ID A0A089ZPJ6_9PSED Unreviewed; 1139 AA.
AC A0A089ZPJ6;
DT 26-NOV-2014, integrated into UniProtKB/TrEMBL.
DT 26-NOV-2014, sequence version 1.
DT 24-JAN-2024, entry version 39.
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 ORFNames=LT40_00670 {ECO:0000313|EMBL:AIS15996.1};
OS Pseudomonas rhizosphaerae.
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Pseudomonadales;
OC Pseudomonadaceae; Pseudomonas.
OX NCBI_TaxID=216142 {ECO:0000313|EMBL:AIS15996.1, ECO:0000313|Proteomes:UP000029499};
RN [1] {ECO:0000313|EMBL:AIS15996.1, ECO:0000313|Proteomes:UP000029499}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 16299 {ECO:0000313|EMBL:AIS15996.1};
RX PubMed=25483321; DOI=10.1016/j.jbiotec.2014.11.031;
RA Kwak Y., Jung B.K., Shin J.H.;
RT "Complete genome sequence of Pseudomonas rhizosphaerae IH5T (=DSM 16299T),
RT a phosphate-solubilizing rhizobacterium for bacterial biofertilizer.";
RL J. Biotechnol. 193:137-138(2015).
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; CP009533; AIS15996.1; -; Genomic_DNA.
DR RefSeq; WP_043185195.1; NZ_CP009533.1.
DR AlphaFoldDB; A0A089ZPJ6; -.
DR STRING; 216142.LT40_00670; -.
DR KEGG; prh:LT40_00670; -.
DR eggNOG; COG1530; Bacteria.
DR HOGENOM; CLU_003468_0_3_6; -.
DR Proteomes; UP000029499; 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; 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; 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:UP000029499};
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 36..114
FT /note="S1 motif"
FT /evidence="ECO:0000259|PROSITE:PS50126"
FT REGION 398..401
FT /note="Required for zinc-mediated homotetramerization and
FT catalytic activity"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00970"
FT REGION 584..827
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 845..1011
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1053..1139
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 592..752
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 845..872
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1095..1115
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 297
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00970"
FT BINDING 340
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00970"
FT BINDING 398
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 401
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 1139 AA; 124548 MW; F4B8C061A88D9936 CRC64;
MLINATQPEE LRVALVDGQR LYDLDIESGA REQKKANIYK GRITRIEPSL EAAFVDFGSE
RHGFLPLKEI SREYFKKNPE GRVNIKEVLS EGQEVIVQVE KEERGNKGAA LTTFISLAGR
YLVLMPNNPR AGGISRRIEG EERNELREAL NGLVAPADMG LIVRTAGLGR SSEEMQWDLD
YLLQLWTAIK EASLDRSAPF LIYQESNVII RAIRDYLRQD IGEVLIDSVE AQDEALTFIR
QVMPQYASKI KLYEDSVPLF NRFQIESQIE TAFQRVVELP SGGSIVIDPT EALVSIDINS
ARATKGSDIE ETALQTNLEA AEEIARQLRL RDIGGLIVID FIDMTPAKNQ RAVEDKVRES
LEADRARVQV GRISRFGLLE MSRQRLRPSL GESSGIVCPR CSGTGIIRDV ESLSLAILRL
IEEEALKDRT AEVRAQVPIP VAAFLLNEKR NSITKIELRT RARIVILPND HLETPHFEVQ
RLRDDSPEAH SGQSSYEIAA AAAEVEEVQP AAATRTLVRQ EAAVKTAPTR TAAPVSAEEA
APVAAAAPTP APAPQIAEPS LFKGLVKSLV SLFATKEAPA APVVVEKPAA TTTERPAREE
RRNGRQQSRN RSNSRRDEER KPREDRAPRE DRSAREDAPA AREERPARAP REERQPRAPR
EDRRPRNGGD DAPRVRELRE PLDAPTAREE RPAREERAPR EERVVREERA PREERAPREE
RPAREERTPG EERPAREERQ PRPAREERVA QQNAAESEVG ATEEALTNDE LLQDDNPEGN
DGDRPRRRSR GQRRRSNRRE RQRDANGDVI EGSEESNESA TEGESNGAAV AAGVAVTAVV
AQSAISASAE AQAHEQAEQA NRSVQPAAAE STAESESLAA PEIVATAPTA EAAVDTPAAA
PAQSDSPAEI ERPATVSAPD TWAAPVNESA APVIEQQPVV EAAKPAETTE PVQQDAAEPV
ELTPPFDTTP TPISPPGADV EVDAPVVVDP AQVSESAFQP PVAQASEEAP SLPVEPALHQ
ISEPAAAEPL SIEPVFVDAV VVEPALVEPV RFEPATSQPV AEPVPASEPV VVAEPEPIQE
AEPAPAVPSN GRAPNDPREV RRRKREAEEA AKNAAFKPEA EVSSAADAQD AHDEPKPQA
//