RNE_SYNY3
ID RNE_SYNY3 Reviewed; 674 AA.
AC P72656;
DT 15-DEC-1998, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1997, sequence version 1.
DT 03-AUG-2022, entry version 121.
DE RecName: Full=Ribonuclease E {ECO:0000303|PubMed:9751718};
DE Short=RNase E;
DE Short=SynRne {ECO:0000303|PubMed:9751718};
DE EC=3.1.26.12 {ECO:0000305|PubMed:17661085};
DE AltName: Full=Ribonuclease E/G {ECO:0000303|PubMed:17661085};
GN Name=rne {ECO:0000303|PubMed:9751718}; OrderedLocusNames=slr1129;
OS Synechocystis sp. (strain PCC 6803 / Kazusa).
OC Bacteria; Cyanobacteria; Synechococcales; Merismopediaceae; Synechocystis;
OC unclassified Synechocystis.
OX NCBI_TaxID=1111708;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=PCC 6803 / Kazusa;
RX PubMed=8905231; DOI=10.1093/dnares/3.3.109;
RA Kaneko T., Sato S., Kotani H., Tanaka A., Asamizu E., Nakamura Y.,
RA Miyajima N., Hirosawa M., Sugiura M., Sasamoto S., Kimura T., Hosouchi T.,
RA Matsuno A., Muraki A., Nakazaki N., Naruo K., Okumura S., Shimpo S.,
RA Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Tabata S.;
RT "Sequence analysis of the genome of the unicellular cyanobacterium
RT Synechocystis sp. strain PCC6803. II. Sequence determination of the entire
RT genome and assignment of potential protein-coding regions.";
RL DNA Res. 3:109-136(1996).
RN [2]
RP FUNCTION AS AN ENDONUCLEASE, FUNCTION IN 5S RRNA MATURATION, RRNA-BINDING,
RP AND EXPRESSION IN E.COLI.
RC STRAIN=PCC 6803 / Kazusa;
RX PubMed=9751718; DOI=10.1073/pnas.95.20.11637;
RA Kaberdin V.R., Miczak A., Jakobsen J.S., Lin-Chao S., McDowall K.J.,
RA von Gabain A.;
RT "The endoribonucleolytic N-terminal half of Escherichia coli RNase E is
RT evolutionarily conserved in Synechocystis sp. and other bacteria but not
RT the C-terminal half, which is sufficient for degradosome assembly.";
RL Proc. Natl. Acad. Sci. U.S.A. 95:11637-11642(1998).
RN [3]
RP FUNCTION, SUBSTRATE SPECIFICITY, AND EXPRESSION IN E.COLI.
RC STRAIN=PCC 6803 / Kazusa;
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 [4]
RP SUBUNIT, AND DISRUPTION PHENOTYPE.
RC STRAIN=PCC 6803 / Kazusa;
RX PubMed=12601000; DOI=10.1074/jbc.m211571200;
RA Rott R., Zipor G., Portnoy V., Liveanu V., Schuster G.;
RT "RNA polyadenylation and degradation in cyanobacteria are similar to the
RT chloroplast but different from Escherichia coli.";
RL J. Biol. Chem. 278:15771-15777(2003).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, AND DISRUPTION PHENOTYPE.
RC STRAIN=PCC 6803 / Kazusa;
RX PubMed=17661085; DOI=10.1007/s00438-007-0254-9;
RA Horie Y., Ito Y., Ono M., Moriwaki N., Kato H., Hamakubo Y., Amano T.,
RA Wachi M., Shirai M., Asayama M.;
RT "Dark-induced mRNA instability involves RNase E/G-type endoribonuclease
RT cleavage at the AU-box and SD sequences in cyanobacteria.";
RL Mol. Genet. Genomics 278:331-346(2007).
RN [6]
RP SUBCELLULAR LOCATION, AND EXPRESSION IN E.COLI.
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 [7]
RP FUNCTION.
RC STRAIN=PCC 6803 / Kazusa;
RX PubMed=25248550; DOI=10.1105/tpc.114.129767;
RA Georg J., Dienst D., Schuergers N., Wallner T., Kopp D., Stazic D.,
RA Kuchmina E., Klaehn S., Lokstein H., Hess W.R., Wilde A.;
RT "The small regulatory RNA SyR1/PsrR1 controls photosynthetic functions in
RT cyanobacteria.";
RL Plant Cell 26:3661-3679(2014).
RN [8]
RP SUBUNIT, AND DOMAIN.
RC STRAIN=PCC 6803 / Kazusa;
RX PubMed=24563514; DOI=10.1261/rna.043513.113;
RA Zhang J.Y., Deng X.M., Li F.P., Wang L., Huang Q.Y., Zhang C.C., Chen W.L.;
RT "RNase E forms a complex with polynucleotide phosphorylase in cyanobacteria
RT via a cyanobacterial-specific nonapeptide in the noncatalytic region.";
RL RNA 20:568-579(2014).
RN [9]
RP SUBCELLULAR LOCATION.
RC STRAIN=PCC 6803 / Kazusa;
RX PubMed=27215789; DOI=10.1128/jb.00267-16;
RA Rosana A.R., Whitford D.S., Fahlman R.P., Owttrim G.W.;
RT "Cyanobacterial RNA Helicase CrhR Localizes to the Thylakoid Membrane
RT Region and Cosediments with Degradosome and Polysome Complexes in
RT Synechocystis sp. Strain PCC 6803.";
RL J. Bacteriol. 198:2089-2099(2016).
RN [10]
RP FUNCTION IN CRRNA MATURATION, DISRUPTION PHENOTYPE, MUTAGENESIS OF PHE-64
RP AND LYS-98, AND RNA-BINDING.
RC STRAIN=PCC 6803 / Kazusa;
RX PubMed=29403013; DOI=10.1038/s41564-017-0103-5;
RA Behler J., Sharma K., Reimann V., Wilde A., Urlaub H., Hess W.R.;
RT "The host-encoded RNase E endonuclease as the crRNA maturation enzyme in a
RT CRISPR-Cas subtype III-Bv system.";
RL Nat. Microbiol. 3:367-377(2018).
RN [11]
RP FUNCTION.
RC STRAIN=PCC 6803 / Kazusa;
RX PubMed=32209657; DOI=10.1074/jbc.ra120.013148;
RA Rosana A.R.R., Whitford D.S., Migur A., Steglich C., Kujat-Choy S.L.,
RA Hess W.R., Owttrim G.W.;
RT "RNA helicase-regulated processing of the Synechocystis rimO-crhR operon
RT results in differential cistron expression and accumulation of two sRNAs.";
RL J. Biol. Chem. 295:6372-6386(2020).
CC -!- FUNCTION: Endoribonuclease that plays a central role in rRNA processing
CC and mRNA decay, and probably tRNA processing (PubMed:9751718,
CC PubMed:17661085, PubMed:25248550, PubMed:32209657). Acts on 9S rRNA
CC (the precursor of 5S rRNA) and RNAI, a molecule that controls the
CC replication of ColE1 plasmid. Upon expression in E.coli does not purify
CC with endogenous degradosome proteins (PubMed:9751718). Prefers 5'-
CC monophosphorylated substrates over 5'-triphosphorylated substrates.
CC Complements an rne temperature-sensitive mutation in E.coli, despite
CC being considerably shorter and not able to interact with the E.coli
CC degradosome (PubMed:10762247). Cleaves AU-rich sequences in vitro,
CC tested with psbA2 mRNA. Complements both an rne temperature-sensitive
CC mutation and an rng deletion in E.coli (PubMed:17661085). Acts in the
CC degradation of psaL mRNA in the presence but not the absence of the
CC sRNA PsrR1 (PubMed:25248550). Cleaves the rimO-crhR transcript,
CC contributing to the very short half-life of rimO mRNA
CC (PubMed:32209657). {ECO:0000269|PubMed:10762247,
CC ECO:0000269|PubMed:17661085, ECO:0000269|PubMed:25248550,
CC ECO:0000269|PubMed:32209657, ECO:0000269|PubMed:9751718}.
CC -!- FUNCTION: mRNA for psbA2, one of the core proteins in photosystem II,
CC is degraded in the dark under control of a cis-acting AU-rich box in
CC its 5'-UTR. RNase E cuts in this box, suggesting it is involved in this
CC dark-induced mRNA instability. {ECO:0000269|PubMed:17661085}.
CC -!- FUNCTION: CRISPR (clustered regularly interspaced short palindromic
CC repeat) is an adaptive immune system that provides protection against
CC mobile genetic elements (viruses, transposable elements and conjugative
CC plasmids). CRISPR clusters contain spacers, sequences complementary to
CC antecedent mobile elements, and target invading nucleic acids. CRISPR
CC clusters are transcribed and processed into CRISPR RNA (crRNA).
CC Endogenous RNase E is required for correct processing of pre-crRNA for
CC the CRISPR3 subtype III-B system in this genome (genes sll7080 to
CC sll7095). This CRISPR3 system does not include a cas6 gene, which is
CC the usual RNase involved in crRNA maturation.
CC {ECO:0000269|PubMed:29403013}.
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:0000305|PubMed:17661085,
CC ECO:0000305|PubMed:29403013};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000250|UniProtKB:P21513};
CC Note=Binds 1 Mg(2+) ion per subunit. {ECO:0000250|UniProtKB:P21513};
CC -!- SUBUNIT: Fractionates in a 250-300 kDa region, which is too small to be
CC the equivalent of an RNA degradosome, as occurs with E.coli RNase E
CC (PubMed:12601000). Interacts with polynucleotide phosphorylase (PNPase,
CC pnp), probably via the C4 Arg-rich motif (residues 665-673)
CC (PubMed:24563514). {ECO:0000269|PubMed:12601000,
CC ECO:0000269|PubMed:24563514}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000305|PubMed:22509045,
CC ECO:0000305|PubMed:27215789}. Cell inner membrane
CC {ECO:0000305|PubMed:22509045}; Peripheral membrane protein
CC {ECO:0000250|UniProtKB:P21513}; Cytoplasmic side
CC {ECO:0000250|UniProtKB:P21513}. Note=Subcellular locations are shown
CC upon expression in E.coli of the N-terminal domain (residues 1-396)
CC (PubMed:22509045). Some of the protein cosediments with polysomes
CC (PubMed:27215789). {ECO:0000269|PubMed:22509045,
CC ECO:0000269|PubMed:27215789}.
CC -!- DISRUPTION PHENOTYPE: Essential, it cannot be deleted (PubMed:12601000,
CC PubMed:17661085, PubMed:29403013). Knockdown experiments show decreased
CC amounts of crRNA precursor processing (PubMed:29403013).
CC {ECO:0000269|PubMed:12601000, ECO:0000269|PubMed:17661085,
CC ECO:0000269|PubMed:29403013}.
CC -!- SIMILARITY: Belongs to the RNase E/G family. {ECO:0000305}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; BA000022; BAA16658.1; -; Genomic_DNA.
DR PIR; S74506; S74506.
DR AlphaFoldDB; P72656; -.
DR SMR; P72656; -.
DR IntAct; P72656; 7.
DR STRING; 1148.1651730; -.
DR PaxDb; P72656; -.
DR EnsemblBacteria; BAA16658; BAA16658; BAA16658.
DR KEGG; syn:slr1129; -.
DR eggNOG; COG1530; Bacteria.
DR InParanoid; P72656; -.
DR OMA; WTNYEAA; -.
DR PhylomeDB; P72656; -.
DR BRENDA; 3.1.26.12; 6192.
DR Proteomes; UP000001425; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005886; C:plasma membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0004519; F:endonuclease activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004540; F:ribonuclease activity; IBA:GO_Central.
DR GO; GO:0019843; F:rRNA binding; IEA:UniProtKB-KW.
DR GO; GO:0000049; F:tRNA binding; IEA:UniProtKB-KW.
DR GO; GO:0051607; P:defense response to virus; IEA:UniProtKB-KW.
DR GO; GO:0006364; P:rRNA processing; IBA:GO_Central.
DR GO; GO:0008033; P:tRNA processing; IEA:UniProtKB-KW.
DR Gene3D; 2.40.50.140; -; 1.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR InterPro; IPR019307; RNA-bd_AU-1/RNase_E/G.
DR InterPro; IPR004659; RNase_E/G.
DR InterPro; IPR022967; S1_dom.
DR InterPro; IPR003029; S1_domain.
DR PANTHER; PTHR30001; PTHR30001; 1.
DR Pfam; PF10150; RNase_E_G; 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 Antiviral defense; Cell inner membrane; Cell membrane; Cytoplasm;
KW Endonuclease; Hydrolase; Magnesium; Membrane; Metal-binding; Nuclease;
KW Reference proteome; RNA-binding; rRNA processing; rRNA-binding;
KW tRNA processing; tRNA-binding; Zinc.
FT CHAIN 1..674
FT /note="Ribonuclease E"
FT /id="PRO_0000097378"
FT DOMAIN 35..117
FT /note="S1 motif"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00180"
FT REGION 458..529
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 626..674
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 665..673
FT /note="C4 Arg-rich motif, probably responsible for
FT interaction with PNPase"
FT /evidence="ECO:0000269|PubMed:24563514"
FT COMPBIAS 470..496
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 497..512
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 515..529
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 296
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:P21513"
FT BINDING 339
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000250|UniProtKB:P21513"
FT BINDING 397
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="ligand shared between dimeric partners"
FT /evidence="ECO:0000250|UniProtKB:P21513"
FT BINDING 400
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="ligand shared between dimeric partners"
FT /evidence="ECO:0000250|UniProtKB:P21513"
FT MUTAGEN 64
FT /note="F->A: Considerable decrease in CRISPR3 crRNA
FT precursor and psbA2 processing; when associated with A-98."
FT /evidence="ECO:0000269|PubMed:29403013"
FT MUTAGEN 98
FT /note="K->A: Considerable decrease in CRISPR3 crRNA
FT precursor and psbA2 processing; when associated with A-64."
FT /evidence="ECO:0000269|PubMed:29403013"
SQ SEQUENCE 674 AA; 74944 MW; 5C03F6087596C2B5 CRC64;
MPKQIVIAEK HQVAAVFWKD QIQELVVSTG SQQVGDIYLG LVDNILPSID AAFINIGDTE
KNGFIHVSDL GPVRLRRTAG SISELLSPQQ RVLVQVMKEP TGNKGPRLTG NISMPGRYMV
LMPYGRGVNL SRRINREEER SRLRALAVLI KPPGMGLLVR TEAEDVPEDA IIEDLENLQK
QWELVQQQAM TRSAPMLLDR DDDFIKRVLR DMYSSEVNRI VVDTPAGMKR IKQQLMNWDQ
GRLPEGVLID CHRESLSILE YFRVNATIRE ALKPRVDLPS GGYIIIEPTE ALTVIDVNSG
SFTHSANSRE TVLWTNYEAA TEIARQLKLR NIGGVIIIDF IDMDSHKDQL QLLEHFNRCL
ETDKARPQIA QLTELGLVEL TRKRQGQNLY ELFGQPCPEC GGLGHLVELP GEKGFVSLSP
TAVNSSIPPR LVEKPILSPP VAKVNDLPKK EEAKISSPLD LLFHPNYQEQ GDRDSNRRRR
RRRGSEFSEK ENIKSVGISR SKGPSPSPTK EKVTGTAPPR RERPSRRVEK TLVPVDVAMT
TLEQDIYARM GISPLIKTEY ADQDPRSFMV SVVTAGAALE GNTNGSGSLV NAVITTVDNG
DNGDNVPSDG LTIVSEVTAP TPVIEQPREE TVEPEQVVLP QLDDETPAAP VAEESAPIET
KKRPGRRRRR SSAE
