ID   B3QH48_RHOPT            Unreviewed;      1053 AA.
AC   B3QH48;
DT   02-SEP-2008, integrated into UniProtKB/TrEMBL.
DT   02-SEP-2008, sequence version 1.
DT   27-MAR-2024, entry version 78.
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   OrderedLocusNames=Rpal_2728 {ECO:0000313|EMBL:ACF01237.1};
OS   Rhodopseudomonas palustris (strain TIE-1).
OC   Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales;
OC   Nitrobacteraceae; Rhodopseudomonas.
OX   NCBI_TaxID=395960 {ECO:0000313|EMBL:ACF01237.1, ECO:0000313|Proteomes:UP000001725};
RN   [1] {ECO:0000313|EMBL:ACF01237.1, ECO:0000313|Proteomes:UP000001725}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=TIE-1 {ECO:0000313|EMBL:ACF01237.1,
RC   ECO:0000313|Proteomes:UP000001725};
RG   US DOE Joint Genome Institute;
RA   Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H.,
RA   Pitluck S., Chain P., Malfatti S., Shin M., Vergez L., Lang D., Schmutz J.,
RA   Larimer F., Land M., Hauser L., Kyrpides N., Mikhailova N., Emerson D.,
RA   Newman D.K., Roden E., Richardson P.;
RT   "Complete sequence of Rhodopseudomonas palustris TIE-1.";
RL   Submitted (MAY-2008) to the EMBL/GenBank/DDBJ databases.
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; Evidence={ECO:0000256|HAMAP-
CC         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; Evidence={ECO:0000256|HAMAP-
CC         Rule:MF_00970};
CC       Note=Binds 2 Zn(2+) ions per homotetramer. {ECO:0000256|HAMAP-
CC       Rule:MF_00970};
CC   -!- SUBUNIT: Homotetramer formed by a dimer of dimers. {ECO:0000256|HAMAP-
CC       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}.
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DR   EMBL; CP001096; ACF01237.1; -; Genomic_DNA.
DR   RefSeq; WP_012495937.1; NC_011004.1.
DR   AlphaFoldDB; B3QH48; -.
DR   KEGG; rpt:Rpal_2728; -.
DR   HOGENOM; CLU_003468_5_0_5; -.
DR   OrthoDB; 9804278at2; -.
DR   Proteomes; UP000001725; 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   Gene3D; 2.40.50.140; Nucleic acid-binding proteins; 2.
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; 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   NCBIfam; TIGR00757; RNaseEG; 1.
DR   PANTHER; PTHR30001; RIBONUCLEASE; 1.
DR   PANTHER; PTHR30001:SF1; RIBONUCLEASE E_G-LIKE PROTEIN, CHLOROPLASTIC; 1.
DR   Pfam; PF10150; RNase_E_G; 1.
DR   Pfam; PF20833; RNase_E_G_Thio; 1.
DR   SUPFAM; SSF50249; Nucleic acid-binding proteins; 1.
PE   3: Inferred from homology;
KW   Cell inner membrane {ECO:0000256|HAMAP-Rule:MF_00970};
KW   Cell membrane {ECO:0000256|HAMAP-Rule:MF_00970};
KW   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|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   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          644..723
FT                   /note="RNase E/G thioredoxin-like"
FT                   /evidence="ECO:0000259|Pfam:PF20833"
FT   REGION          94..128
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          213..314
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          645..648
FT                   /note="Required for zinc-mediated homotetramerization and
FT                   catalytic activity"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00970"
FT   REGION          774..1053
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        94..110
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        228..277
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        278..313
FT                   /note="Acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        832..850
FT                   /note="Acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        958..976
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   BINDING         544
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_note="catalytic"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00970"
FT   BINDING         587
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_note="catalytic"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00970"
FT   BINDING         645
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         648
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   1053 AA;  115731 MW;  630391D431EEC8AE CRC64;
     MANKMLIDAT HPEETRVVVV RGNRVEEFDF ETAQRKQLRG NIYLAKVTRV EPSLQAAFIE
     YGGNRHGFLA FSEIHPDYYQ IPVADRQALI EADERAHREA EEENEQRSSR RRSRHRSHRR
     RNNGERVQSE IVEAATDVAA EQPHEAADHH EAHEAGAHAE AERLMHELPE GETAEQHDAE
     YAADHEHTHV EAAPSEPQVS AAAEPVTIEQ PAAAEAPAPV EAPQAAASHD ETDAHDDDHG
     EDSANYAEDA PFPIDEHHEA EDEHEAHDDH VEGEHEVETD SDSDTEAEAE DDEEEDDEEE
     AEEDVVESVG GDDVLEEVPE RAFRPRRQYK IQEVIKRRQV MLVQVVKEER GNKGAALTTY
     LSLAGRYAVL MPNTARGGGI SRKITSAQDR SRLKEVVQDL DVPEGMGVIL RTAGASRTKP
     EIKRDFEYLI RMWETVRDVT LNSQAPKLVY EEGSLIKRSL RDLYNKEIDE VLVAGEAGYR
     EARDFMHMLM PSQVRAVKLY RDGQPLFSRM GVESQLDAMF SPTVQLRSGG YIVINQTEAL
     VSIDVNSGRS TREHHIEDTA LKTNMEAAEE VARQLRLRDL AGLIVIDFID MDEKRNNRAV
     ERKLSDCLRQ DRARIQVGRI SHFGLLEMSR QRIRASVLES STEPCPHCGG SGHVRSVSSV
     ALQLLRGLEE VLMKGATHNL IVRTRTDVAL YVLNHKRGHL RDLETGFRVS LSVLADPTVS
     GQQSFVIDRG EQVHTLETAK ALLAAQIAAS PAPLDEPEDD DGYDFEAEIE TDETVGLAED
     QGSEAGESES EGRKRRRRRR RRRSGEPREA AEAGAVGEDG EQPFVSEGVE QVGEADEGDE
     AGEDDSDAEA RADQGENGER RPRRRGRRGG RRRRGNAEAG ENEAGVVGSI SDELSPTDEA
     EAADAVADFD GGSPSVQPSF EPAAEAEQPH DAPPHDIVPS EPQHTAATAA PDTSDPSAED
     DSAAKKAARR RSTVREKVSF GASAAASETT AEAAAEVQPE PTAQAEQPAT AAPAVEAPAA
     EAAPQAAAQP AEEPSSAAPR RVGWWSRRFG GGN
//