RNE_ECOLI
ID RNE_ECOLI Reviewed; 1061 AA.
AC P21513; P77591;
DT 01-MAY-1991, integrated into UniProtKB/Swiss-Prot.
DT 29-AUG-2003, sequence version 6.
DT 03-AUG-2022, entry version 207.
DE RecName: Full=Ribonuclease E {ECO:0000255|HAMAP-Rule:MF_00970};
DE Short=RNase E {ECO:0000255|HAMAP-Rule:MF_00970};
DE EC=3.1.26.12 {ECO:0000255|HAMAP-Rule:MF_00970};
GN Name=rne {ECO:0000255|HAMAP-Rule:MF_00970, ECO:0000303|PubMed:2011493};
GN Synonyms=ams {ECO:0000303|PubMed:1704367}, hmp1;
GN OrderedLocusNames=b1084, JW1071;
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 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=8905232; DOI=10.1093/dnares/3.3.137;
RA Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K.,
RA Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S.,
RA Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K., Mori H.,
RA Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G.,
RA Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M.,
RA Horiuchi T.;
RT "A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 12.7-28.0 min region on the linkage map.";
RL DNA Res. 3:137-155(1996).
RN [2]
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 [3]
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 [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-1025.
RC STRAIN=K12;
RX PubMed=1447789; DOI=10.1016/0022-2836(92)90489-7;
RA Casaregola S., Jacq A., Laoudj D., McGurk G., Margarson S., Tempete M.,
RA Norris V., Holland I.B.;
RT "Cloning and analysis of the entire Escherichia coli ams gene. ams is
RT identical to hmp1 and encodes a 114 kDa protein that migrates as a 180 kDa
RT protein.";
RL J. Mol. Biol. 228:30-40(1992).
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-844.
RC STRAIN=K12;
RX PubMed=1704367; DOI=10.1016/s0021-9258(18)49924-3;
RA Claverie-Martin F., Diaz-Torres M., Yancey S.D., Kushner S.R.;
RT "Analysis of the altered mRNA stability (ams) gene from Escherichia coli.
RT Nucleotide sequence, transcriptional analysis, and homology of its product
RT to MRP3, a mitochondrial ribosomal protein from Neurospora crassa.";
RL J. Biol. Chem. 266:2843-2851(1991).
RN [6]
RP PARTIAL NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PROTEIN SEQUENCE OF 1-27.
RC STRAIN=K12;
RX PubMed=2011493; DOI=10.1093/nar/19.1.125;
RA Chauhan A.K., Miczak A., Taraseviciene L., Apirion D.;
RT "Sequencing and expression of the rne gene of Escherichia coli.";
RL Nucleic Acids Res. 19:125-129(1991).
RN [7]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 844-1061, AND CHARACTERIZATION.
RC STRAIN=K12;
RX PubMed=8415644; DOI=10.1073/pnas.90.19.9006;
RA Cormack R.S., Genereaux J.L., Mackie G.A.;
RT "RNase E activity is conferred by a single polypeptide: overexpression,
RT purification, and properties of the ams/rne/hmp1 gene product.";
RL Proc. Natl. Acad. Sci. U.S.A. 90:9006-9010(1993).
RN [8]
RP FUNCTION IN 5S RRNA MATURATION.
RX PubMed=6339234; DOI=10.1111/j.1432-1033.1983.tb07238.x;
RA Roy M.K., Singh B., Ray B.K., Apirion D.;
RT "Maturation of 5-S rRNA: ribonuclease E cleavages and their dependence on
RT precursor sequences.";
RL Eur. J. Biochem. 131:119-127(1983).
RN [9]
RP FUNCTION IN PROCESSING OF DICF-RNA.
RX PubMed=1691299; DOI=10.1016/0022-2836(90)90325-g;
RA Faubladier M., Cam K., Bouche J.P.;
RT "Escherichia coli cell division inhibitor DicF-RNA of the dicB operon.
RT Evidence for its generation in vivo by transcription termination and by
RT RNase III and RNase E-dependent processing.";
RL J. Mol. Biol. 212:461-471(1990).
RN [10]
RP FUNCTION.
RX PubMed=1708438; DOI=10.1111/j.1365-2958.1990.tb00574.x;
RA Mudd E.A., Krisch H.M., Higgins C.F.;
RT "RNase E, an endoribonuclease, has a general role in the chemical decay of
RT Escherichia coli mRNA: evidence that rne and ams are the same genetic
RT locus.";
RL Mol. Microbiol. 4:2127-2135(1990).
RN [11]
RP FUNCTION, INTERACTION WITH RHLB; PNPASE AND ENOLASE, AND DOMAIN.
RX PubMed=9732274; DOI=10.1101/gad.12.17.2770;
RA Vanzo N.F., Li Y.S., Py B., Blum E., Higgins C.F., Raynal L.C.,
RA Krisch H.M., Carpousis A.J.;
RT "Ribonuclease E organizes the protein interactions in the Escherichia coli
RT RNA degradosome.";
RL Genes Dev. 12:2770-2781(1998).
RN [12]
RP FUNCTION IN 16S RRNA MATURATION, AND DISRUPTION PHENOTYPE.
RC STRAIN=K12;
RX PubMed=10329633; DOI=10.1093/emboj/18.10.2878;
RA Li Z., Pandit S., Deutscher M.P.;
RT "RNase G (CafA protein) and RNase E are both required for the 5' maturation
RT of 16S ribosomal RNA.";
RL EMBO J. 18:2878-2885(1999).
RN [13]
RP FUNCTION AS AN ENDONUCLEASE, AND SUBSTRATE SPECIFICITY.
RX PubMed=10762247; DOI=10.1128/jb.182.9.2468-2475.2000;
RA Jiang X., Diwa A., Belasco J.G.;
RT "Regions of RNase E important for 5'-end-dependent RNA cleavage and
RT autoregulated synthesis.";
RL J. Bacteriol. 182:2468-2475(2000).
RN [14]
RP SUBUNIT, AND SUBCELLULAR LOCATION.
RX PubMed=11134527; DOI=10.1073/pnas.98.1.63;
RA Liou G.G., Jane W.N., Cohen S.N., Lin N.S., Lin-Chao S.;
RT "RNA degradosomes exist in vivo in Escherichia coli as multicomponent
RT complexes associated with the cytoplasmic membrane via the N-terminal
RT region of ribonuclease E.";
RL Proc. Natl. Acad. Sci. U.S.A. 98:63-68(2001).
RN [15]
RP FUNCTION IN CLEAVAGE OF POLY(A).
RX PubMed=11328869; DOI=10.1093/nar/29.9.1864;
RA Walsh A.P., Tock M.R., Mallen M.H., Kaberdin V.R., Gabain Av A.,
RA McDowall K.J.;
RT "Cleavage of poly(A) tails on the 3'-end of RNA by ribonuclease E of
RT Escherichia coli.";
RL Nucleic Acids Res. 29:1864-1871(2001).
RN [16]
RP FUNCTION IN TRNA MATURATION.
RC STRAIN=K12;
RX PubMed=11871663; DOI=10.1017/s1355838202014929;
RA Li Z., Deutscher M.P.;
RT "RNase E plays an essential role in the maturation of Escherichia coli tRNA
RT precursors.";
RL RNA 8:97-109(2002).
RN [17]
RP INTERACTION WITH DEAD.
RC STRAIN=CF881;
RX PubMed=15554978; DOI=10.1111/j.1365-2958.2004.04360.x;
RA Prud'homme-Genereux A., Beran R.K., Iost I., Ramey C.S., Mackie G.A.,
RA Simons R.W.;
RT "Physical and functional interactions among RNase E, polynucleotide
RT phosphorylase and the cold-shock protein, CsdA: evidence for a 'cold shock
RT degradosome'.";
RL Mol. Microbiol. 54:1409-1421(2004).
RN [18]
RP ACTIVITY REGULATION, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=15197283; DOI=10.1073/pnas.0401382101;
RA Jiang X., Belasco J.G.;
RT "Catalytic activation of multimeric RNase E and RNase G by 5'-
RT monophosphorylated RNA.";
RL Proc. Natl. Acad. Sci. U.S.A. 101:9211-9216(2004).
RN [19]
RP CATALYTIC ACTIVITY, RNA-BINDING, SUBUNIT, ZINC-BINDING, COFACTOR,
RP IDENTIFICATION BY MASS SPECTROMETRY, AND MUTAGENESIS OF CYS-404 AND
RP CYS-407.
RX PubMed=15779893; DOI=10.1021/bi0478244;
RA Callaghan A.J., Redko Y., Murphy L.M., Grossmann J.G., Yates D., Garman E.,
RA Ilag L.L., Robinson C.V., Symmons M.F., McDowall K.J., Luisi B.F.;
RT "'Zn-link': a metal-sharing interface that organizes the quaternary
RT structure and catalytic site of the endoribonuclease, RNase E.";
RL Biochemistry 44:4667-4675(2005).
RN [20]
RP INTERACTION WITH RHLB; PNPASE AND ENOLASE.
RX PubMed=18337249; DOI=10.1074/jbc.m709118200;
RA Taghbalout A., Rothfield L.;
RT "RNaseE and RNA helicase B play central roles in the cytoskeletal
RT organization of the RNA degradosome.";
RL J. Biol. Chem. 283:13850-13855(2008).
RN [21]
RP CATALYTIC ACTIVITY, FUNCTION, AND MUTAGENESIS OF THR-170.
RX PubMed=19889093; DOI=10.1111/j.1365-2958.2009.06935.x;
RA Kime L., Jourdan S.S., Stead J.A., Hidalgo-Sastre A., McDowall K.J.;
RT "Rapid cleavage of RNA by RNase E in the absence of 5' monophosphate
RT stimulation.";
RL Mol. Microbiol. 76:590-604(2010).
RN [22]
RP ACTIVITY REGULATION, AND SUBCELLULAR LOCATION.
RX PubMed=22509045; DOI=10.1073/pnas.1120181109;
RA Murashko O.N., Kaberdin V.R., Lin-Chao S.;
RT "Membrane binding of Escherichia coli RNase E catalytic domain stabilizes
RT protein structure and increases RNA substrate affinity.";
RL Proc. Natl. Acad. Sci. U.S.A. 109:7019-7024(2012).
RN [23]
RP SUBSTRATE SPECIFICITY.
RX PubMed=26694614; DOI=10.1074/jbc.m115.702555;
RA Richards J., Belasco J.G.;
RT "Distinct Requirements for 5'-Monophosphate-assisted RNA Cleavage by
RT Escherichia coli RNase E and RNase G.";
RL J. Biol. Chem. 291:5038-5048(2016).
RN [24]
RP ERRATUM.
RX PubMed=27664066; DOI=10.1074/jbc.a115.702555;
RA Richards J., Belasco J.G.;
RT "Distinct requirements for 5'-monophosphate-assisted RNA cleavage by
RT Escherichia coli RNase E and RNase G.";
RL J. Biol. Chem. 291:20825-20825(2016).
RN [25]
RP FUNCTION IN TRNA(PRO) 3' PROCESSING.
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=27288443; DOI=10.1093/nar/gkw517;
RA Mohanty B.K., Petree J.R., Kushner S.R.;
RT "Endonucleolytic cleavages by RNase E generate the mature 3' termini of the
RT three proline tRNAs in Escherichia coli.";
RL Nucleic Acids Res. 44:6350-6362(2016).
RN [26]
RP FUNCTION IN RRNA DEGRADATION.
RC STRAIN=K12 / MG1655(Seq)*;
RX PubMed=27298395; DOI=10.1261/rna.056275.116;
RA Sulthana S., Basturea G.N., Deutscher M.P.;
RT "Elucidation of pathways of ribosomal RNA degradation: an essential role
RT for RNase E.";
RL RNA 22:1163-1171(2016).
RN [27]
RP X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) OF 35-125, STRUCTURE BY NMR OF
RP 35-125, SUBUNIT, RNA-BINDING, DOMAIN, AND MUTAGENESIS OF GLY-66.
RX PubMed=15312761; DOI=10.1016/j.jmb.2004.05.061;
RA Schubert M., Edge R.E., Lario P., Cook M.A., Strynadka N.C., Mackie G.A.,
RA McIntosh L.P.;
RT "Structural characterization of the RNase E S1 domain and identification of
RT its oligonucleotide-binding and dimerization interfaces.";
RL J. Mol. Biol. 341:37-54(2004).
RN [28]
RP X-RAY CRYSTALLOGRAPHY (2.85 ANGSTROMS) OF 1-510 IN COMPLEXES WITH RNA; ZINC
RP AND MAGNESIUM IONS, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, SUBUNIT, AND
RP MUTAGENESIS OF PHE-57; PHE-67; LYS-112; THR-170; ASP-303; ASN-305; ASP-346
RP AND ARG-373.
RX PubMed=16237448; DOI=10.1038/nature04084;
RA Callaghan A.J., Marcaida M.J., Stead J.A., McDowall K.J., Scott W.G.,
RA Luisi B.F.;
RT "Structure of Escherichia coli RNase E catalytic domain and implications
RT for RNA turnover.";
RL Nature 437:1187-1191(2005).
RN [29]
RP X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) OF 833-850 IN COMPLEX WITH ENO, AND
RP SUBUNIT.
RX PubMed=16516921; DOI=10.1016/j.jmb.2006.02.012;
RA Chandran V., Luisi B.F.;
RT "Recognition of enolase in the Escherichia coli RNA degradosome.";
RL J. Mol. Biol. 358:8-15(2006).
RN [30]
RP X-RAY CRYSTALLOGRAPHY (3.30 ANGSTROMS) OF 1-515 IN COMPLEX WITH RNA AND
RP ZINC IONS, AND SUBUNIT.
RX PubMed=18682225; DOI=10.1016/j.str.2008.04.017;
RA Koslover D.J., Callaghan A.J., Marcaida M.J., Garman E.F., Martick M.,
RA Scott W.G., Luisi B.F.;
RT "The crystal structure of the Escherichia coli RNase E apoprotein and a
RT mechanism for RNA degradation.";
RL Structure 16:1238-1244(2008).
RN [31]
RP X-RAY CRYSTALLOGRAPHY (2.4 ANGSTROMS) OF 1021-1061 IN COMPLEXES WITH PNP
RP AND RNA, AND SUBUNIT.
RX PubMed=19327365; DOI=10.1016/j.jmb.2009.03.051;
RA Nurmohamed S., Vaidialingam B., Callaghan A.J., Luisi B.F.;
RT "Crystal structure of Escherichia coli polynucleotide phosphorylase core
RT bound to RNase E, RNA and manganese: implications for catalytic mechanism
RT and RNA degradosome assembly.";
RL J. Mol. Biol. 389:17-33(2009).
RN [32]
RP X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) OF 823-850 IN COMPLEX WITH ENO,
RP INTERACTION WITH ENO, IDENTIFICATION BY MASS SPECTROMETRY, AND SUBUNIT.
RX PubMed=20823555; DOI=10.1107/s0907444910030015;
RA Nurmohamed S., McKay A.R., Robinson C.V., Luisi B.F.;
RT "Molecular recognition between Escherichia coli enolase and ribonuclease
RT E.";
RL Acta Crystallogr. D 66:1036-1040(2010).
CC -!- FUNCTION: Endoribonuclease that plays a central role in RNA processing
CC and decay. Required for the maturation of 5S and 16S rRNAs and the
CC majority of tRNAs. Also involved in the degradation of most mRNAs. Can
CC also process other RNA species, such as RNAI, a molecule that controls
CC the replication of ColE1 plasmid, and the cell division inhibitor DicF-
CC RNA. It initiates the decay of RNAs by cutting them internally near
CC their 5'-end. It is able to remove poly(A) tails by an endonucleolytic
CC process. Required to initiate rRNA degradation during both starvation
CC and quality control; acts after RNase PH (rph) exonucleolytically
CC digests the 3'-end of the 16S rRNA (PubMed:27298395). Degradation of
CC 16S rRNA leads to 23S rRNA degradation (PubMed:27298395). Processes the
CC 3 tRNA(Pro) precursors immediately after the 3'-CCA to generate the
CC mature ends (PubMed:27288443). {ECO:0000255|HAMAP-Rule:MF_00970,
CC ECO:0000269|PubMed:10329633, ECO:0000269|PubMed:10762247,
CC ECO:0000269|PubMed:11328869, ECO:0000269|PubMed:11871663,
CC ECO:0000269|PubMed:16237448, ECO:0000269|PubMed:1691299,
CC ECO:0000269|PubMed:1708438, ECO:0000269|PubMed:19889093,
CC ECO:0000269|PubMed:27288443, ECO:0000269|PubMed:27298395,
CC ECO:0000269|PubMed:6339234, ECO:0000269|PubMed:9732274}.
CC -!- FUNCTION: Prefers 5'-monophosphorylated substrates over 5'-
CC triphosphorylated substrates (PubMed:10762247). 5'-monophosphate-
CC assisted cleavage requires at least 2 and preferably 3 or more unpaired
CC 5'-terminal nucleotides. The optimal spacing between the 5' end and the
CC scissile phosphate appears to be 8 nucleotides. Any sequence of
CC unpaired nucleotides at the 5'-end is tolerated (PubMed:26694614).
CC {ECO:0000269|PubMed:10762247, ECO:0000269|PubMed:26694614}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Endonucleolytic cleavage of single-stranded RNA in A- and U-
CC rich regions.; EC=3.1.26.12; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_00970, ECO:0000269|PubMed:15779893,
CC ECO:0000269|PubMed:16237448, ECO:0000269|PubMed:19889093};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000269|PubMed:15779893, ECO:0000269|PubMed:16237448,
CC ECO:0000269|PubMed:18682225};
CC Note=Binds 2 Zn(2+) ions per homotetramer. Zinc ions are bound between
CC subunits and are essential for homotetramerization and catalytic
CC activity, but not for RNA binding. In the absence of zinc, the protein
CC dissociates into inactive dimers. {ECO:0000269|PubMed:15779893};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:16237448};
CC Note=Binds 1 Mg(2+) ion per subunit. {ECO:0000269|PubMed:16237448};
CC -!- ACTIVITY REGULATION: The presence of a 5'-monophosphate on substrate
CC RNA accelerates its cleavage by catalytically activating the enzyme
CC (PubMed:15197283). Binding to the membrane stabilizes protein structure
CC and increases affinity for the substrate. {ECO:0000269|PubMed:15197283,
CC ECO:0000269|PubMed:22509045}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.60 uM for 5'-phosphorylated fluorogenic substrate
CC {ECO:0000269|PubMed:15197283};
CC KM=0.57 uM for 5'-OH fluorogenic substrate
CC {ECO:0000269|PubMed:15197283};
CC Note=kcat is 0.83 min(-1) for 5'-PO(4) substrate and 0.088 min(-1)
CC for 5-OH substrate. {ECO:0000269|PubMed:15197283};
CC -!- SUBUNIT: Component of the RNA degradosome, which is a multiprotein
CC complex involved in RNA processing and mRNA degradation. Within the RNA
CC degradosome, RNase E assembles into a homotetramer formed by a dimer of
CC dimers. Tetramerization is essential for catalytic activity, but not
CC for RNA-binding. Interacts with RhlB, PNPase (pnp) and enolase (eno).
CC Interacts with DeaD at reduced temperature. {ECO:0000255|HAMAP-
CC Rule:MF_00970, ECO:0000269|PubMed:11134527,
CC ECO:0000269|PubMed:15312761, ECO:0000269|PubMed:15554978,
CC ECO:0000269|PubMed:15779893, ECO:0000269|PubMed:16237448,
CC ECO:0000269|PubMed:16516921, ECO:0000269|PubMed:18337249,
CC ECO:0000269|PubMed:18682225, ECO:0000269|PubMed:19327365,
CC ECO:0000269|PubMed:20823555, ECO:0000269|PubMed:9732274}.
CC -!- INTERACTION:
CC P21513; P0A6Y8: dnaK; NbExp=10; IntAct=EBI-549958, EBI-542092;
CC P21513; P0A6P9: eno; NbExp=17; IntAct=EBI-549958, EBI-368855;
CC P21513; P05055: pnp; NbExp=13; IntAct=EBI-549958, EBI-548080;
CC P21513; P0A8J8: rhlB; NbExp=18; IntAct=EBI-549958, EBI-555806;
CC P21513; P21513: rne; NbExp=2; IntAct=EBI-549958, EBI-549958;
CC P21513; P21507: srmB; NbExp=3; IntAct=EBI-549958, EBI-546628;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:11134527}. Cell
CC inner membrane {ECO:0000269|PubMed:11134527,
CC ECO:0000269|PubMed:22509045}; Peripheral membrane protein
CC {ECO:0000269|PubMed:11134527, ECO:0000269|PubMed:22509045}; Cytoplasmic
CC side {ECO:0000269|PubMed:11134527, ECO:0000269|PubMed:22509045}.
CC Note=Associated with the cytoplasmic membrane via the N- and C-terminal
CC regions. {ECO:0000269|PubMed:11134527, ECO:0000269|PubMed:22509045}.
CC -!- DOMAIN: The N-terminal S1 motif binds RNA, and can also bind single-
CC stranded DNA (in vitro). The C-terminal region interacts with the other
CC degradosomal components. {ECO:0000269|PubMed:15312761,
CC ECO:0000269|PubMed:9732274}.
CC -!- DISRUPTION PHENOTYPE: Essential, it cannot be deleted. In a temperature
CC sensitive mutant at non-permissive temperature, slow processing of the
CC 17S rRNA precursor to 16S rRNA; a double rne-rng mutated strain no
CC longer processes the 17S rRNA precursor. {ECO:0000269|PubMed:10329633}.
CC -!- MISCELLANEOUS: In K12 strains that are derived from W1485 (including
CC MG1655 and W3110) the rph gene has a frameshift that leads to loss of
CC its ribonuclease PH activity. In strain K12 / MG1655(Seq)* the wild-
CC type Rph protein has been restored (PubMed:27298395).
CC {ECO:0000269|PubMed:27298395}.
CC -!- SIMILARITY: Belongs to the RNase E/G family. RNase E subfamily.
CC {ECO:0000255|HAMAP-Rule:MF_00970}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAA23443.1; Type=Frameshift; Evidence={ECO:0000305};
CC Sequence=CAA38206.1; Type=Frameshift; Evidence={ECO:0000305};
CC Sequence=CAA47818.1; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; U00096; AAC74168.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA35893.1; -; Genomic_DNA.
DR EMBL; X67470; CAA47818.1; ALT_FRAME; Genomic_DNA.
DR EMBL; M62747; AAA23443.1; ALT_FRAME; Genomic_DNA.
DR EMBL; X54309; CAA38206.1; ALT_FRAME; Genomic_DNA.
DR EMBL; L23942; AAA03347.1; -; Genomic_DNA.
DR PIR; A64852; S27311.
DR RefSeq; NP_415602.1; NC_000913.3.
DR RefSeq; WP_000827360.1; NZ_LN832404.1.
DR PDB; 1SLJ; NMR; -; A=35-125.
DR PDB; 1SMX; X-ray; 1.80 A; A/B=35-125.
DR PDB; 1SN8; X-ray; 2.00 A; A/B=35-125.
DR PDB; 2BX2; X-ray; 2.85 A; L=1-510.
DR PDB; 2C0B; X-ray; 3.18 A; L=1-510.
DR PDB; 2C4R; X-ray; 3.60 A; L=1-510.
DR PDB; 2FYM; X-ray; 1.60 A; B/E=833-850.
DR PDB; 2VMK; X-ray; 3.30 A; A/B/C/D=1-515.
DR PDB; 2VRT; X-ray; 3.50 A; A/B/C/D=1-509.
DR PDB; 3GCM; X-ray; 2.50 A; D/E/F=1021-1061.
DR PDB; 3GME; X-ray; 2.40 A; D=1021-1061.
DR PDB; 3H1C; X-ray; 3.57 A; D/E/F/H/J/L/N/P/S/U/W/Y=1021-1061.
DR PDB; 3H8A; X-ray; 1.90 A; E/F=823-850.
DR PDB; 5F6C; X-ray; 3.00 A; A=1-510, B=1-511.
DR PDB; 6G63; X-ray; 3.95 A; A/G/L/N=1-510.
DR PDBsum; 1SLJ; -.
DR PDBsum; 1SMX; -.
DR PDBsum; 1SN8; -.
DR PDBsum; 2BX2; -.
DR PDBsum; 2C0B; -.
DR PDBsum; 2C4R; -.
DR PDBsum; 2FYM; -.
DR PDBsum; 2VMK; -.
DR PDBsum; 2VRT; -.
DR PDBsum; 3GCM; -.
DR PDBsum; 3GME; -.
DR PDBsum; 3H1C; -.
DR PDBsum; 3H8A; -.
DR PDBsum; 5F6C; -.
DR PDBsum; 6G63; -.
DR AlphaFoldDB; P21513; -.
DR BMRB; P21513; -.
DR SASBDB; P21513; -.
DR SMR; P21513; -.
DR BioGRID; 4261023; 251.
DR BioGRID; 850013; 1.
DR ComplexPortal; CPX-403; RNA degradosome.
DR DIP; DIP-10727N; -.
DR IntAct; P21513; 63.
DR MINT; P21513; -.
DR STRING; 511145.b1084; -.
DR jPOST; P21513; -.
DR PaxDb; P21513; -.
DR PRIDE; P21513; -.
DR EnsemblBacteria; AAC74168; AAC74168; b1084.
DR EnsemblBacteria; BAA35893; BAA35893; BAA35893.
DR GeneID; 945641; -.
DR KEGG; ecj:JW1071; -.
DR KEGG; eco:b1084; -.
DR PATRIC; fig|1411691.4.peg.1184; -.
DR EchoBASE; EB0852; -.
DR eggNOG; COG1530; Bacteria.
DR HOGENOM; CLU_003468_1_2_6; -.
DR InParanoid; P21513; -.
DR OMA; SDWVRPA; -.
DR PhylomeDB; P21513; -.
DR BioCyc; EcoCyc:EG10859-MON; -.
DR BioCyc; MetaCyc:EG10859-MON; -.
DR BRENDA; 3.1.26.12; 2026.
DR EvolutionaryTrace; P21513; -.
DR PRO; PR:P21513; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:1990061; C:bacterial degradosome; IDA:EcoCyc.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0009898; C:cytoplasmic side of plasma membrane; IEA:UniProtKB-UniRule.
DR GO; GO:1902555; C:endoribonuclease complex; IDA:EcoCyc.
DR GO; GO:0016020; C:membrane; IDA:ComplexPortal.
DR GO; GO:0008312; F:7S RNA binding; IMP:CAFA.
DR GO; GO:0017151; F:DEAD/H-box RNA helicase binding; IPI:CAFA.
DR GO; GO:0004521; F:endoribonuclease activity; IEA:UniProtKB-UniRule.
DR GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR GO; GO:0000287; F:magnesium ion binding; IMP:EcoCyc.
DR GO; GO:0004540; F:ribonuclease activity; IBA:GO_Central.
DR GO; GO:0008995; F:ribonuclease E activity; IDA:EcoCyc.
DR GO; GO:0003723; F:RNA binding; IMP:CAFA.
DR GO; GO:0019843; F:rRNA binding; IEA:UniProtKB-KW.
DR GO; GO:0000049; F:tRNA binding; IEA:UniProtKB-KW.
DR GO; GO:0008270; F:zinc ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0006402; P:mRNA catabolic process; IMP:EcoCyc.
DR GO; GO:1902280; P:regulation of RNA helicase activity; IMP:CAFA.
DR GO; GO:0006401; P:RNA catabolic process; IDA:EcoCyc.
DR GO; GO:0006396; P:RNA processing; IC:ComplexPortal.
DR GO; GO:0000967; P:rRNA 5'-end processing; IMP:EcoCyc.
DR GO; GO:0006364; P:rRNA processing; IBA:GO_Central.
DR GO; GO:0008033; P:tRNA processing; IMP:EcoCyc.
DR DisProt; DP00207; -.
DR Gene3D; 2.40.50.140; -; 1.
DR HAMAP; MF_00970; RNase_E; 1.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR InterPro; IPR021968; PNPase_C.
DR InterPro; IPR019307; RNA-bd_AU-1/RNase_E/G.
DR InterPro; IPR028878; RNase_E.
DR InterPro; IPR004659; RNase_E/G.
DR InterPro; IPR022967; S1_dom.
DR InterPro; IPR003029; S1_domain.
DR PANTHER; PTHR30001; PTHR30001; 1.
DR Pfam; PF12111; PNPase_C; 1.
DR Pfam; PF10150; RNase_E_G; 1.
DR Pfam; PF00575; S1; 1.
DR SMART; SM00316; S1; 1.
DR SUPFAM; SSF50249; SSF50249; 1.
DR TIGRFAMs; TIGR00757; RNaseEG; 1.
DR PROSITE; PS50126; S1; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cell inner membrane; Cell membrane; Cytoplasm;
KW Direct protein sequencing; Endonuclease; Hydrolase; Magnesium; Membrane;
KW Metal-binding; Nuclease; Reference proteome; RNA-binding; rRNA processing;
KW rRNA-binding; tRNA processing; tRNA-binding; Zinc.
FT CHAIN 1..1061
FT /note="Ribonuclease E"
FT /id="PRO_0000097373"
FT DOMAIN 39..119
FT /note="S1 motif"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00970"
FT REGION 57..112
FT /note="Interaction with RNA"
FT REGION 169..170
FT /note="Interaction with RNA 5'-terminal monophosphate"
FT REGION 404..407
FT /note="Required for zinc-mediated homotetramerization and
FT catalytic activity"
FT REGION 532..565
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 586..731
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 752..822
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 833..850
FT /note="Interaction with enolase"
FT REGION 1021..1061
FT /note="Interaction with PNPase"
FT REGION 1031..1061
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 534..562
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 592..650
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 657..694
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 783..797
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 303
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:16237448"
FT BINDING 346
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000269|PubMed:16237448"
FT BINDING 404
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="ligand shared between dimeric partners"
FT /evidence="ECO:0000269|PubMed:15779893,
FT ECO:0000269|PubMed:18682225"
FT BINDING 407
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="ligand shared between dimeric partners"
FT /evidence="ECO:0000269|PubMed:15779893,
FT ECO:0000269|PubMed:18682225"
FT MUTAGEN 57
FT /note="F->A: Reduces RNA cleavage by over 98%."
FT /evidence="ECO:0000269|PubMed:16237448"
FT MUTAGEN 66
FT /note="G->S: Disrupts folding of the S1 motif."
FT /evidence="ECO:0000269|PubMed:15312761"
FT MUTAGEN 67
FT /note="F->A: Reduces RNA cleavage by over 98%."
FT /evidence="ECO:0000269|PubMed:16237448"
FT MUTAGEN 112
FT /note="K->A: Reduces RNA cleavage by 98%."
FT /evidence="ECO:0000269|PubMed:16237448"
FT MUTAGEN 170
FT /note="T->V: Abolishes enzyme activity toward RNA
FT substrates with a 5' monophosphate (PubMed:16237448).
FT Strongly reduces enzyme activity toward cspA mRNA
FT (PubMed:19889093)."
FT /evidence="ECO:0000269|PubMed:16237448,
FT ECO:0000269|PubMed:19889093"
FT MUTAGEN 303
FT /note="D->N: Reduces RNA cleavage by over 96%."
FT /evidence="ECO:0000269|PubMed:16237448"
FT MUTAGEN 305
FT /note="N->D,L: Reduces RNA cleavage by over 96%."
FT /evidence="ECO:0000269|PubMed:16237448"
FT MUTAGEN 346
FT /note="D->N: Reduces RNA cleavage by over 96%."
FT /evidence="ECO:0000269|PubMed:16237448"
FT MUTAGEN 373
FT /note="R->A,D: Reduces RNA cleavage by 89%."
FT /evidence="ECO:0000269|PubMed:16237448"
FT MUTAGEN 404
FT /note="C->A: Reduces zinc-binding. Abolishes
FT homotetramerization and enzyme activity."
FT /evidence="ECO:0000269|PubMed:15779893"
FT MUTAGEN 407
FT /note="C->A: Reduces zinc-binding. Abolishes
FT homotetramerization and enzyme activity."
FT /evidence="ECO:0000269|PubMed:15779893"
FT CONFLICT 390
FT /note="Q -> H (in Ref. 5; AAA23443)"
FT /evidence="ECO:0000305"
FT CONFLICT 487
FT /note="L -> V (in Ref. 4; CAA47818 and 5; AAA23443)"
FT /evidence="ECO:0000305"
FT CONFLICT 564
FT /note="A -> R (in Ref. 4; CAA47818)"
FT /evidence="ECO:0000305"
FT CONFLICT 784
FT /note="N -> K (in Ref. 4; CAA47818)"
FT /evidence="ECO:0000305"
FT CONFLICT 838
FT /note="A -> R (in Ref. 5; AAA23443)"
FT /evidence="ECO:0000305"
FT CONFLICT 905
FT /note="P -> R (in Ref. 4; CAA47818)"
FT /evidence="ECO:0000305"
FT CONFLICT 1048
FT /note="H -> R (in Ref. 7; AAA03347)"
FT /evidence="ECO:0000305"
FT STRAND 2..7
FT /evidence="ECO:0007829|PDB:2BX2"
FT STRAND 10..12
FT /evidence="ECO:0007829|PDB:2VMK"
FT STRAND 14..20
FT /evidence="ECO:0007829|PDB:2BX2"
FT STRAND 23..30
FT /evidence="ECO:0007829|PDB:2BX2"
FT STRAND 32..34
FT /evidence="ECO:0007829|PDB:2BX2"
FT STRAND 36..39
FT /evidence="ECO:0007829|PDB:1SLJ"
FT STRAND 42..50
FT /evidence="ECO:0007829|PDB:1SMX"
FT HELIX 51..53
FT /evidence="ECO:0007829|PDB:1SMX"
FT STRAND 55..64
FT /evidence="ECO:0007829|PDB:1SMX"
FT STRAND 66..69
FT /evidence="ECO:0007829|PDB:1SMX"
FT HELIX 70..72
FT /evidence="ECO:0007829|PDB:1SMX"
FT HELIX 75..77
FT /evidence="ECO:0007829|PDB:1SMX"
FT STRAND 84..86
FT /evidence="ECO:0007829|PDB:1SMX"
FT HELIX 90..92
FT /evidence="ECO:0007829|PDB:1SMX"
FT STRAND 99..106
FT /evidence="ECO:0007829|PDB:1SMX"
FT STRAND 109..112
FT /evidence="ECO:0007829|PDB:5F6C"
FT STRAND 115..118
FT /evidence="ECO:0007829|PDB:1SMX"
FT STRAND 125..130
FT /evidence="ECO:0007829|PDB:2BX2"
FT STRAND 134..136
FT /evidence="ECO:0007829|PDB:2C0B"
FT STRAND 137..139
FT /evidence="ECO:0007829|PDB:5F6C"
FT TURN 145..148
FT /evidence="ECO:0007829|PDB:2VRT"
FT HELIX 151..155
FT /evidence="ECO:0007829|PDB:2BX2"
FT STRAND 165..168
FT /evidence="ECO:0007829|PDB:2BX2"
FT HELIX 170..174
FT /evidence="ECO:0007829|PDB:2BX2"
FT HELIX 177..199
FT /evidence="ECO:0007829|PDB:2BX2"
FT STRAND 205..208
FT /evidence="ECO:0007829|PDB:2BX2"
FT STRAND 210..212
FT /evidence="ECO:0007829|PDB:2VMK"
FT HELIX 213..221
FT /evidence="ECO:0007829|PDB:2BX2"
FT STRAND 226..232
FT /evidence="ECO:0007829|PDB:2BX2"
FT HELIX 234..246
FT /evidence="ECO:0007829|PDB:2BX2"
FT HELIX 250..255
FT /evidence="ECO:0007829|PDB:2BX2"
FT STRAND 256..258
FT /evidence="ECO:0007829|PDB:2BX2"
FT HELIX 265..268
FT /evidence="ECO:0007829|PDB:2BX2"
FT HELIX 272..277
FT /evidence="ECO:0007829|PDB:2BX2"
FT STRAND 281..284
FT /evidence="ECO:0007829|PDB:2BX2"
FT STRAND 290..295
FT /evidence="ECO:0007829|PDB:2BX2"
FT STRAND 300..305
FT /evidence="ECO:0007829|PDB:2BX2"
FT STRAND 311..313
FT /evidence="ECO:0007829|PDB:5F6C"
FT HELIX 315..336
FT /evidence="ECO:0007829|PDB:2BX2"
FT STRAND 341..346
FT /evidence="ECO:0007829|PDB:2BX2"
FT HELIX 353..366
FT /evidence="ECO:0007829|PDB:2BX2"
FT TURN 367..369
FT /evidence="ECO:0007829|PDB:2BX2"
FT STRAND 374..379
FT /evidence="ECO:0007829|PDB:2BX2"
FT STRAND 383..389
FT /evidence="ECO:0007829|PDB:2BX2"
FT HELIX 396..400
FT /evidence="ECO:0007829|PDB:2BX2"
FT STRAND 401..403
FT /evidence="ECO:0007829|PDB:5F6C"
FT STRAND 405..411
FT /evidence="ECO:0007829|PDB:2BX2"
FT HELIX 416..432
FT /evidence="ECO:0007829|PDB:2BX2"
FT STRAND 433..435
FT /evidence="ECO:0007829|PDB:5F6C"
FT STRAND 436..443
FT /evidence="ECO:0007829|PDB:2BX2"
FT HELIX 445..451
FT /evidence="ECO:0007829|PDB:2BX2"
FT TURN 452..455
FT /evidence="ECO:0007829|PDB:2BX2"
FT HELIX 456..465
FT /evidence="ECO:0007829|PDB:2BX2"
FT TURN 466..468
FT /evidence="ECO:0007829|PDB:2BX2"
FT STRAND 470..475
FT /evidence="ECO:0007829|PDB:2BX2"
FT STRAND 485..490
FT /evidence="ECO:0007829|PDB:2BX2"
FT TURN 491..493
FT /evidence="ECO:0007829|PDB:2C0B"
FT HELIX 499..501
FT /evidence="ECO:0007829|PDB:2BX2"
FT HELIX 502..506
FT /evidence="ECO:0007829|PDB:2BX2"
FT TURN 507..509
FT /evidence="ECO:0007829|PDB:2BX2"
FT HELIX 831..833
FT /evidence="ECO:0007829|PDB:3H8A"
FT HELIX 835..838
FT /evidence="ECO:0007829|PDB:2FYM"
SQ 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
