUBUNIT.
PubMed=18682225; DOI=10.1016/j.str.2008.04.017;
Koslover D.J., Callaghan A.J., Marcaida M.J., Garman E.F., Martick M.,
Scott W.G., Luisi B.F.;
"The crystal structure of the Escherichia coli RNase E apoprotein and
a mechanism for RNA degradation.";
Structure 16:1238-1244(2008).
[25] {ECO:0000244|PDB:3H1C}
X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF 1021-1061 IN COMPLEXES WITH
PNP AND RNA, AND SUBUNIT.
PubMed=19327365; DOI=10.1016/j.jmb.2009.03.051;
Nurmohamed S., Vaidialingam B., Callaghan A.J., Luisi B.F.;
"Crystal structure of Escherichia coli polynucleotide phosphorylase
core bound to RNase E, RNA and manganese: implications for catalytic
mechanism and RNA degradosome assembly.";
J. Mol. Biol. 389:17-33(2009).
[26] {ECO:0000244|PDB:3H8A}
X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) OF 823-850 IN COMPLEX WITH ENO,
INTERACTION WITH ENO, IDENTIFICATION BY MASS SPECTROMETRY, AND
SUBUNIT.
PubMed=20823555; DOI=10.1107/S0907444910030015;
Nurmohamed S., McKay A.R., Robinson C.V., Luisi B.F.;
"Molecular recognition between Escherichia coli enolase and
ribonuclease E.";
Acta Crystallogr. D 66:1036-1040(2010).
-!- FUNCTION: Endoribonuclease that plays a central role in RNA
processing and decay. Required for the maturation of 5S and 16S
rRNAs and the majority of tRNAs. Also involved in the degradation
of most mRNAs. Can also process other RNA species, such as RNAI, a
molecule that controls the replication of ColE1 plasmid, and the
cell division inhibitor DicF-RNA. It initiates the decay of RNAs
by cutting them internally near their 5'-end. It is able to remove
poly(A) tails by an endonucleolytic process. {ECO:0000255|HAMAP-
Rule:MF_00970, ECO:0000269|PubMed:10329633,
ECO:0000269|PubMed:11328869, ECO:0000269|PubMed:11871663,
ECO:0000269|PubMed:16237448, ECO:0000269|PubMed:1691299,
ECO:0000269|PubMed:1708438, ECO:0000269|PubMed:19889093,
ECO:0000269|PubMed:6339234, ECO:0000269|PubMed:9732274}.
-!- CATALYTIC ACTIVITY: Endonucleolytic cleavage of single-stranded
RNA in A- and U-rich regions. {ECO:0000255|HAMAP-Rule:MF_00970,
ECO:0000269|PubMed:15779893, ECO:0000269|PubMed:16237448,
ECO:0000269|PubMed:19889093}.
-!- COFACTOR:
Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
Evidence={ECO:0000269|PubMed:15779893,
ECO:0000269|PubMed:16237448, ECO:0000269|PubMed:18682225};
Note=Binds 2 Zn(2+) ions per homotetramer. Zinc ions are bound
between subunits and are essential for homotetramerization and
catalytic activity, but not for RNA binding. In the absence of
zinc, the protein dissociates into inactive dimers.
{ECO:0000269|PubMed:15779893};
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
Evidence={ECO:0000269|PubMed:16237448};
Note=Binds 1 Mg(2+) ion per subunit.
{ECO:0000269|PubMed:16237448};
-!- ENZYME REGULATION: Binding to the membrane stabilizes protein
structure and increases affinity for the substrate.
{ECO:0000269|PubMed:22509045}.
-!- SUBUNIT: Component of the RNA degradosome, which is a multiprotein
complex involved in RNA processing and mRNA degradation. Within
the RNA degradosome, Rnase E assembles into a homotetramer formed
by a dimer of dimers. Tetramerization is essential for catalytic
activity, but not for RNA-binding. Interacts with RhlB, PNPase
(pnp) and enolase (eno). Interacts with DeaD at reduced
temperature. {ECO:0000255|HAMAP-Rule:MF_00970,
ECO:0000269|PubMed:11134527, ECO:0000269|PubMed:15312761,
ECO:0000269|PubMed:15554978, ECO:0000269|PubMed:15779893,
ECO:0000269|PubMed:16237448, ECO:0000269|PubMed:16516921,
ECO:0000269|PubMed:18337249, ECO:0000269|PubMed:18682225,
ECO:0000269|PubMed:19327365, ECO:0000269|PubMed:20823555,
ECO:0000269|PubMed:9732274}.
-!- INTERACTION:
Self; NbExp=2; IntAct=EBI-549958, EBI-549958;
P0A6Y8:dnaK; NbExp=10; IntAct=EBI-549958, EBI-542092;
P0A6P9:eno; NbExp=17; IntAct=EBI-549958, EBI-368855;
P05055:pnp; NbExp=13; IntAct=EBI-549958, EBI-548080;
P0A8J8:rhlB; NbExp=18; IntAct=EBI-549958, EBI-555806;
P21507:srmB; NbExp=3; IntAct=EBI-549958, EBI-546628;
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:11134527}.
Cell inner membrane {ECO:0000269|PubMed:11134527,
ECO:0000269|PubMed:22509045}; Peripheral membrane protein
{ECO:0000269|PubMed:11134527, ECO:0000269|PubMed:22509045};
Cytoplasmic side {ECO:0000269|PubMed:11134527,
ECO:0000269|PubMed:22509045}. Note=Associated with the cytoplasmic
membrane via the N- and C-terminal regions.
{ECO:0000269|PubMed:11134527, ECO:0000269|PubMed:22509045}.
-!- DOMAIN: The N-terminal S1 motif binds RNA, and can also bind
single-stranded DNA (in vitro). The C-terminal region interacts
with the other degradosomal components.
{ECO:0000269|PubMed:15312761, ECO:0000269|PubMed:9732274}.
-!- SIMILARITY: Belongs to the RNase E/G family. RNase E subfamily.
{ECO:0000255|HAMAP-Rule:MF_00970}.
-!- SEQUENCE CAUTION:
Sequence=AAA23443.1; Type=Frameshift; Positions=796; Evidence={ECO:0000305};
Sequence=CAA38206.1; Type=Frameshift; Positions=Several; Evidence={ECO:0000305};
Sequence=CAA47818.1; Type=Frameshift; Positions=1003; Evidence={ECO:0000305};
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EMBL; U00096; AAC74168.1; -; Genomic_DNA.
EMBL; AP009048; BAA35893.1; -; Genomic_DNA.
EMBL; X67470; CAA47818.1; ALT_FRAME; Genomic_DNA.
EMBL; M62747; AAA23443.1; ALT_FRAME; Genomic_DNA.
EMBL; X54309; CAA38206.1; ALT_FRAME; Genomic_DNA.
EMBL; L23942; AAA03347.1; -; Genomic_DNA.
PIR; A64852; S27311.
RefSeq; NP_415602.1; NC_000913.3.
RefSeq; WP_000827360.1; NZ_LN832404.1.
PDB; 1SLJ; NMR; -; A=35-125.
PDB; 1SMX; X-ray; 1.80 A; A/B=35-125.
PDB; 1SN8; X-ray; 2.00 A; A/B=35-125.
PDB; 2BX2; X-ray; 2.85 A; L=1-510.
PDB; 2C0B; X-ray; 3.18 A; L=1-510.
PDB; 2C4R; X-ray; 3.60 A; L=1-510.
PDB; 2FYM; X-ray; 1.60 A; B/E=833-850.
PDB; 2VMK; X-ray; 3.30 A; A/B/C/D=1-515.
PDB; 2VRT; X-ray; 3.50 A; A/B/C/D=1-509.
PDB; 3GCM; X-ray; 2.50 A; D/E/F=1021-1061.
PDB; 3GME; X-ray; 2.40 A; D=1021-1061.
PDB; 3H1C; X-ray; 3.57 A; D/E/F/H/J/L/N/P/S/U/W/Y=1021-1061.
PDB; 3H8A; X-ray; 1.90 A; E/F=823-850.
PDB; 5F6C; X-ray; 3.00 A; A=1-510, B=1-511.
PDBsum; 1SLJ; -.
PDBsum; 1SMX; -.
PDBsum; 1SN8; -.
PDBsum; 2BX2; -.
PDBsum; 2C0B; -.
PDBsum; 2C4R; -.
PDBsum; 2FYM; -.
PDBsum; 2VMK; -.
PDBsum; 2VRT; -.
PDBsum; 3GCM; -.
PDBsum; 3GME; -.
PDBsum; 3H1C; -.
PDBsum; 3H8A; -.
PDBsum; 5F6C; -.
DisProt; DP00207; -.
ProteinModelPortal; P21513; -.
SMR; P21513; -.
BioGrid; 4261023; 222.
DIP; DIP-10727N; -.
IntAct; P21513; 63.
MINT; MINT-1220086; -.
STRING; 316385.ECDH10B_1155; -.
PaxDb; P21513; -.
PRIDE; P21513; -.
EnsemblBacteria; AAC74168; AAC74168; b1084.
EnsemblBacteria; BAA35893; BAA35893; BAA35893.
GeneID; 945641; -.
KEGG; ecj:JW1071; -.
KEGG; eco:b1084; -.
PATRIC; fig|1411691.4.peg.1184; -.
EchoBASE; EB0852; -.
EcoGene; EG10859; rne.
eggNOG; ENOG4107QQB; Bacteria.
eggNOG; COG1530; LUCA.
HOGENOM; HOG000258027; -.
InParanoid; P21513; -.
KO; K08300; -.
BioCyc; EcoCyc:EG10859-MONOMER; -.
BioCyc; MetaCyc:EG10859-MONOMER; -.
BRENDA; 3.1.26.12; 2026.
EvolutionaryTrace; P21513; -.
PRO; PR:P21513; -.
Proteomes; UP000000318; Chromosome.
Proteomes; UP000000625; Chromosome.
GO; GO:0000015; C:phosphopyruvate hydratase complex; IDA:CAFA.
GO; GO:0005886; C:plasma membrane; IEA:UniProtKB-SubCell.
GO; GO:0008312; F:7S RNA binding; IMP:CAFA.
GO; GO:0017151; F:DEAD/H-box RNA helicase binding; IPI:CAFA.
GO; GO:0004519; F:endonuclease activity; IEA:UniProtKB-KW.
GO; GO:0042802; F:identical protein binding; IPI:IntAct.
GO; GO:0000287; F:magnesium ion binding; IMP:EcoCyc.
GO; GO:0004540; F:ribonuclease activity; IBA:GO_Central.
GO; GO:0008995; F:ribonuclease E activity; IDA:EcoCyc.
GO; GO:0003723; F:RNA binding; IMP:CAFA.
GO; GO:0006402; P:mRNA catabolic process; IMP:EcoCyc.
GO; GO:0051289; P:protein homotetramerization; IPI:EcoCyc.
GO; GO:1902280; P:regulation of ATP-dependent RNA helicase activity; IMP:CAFA.
GO; GO:0006401; P:RNA catabolic process; IDA:EcoCyc.
GO; GO:0000967; P:rRNA 5'-end processing; IMP:EcoCyc.
GO; GO:0008033; P:tRNA processing; IMP:EcoCyc.
HAMAP; MF_00970; RNase_E; 1.
InterPro; IPR012340; NA-bd_OB-fold.
InterPro; IPR021968; PNPase_C.
InterPro; IPR019307; RNA-bd_AU-1/RNase_E/G.
InterPro; IPR028878; RNase_E.
InterPro; IPR004659; RNase_E/G.
InterPro; IPR022967; S1_dom.
InterPro; IPR003029; S1_domain.
Pfam; PF12111; PNPase_C; 1.
Pfam; PF10150; RNase_E_G; 1.
Pfam; PF00575; S1; 1.
SMART; SM00316; S1; 1.
SUPFAM; SSF50249; SSF50249; 1.
TIGRFAMs; TIGR00757; RNaseEG; 1.
PROSITE; PS50126; S1; 1.
1: Evidence at protein level;
3D-structure; Cell inner membrane; Cell membrane; Complete proteome;
Cytoplasm; Direct protein sequencing; Endonuclease; Hydrolase;
Magnesium; Membrane; Metal-binding; Nuclease; Reference proteome;
RNA-binding; rRNA processing; tRNA processing; Zinc.
CHAIN 1 1061 Ribonuclease E.
/FTId=PRO_0000097373.
DOMAIN 39 119 S1 motif. {ECO:0000255|HAMAP-
Rule:MF_00970}.
REGION 57 112 Interaction with RNA.
REGION 169 170 Interaction with RNA 5'-terminal
monophosphate.
REGION 404 407 Required for zinc-mediated
homotetramerization and catalytic
activity.
REGION 833 850 Interaction with enolase.
REGION 1021 1061 Interaction with PNPase.
METAL 303 303 Magnesium; catalytic.
{ECO:0000269|PubMed:16237448}.
METAL 346 346 Magnesium; catalytic.
{ECO:0000269|PubMed:16237448}.
METAL 404 404 Zinc; shared with dimeric partner.
{ECO:0000269|PubMed:15779893,
ECO:0000269|PubMed:18682225}.
METAL 407 407 Zinc; shared with dimeric partner.
{ECO:0000269|PubMed:15779893,
ECO:0000269|PubMed:18682225}.
MUTAGEN 57 57 F->A: Reduces RNA cleavage by over 98%.
{ECO:0000269|PubMed:16237448}.
MUTAGEN 66 66 G->S: Disrupts folding of the S1 motif.
{ECO:0000269|PubMed:15312761}.
MUTAGEN 67 67 F->A: Reduces RNA cleavage by over 98%.
{ECO:0000269|PubMed:16237448}.
MUTAGEN 112 112 K->A: Reduces RNA cleavage by 98%.
{ECO:0000269|PubMed:16237448}.
MUTAGEN 170 170 T->V: Abolishes enzyme activity toward
RNA substrates with a 5' monophosphate
(PubMed:16237448). Strongly reduces
enzyme activity toward cspA mRNA
(PubMed:19889093).
{ECO:0000269|PubMed:16237448,
ECO:0000269|PubMed:19889093}.
MUTAGEN 303 303 D->N: Reduces RNA cleavage by over 96%.
{ECO:0000269|PubMed:16237448}.
MUTAGEN 305 305 N->D,L: Reduces RNA cleavage by over 96%.
{ECO:0000269|PubMed:16237448}.
MUTAGEN 346 346 D->N: Reduces RNA cleavage by over 96%.
{ECO:0000269|PubMed:16237448}.
MUTAGEN 373 373 R->A,D: Reduces RNA cleavage by 89%.
{ECO:0000269|PubMed:16237448}.
MUTAGEN 404 404 C->A: Reduces zinc-binding. Abolishes
homotetramerization and enzyme activity.
{ECO:0000269|PubMed:15779893}.
MUTAGEN 407 407 C->A: Reduces zinc-binding. Abolishes
homotetramerization and enzyme activity.
{ECO:0000269|PubMed:15779893}.
CONFLICT 390 390 Q -> H (in Ref. 5; AAA23443).
{ECO:0000305}.
CONFLICT 487 487 L -> V (in Ref. 4; CAA47818 and 5;
AAA23443). {ECO:0000305}.
CONFLICT 564 564 A -> R (in Ref. 4; CAA47818).
{ECO:0000305}.
CONFLICT 784 784 N -> K (in Ref. 4; CAA47818).
{ECO:0000305}.
CONFLICT 838 838 A -> R (in Ref. 5; AAA23443).
{ECO:0000305}.
CONFLICT 905 905 P -> R (in Ref. 4; CAA47818).
{ECO:0000305}.
CONFLICT 1048 1048 H -> R (in Ref. 7; AAA03347).
{ECO:0000305}.
STRAND 2 7 {ECO:0000244|PDB:2BX2}.
STRAND 10 12 {ECO:0000244|PDB:2VMK}.
STRAND 14 20 {ECO:0000244|PDB:2BX2}.
STRAND 23 30 {ECO:0000244|PDB:2BX2}.
STRAND 32 34 {ECO:0000244|PDB:2BX2}.
STRAND 36 39 {ECO:0000244|PDB:1SLJ}.
STRAND 42 50 {ECO:0000244|PDB:1SMX}.
HELIX 51 53 {ECO:0000244|PDB:1SMX}.
STRAND 55 64 {ECO:0000244|PDB:1SMX}.
STRAND 66 69 {ECO:0000244|PDB:1SMX}.
HELIX 70 72 {ECO:0000244|PDB:1SMX}.
HELIX 75 77 {ECO:0000244|PDB:1SMX}.
STRAND 84 86 {ECO:0000244|PDB:1SMX}.
HELIX 90 92 {ECO:0000244|PDB:1SMX}.
STRAND 99 106 {ECO:0000244|PDB:1SMX}.
STRAND 109 112 {ECO:0000244|PDB:5F6C}.
STRAND 115 118 {ECO:0000244|PDB:1SMX}.
STRAND 125 130 {ECO:0000244|PDB:2BX2}.
STRAND 134 136 {ECO:0000244|PDB:2C0B}.
STRAND 137 139 {ECO:0000244|PDB:5F6C}.
TURN 145 148 {ECO:0000244|PDB:2VRT}.
HELIX 151 155 {ECO:0000244|PDB:2BX2}.
STRAND 165 168 {ECO:0000244|PDB:2BX2}.
HELIX 170 174 {ECO:0000244|PDB:2BX2}.
HELIX 177 199 {ECO:0000244|PDB:2BX2}.
STRAND 205 208 {ECO:0000244|PDB:2BX2}.
STRAND 210 212 {ECO:0000244|PDB:2VMK}.
HELIX 213 221 {ECO:0000244|PDB:2BX2}.
STRAND 226 232 {ECO:0000244|PDB:2BX2}.
HELIX 234 246 {ECO:0000244|PDB:2BX2}.
HELIX 250 255 {ECO:0000244|PDB:2BX2}.
STRAND 256 258 {ECO:0000244|PDB:2BX2}.
HELIX 265 268 {ECO:0000244|PDB:2BX2}.
HELIX 272 277 {ECO:0000244|PDB:2BX2}.
STRAND 281 284 {ECO:0000244|PDB:2BX2}.
STRAND 290 295 {ECO:0000244|PDB:2BX2}.
STRAND 300 305 {ECO:0000244|PDB:2BX2}.
STRAND 311 313 {ECO:0000244|PDB:5F6C}.
HELIX 315 336 {ECO:0000244|PDB:2BX2}.
STRAND 341 346 {ECO:0000244|PDB:2BX2}.
HELIX 353 366 {ECO:0000244|PDB:2BX2}.
TURN 367 369 {ECO:0000244|PDB:2BX2}.
STRAND 374 379 {ECO:0000244|PDB:2BX2}.
STRAND 383 389 {ECO:0000244|PDB:2BX2}.
HELIX 396 400 {ECO:0000244|PDB:2BX2}.
STRAND 401 403 {ECO:0000244|PDB:5F6C}.
STRAND 405 411 {ECO:0000244|PDB:2BX2}.
HELIX 416 432 {ECO:0000244|PDB:2BX2}.
STRAND 433 435 {ECO:0000244|PDB:5F6C}.
STRAND 436 443 {ECO:0000244|PDB:2BX2}.
HELIX 445 451 {ECO:0000244|PDB:2BX2}.
TURN 452 455 {ECO:0000244|PDB:2BX2}.
HELIX 456 465 {ECO:0000244|PDB:2BX2}.
TURN 466 468 {ECO:0000244|PDB:2BX2}.
STRAND 470 475 {ECO:0000244|PDB:2BX2}.
STRAND 485 490 {ECO:0000244|PDB:2BX2}.
TURN 491 493 {ECO:0000244|PDB:2C0B}.
HELIX 499 501 {ECO:0000244|PDB:2BX2}.
HELIX 502 506 {ECO:0000244|PDB:2BX2}.
TURN 507 509 {ECO:0000244|PDB:2BX2}.
HELIX 831 833 {ECO:0000244|PDB:3H8A}.
HELIX 835 838 {ECO:0000244|PDB:2FYM}.
SEQUENCE 1061 AA; 118197 MW; D4066D80E1DE7D37 CRC64;
MKRMLINATQ QEELRVALVD GQRLYDLDIE SPGHEQKKAN IYKGKITRIE PSLEAAFVDY
GAERHGFLPL KEIAREYFPA NYSAHGRPNI KDVLREGQEV IVQIDKEERG NKGAALTTFI
SLAGSYLVLM PNNPRAGGIS RRIEGDDRTE LKEALASLEL PEGMGLIVRT AGVGKSAEAL
QWDLSFRLKH WEAIKKAAES RPAPFLIHQE SNVIVRAFRD YLRQDIGEIL IDNPKVLELA
RQHIAALGRP DFSSKIKLYT GEIPLFSHYQ IESQIESAFQ REVRLPSGGS IVIDSTEALT
AIDINSARAT RGGDIEETAF NTNLEAADEI ARQLRLRDLG GLIVIDFIDM TPVRHQRAVE
NRLREAVRQD RARIQISHIS RFGLLEMSRQ RLSPSLGESS HHVCPRCSGT GTVRDNESLS
LSILRLIEEE ALKENTQEVH AIVPVPIASY LLNEKRSAVN AIETRQDGVR CVIVPNDQME
TPHYHVLRVR KGEETPTLSY MLPKLHEEAM ALPSEEEFAE RKRPEQPALA TFAMPDVPPA
PTPAEPAAPV VAPAPKAAPA TPAAPAQPGL LSRFFGALKA LFSGGEETKP TEQPAPKAEA
KPERQQDRRK PRQNNRRDRN ERRDTRSERT EGSDNREENR RNRRQAQQQT AETRESRQQA
EVTEKARTAD EQQAPRRERS RRRNDDKRQA QQEAKALNVE EQSVQETEQE ERVRPVQPRR
KQRQLNQKVR YEQSVAEEAV VAPVVEETVA AEPIVQEAPA PRTELVKVPL PVVAQTAPEQ
QEENNADNRD NGGMPRRSRR SPRHLRVSGQ RRRRYRDERY PTQSPMPLTV ACASPELASG
KVWIRYPIVR PQDVQVEEQR EQEEVHVQPM VTEVPVAAAI EPVVSAPVVE EVAGVVEAPV
QVAEPQPEVV ETTHPEVIAA AVTEQPQVIT ESDVAVAQEV AEQAEPVVEP QEETADIEEV
VETAEVVVAE PEVVAQPAAP VVAEVAAEVE TVAAVEPEVT VEHNHATAPM TRAPAPEYVP
EAPRHSDWQR PTFAFEGKGA AGGHTATHHA SAAPARPQPV E


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