ID W0HPI9_9GAMM Unreviewed; 1175 AA.
AC W0HPI9;
DT 19-MAR-2014, integrated into UniProtKB/TrEMBL.
DT 19-MAR-2014, sequence version 1.
DT 27-MAR-2024, entry version 46.
DE RecName: Full=Ribonuclease E {ECO:0000256|HAMAP-Rule:MF_00970};
DE Short=RNase E {ECO:0000256|HAMAP-Rule:MF_00970};
DE EC=3.1.26.12 {ECO:0000256|HAMAP-Rule:MF_00970};
GN Name=rne {ECO:0000256|HAMAP-Rule:MF_00970,
GN ECO:0000313|EMBL:AHF74023.1};
GN ORFNames=SOPEG_2138 {ECO:0000313|EMBL:AHF74023.1};
OS Candidatus Sodalis pierantonius str. SOPE.
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
OC Bruguierivoracaceae; Sodalis.
OX NCBI_TaxID=2342 {ECO:0000313|EMBL:AHF74023.1, ECO:0000313|Proteomes:UP000019025};
RN [1] {ECO:0000313|EMBL:AHF74023.1, ECO:0000313|Proteomes:UP000019025}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=none {ECO:0000313|Proteomes:UP000019025};
RX PubMed=24407854; DOI=10.1093/gbe/evt210;
RA Oakeson K.F., Gil R., Clayton A.L., Dunn D.M., von Niederhausern A.C.,
RA Hamil C., Aoyagi A., Duval B., Baca A., Silva F.J., Vallier A.,
RA Jackson D.G., Latorre A., Weiss R.B., Heddi A., Moya A., Dale C.;
RT "Genome degeneration and adaptation in a nascent stage of symbiosis.";
RL Genome Biol. Evol. 6:76-93(2014).
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.
CC {ECO:0000256|HAMAP-Rule:MF_00970}.
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:0000256|HAMAP-
CC Rule:MF_00970};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_00970};
CC Note=Binds 1 Mg(2+) ion per subunit. {ECO:0000256|HAMAP-Rule:MF_00970};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_00970};
CC Note=Binds 2 Zn(2+) ions per homotetramer. {ECO:0000256|HAMAP-
CC Rule:MF_00970};
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. {ECO:0000256|HAMAP-Rule:MF_00970}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00970}. Cell
CC inner membrane {ECO:0000256|HAMAP-Rule:MF_00970}; Peripheral membrane
CC protein {ECO:0000256|HAMAP-Rule:MF_00970}; Cytoplasmic side
CC {ECO:0000256|HAMAP-Rule:MF_00970}.
CC -!- SIMILARITY: Belongs to the RNase E/G family. RNase E subfamily.
CC {ECO:0000256|HAMAP-Rule:MF_00970}.
CC -!- SIMILARITY: Belongs to the RNase E/G family. RNase G subfamily.
CC {ECO:0000256|ARBA:ARBA00005663}.
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DR EMBL; CP006568; AHF74023.1; -; Genomic_DNA.
DR RefSeq; WP_025245436.1; NZ_CP006568.1.
DR AlphaFoldDB; W0HPI9; -.
DR STRING; 2342.SOPEG_2138; -.
DR KEGG; pes:SOPEG_2138; -.
DR PATRIC; fig|2342.5.peg.2266; -.
DR eggNOG; COG1530; Bacteria.
DR HOGENOM; CLU_003468_1_3_6; -.
DR Proteomes; UP000019025; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0009898; C:cytoplasmic side of plasma membrane; IEA:UniProtKB-UniRule.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0008995; F:ribonuclease E activity; IEA:InterPro.
DR GO; GO:0004521; F:RNA endonuclease activity; IEA:UniProtKB-UniRule.
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; IEA:UniProtKB-UniRule.
DR GO; GO:0006364; P:rRNA processing; IEA:UniProtKB-UniRule.
DR GO; GO:0008033; P:tRNA processing; IEA:UniProtKB-UniRule.
DR CDD; cd04453; S1_RNase_E; 1.
DR Gene3D; 2.40.50.140; Nucleic acid-binding proteins; 1.
DR Gene3D; 3.40.1260.20; Ribonuclease E, catalytic domain; 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; IPR048583; RNase_E_G_thioredoxin-like.
DR InterPro; IPR003029; S1_domain.
DR NCBIfam; TIGR00757; RNaseEG; 1.
DR PANTHER; PTHR30001; RIBONUCLEASE; 1.
DR PANTHER; PTHR30001:SF1; RIBONUCLEASE E_G-LIKE PROTEIN, CHLOROPLASTIC; 1.
DR Pfam; PF12111; PNPase_C; 1.
DR Pfam; PF10150; RNase_E_G; 1.
DR Pfam; PF20833; RNase_E_G_Thio; 1.
DR Pfam; PF00575; S1; 1.
DR SMART; SM00316; S1; 1.
DR SUPFAM; SSF50249; Nucleic acid-binding proteins; 1.
DR PROSITE; PS50126; S1; 1.
PE 3: Inferred from homology;
KW Cell inner membrane {ECO:0000256|ARBA:ARBA00022519, ECO:0000256|HAMAP-
KW Rule:MF_00970};
KW Cell membrane {ECO:0000256|ARBA:ARBA00022475, ECO:0000256|HAMAP-
KW Rule:MF_00970}; Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00970};
KW Endonuclease {ECO:0000256|HAMAP-Rule:MF_00970};
KW Hydrolase {ECO:0000256|ARBA:ARBA00022801, ECO:0000256|HAMAP-Rule:MF_00970};
KW Magnesium {ECO:0000256|ARBA:ARBA00022842, ECO:0000256|HAMAP-Rule:MF_00970};
KW Membrane {ECO:0000256|ARBA:ARBA00023136, ECO:0000256|HAMAP-Rule:MF_00970};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723, ECO:0000256|HAMAP-
KW Rule:MF_00970}; Nuclease {ECO:0000256|HAMAP-Rule:MF_00970};
KW Reference proteome {ECO:0000313|Proteomes:UP000019025};
KW RNA-binding {ECO:0000256|ARBA:ARBA00022884, ECO:0000256|HAMAP-
KW Rule:MF_00970}; rRNA processing {ECO:0000256|HAMAP-Rule:MF_00970};
KW rRNA-binding {ECO:0000256|HAMAP-Rule:MF_00970};
KW tRNA processing {ECO:0000256|HAMAP-Rule:MF_00970};
KW tRNA-binding {ECO:0000256|HAMAP-Rule:MF_00970};
KW Zinc {ECO:0000256|HAMAP-Rule:MF_00970}.
FT DOMAIN 39..119
FT /note="S1 motif"
FT /evidence="ECO:0000259|PROSITE:PS50126"
FT REGION 404..407
FT /note="Required for zinc-mediated homotetramerization and
FT catalytic activity"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00970"
FT REGION 588..826
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 893..1175
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 603..655
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 660..674
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 675..694
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:0000256|HAMAP-Rule:MF_00970"
FT BINDING 346
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00970"
FT BINDING 404
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="ligand shared between dimeric partners"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00970"
FT BINDING 407
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_note="ligand shared between dimeric partners"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00970"
SQ SEQUENCE 1175 AA; 127684 MW; 121494F7A1758E43 CRC64;
MKRMLINATQ QEELRVALVD GQRLYDLDIE SPGHEQKKAN IYKGKITRIE PSLEAAFVDY
GAERHGFLPL KEISREYFPP QYSSHGRPNI KDVLREGQEV IVQVDKEERG NKGAALTTFI
SLAGSYLVLM PNNPRAGGIS RRIEGDDRTE LKEALSSLEL PDGMGLIVRT AGVGKSADAL
QWDLAFRLKH WQAIKKAAEG RPAPFLIHQE SNVIVRAFRD YLRPDIGEIL IDNPKVLDLA
KEHIASLGRP DFTSKIKLYS GEIPLFSHYQ IESQIESAFQ REVRLPSGGS IVIDTTEALT
AIDINSARST RGGDIEETAF NTNLEAADEI ARQLRLRDLG GLIVIDFIDM TPVRHQREVE
NCLRESVRQD RARIQIGRIS RFGLLELSRQ RLSPSLGESS HHVCPRCGGT GTIRDNESLS
LSILRLIEEE ALKENTLEVH AIVPVPIASY LLNEKREAVN AIEKRQGGVR AIIVPNDQMQ
TPHYAVLRVR KGEEAPTLSY LLPQLHEVEM IQPSEEPAAE RKRPEQPALA AFVMPDPPLA
SEKPAAAETV VQAAPAAAVK AAGASRGLFG RLVAGFKSLI GTPAQQTETN AAEAVVVEMP
PETETPRRQD RRGQRRQPSG RREHNNESTR AGQESRQPRE GRDDTRRKRP QAVTETETEG
EMIGETQQEG QVQQSRREPR QDRQRRRQQE PKAQVAEQEL KTLPAEIAPD DTASEEDKPI
QAQPRRQRRA LNRKIRVGDR AAPTSDAAES ATAAFNAAVE SQDDDIGGLQ SENDVALEAG
NADGGRNGNE AGLPRRSRRS PRHLRVSGQR RRRYRDERYP LSSPVPLTSA VVSPEMASGK
VWVSYPVTPI EQPEHDAGAD VAAGTDATVG QKQAAFAVTP AGEAAAATVS EALNSQQLPP
STLIPSPAQE AAADDVPPVI APGEQPMAQR QIERAEPAAG SAVTPTADDG DDVSQAPAQP
IAAPATPNAE TAPLSLEQRD EERHADSVPA SQPVTVHEEE RSADLASPSQ PVASHDDERP
VNSAQDVTPP ETHDASRPDD TANADAVAVS EPFLGAALPP VVPAADGQNV GTAQPTPSAA
AEDAARHMPP PVSPPLTQEG RPLPVSPDTP AMRFKHHASA PMTKAPAPAY TPSPLPVSDW
QRPDYRFDDH GAAGGHAADK QATAPATRPD TPDPL
//
