ID Q89M88_BRADU Unreviewed; 1032 AA.
AC Q89M88;
DT 01-JUN-2003, integrated into UniProtKB/TrEMBL.
DT 01-JUN-2003, sequence version 1.
DT 27-MAR-2024, entry version 117.
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=bll4305 {ECO:0000313|EMBL:BAC49570.1};
OS Bradyrhizobium diazoefficiens (strain JCM 10833 / BCRC 13528 / IAM 13628 /
OS NBRC 14792 / USDA 110).
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales;
OC Nitrobacteraceae; Bradyrhizobium.
OX NCBI_TaxID=224911 {ECO:0000313|EMBL:BAC49570.1, ECO:0000313|Proteomes:UP000002526};
RN [1] {ECO:0000313|Proteomes:UP000002526}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=JCM 10833 / BCRC 13528 / IAM 13628 / NBRC 14792 / USDA 110
RC {ECO:0000313|Proteomes:UP000002526};
RX PubMed=12597275; DOI=10.1093/dnares/9.6.189;
RA Kaneko T., Nakamura Y., Sato S., Minamisawa K., Uchiumi T., Sasamoto S.,
RA Watanabe A., Idesawa K., Iriguchi M., Kawashima K., Kohara M.,
RA Matsumoto M., Shimpo S., Tsuruoka H., Wada T., Yamada M., Tabata S.;
RT "Complete genomic sequence of nitrogen-fixing symbiotic bacterium
RT Bradyrhizobium japonicum USDA110.";
RL DNA Res. 9:189-197(2002).
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: 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; BA000040; BAC49570.1; -; Genomic_DNA.
DR RefSeq; NP_770945.1; NC_004463.1.
DR AlphaFoldDB; Q89M88; -.
DR STRING; 224911.AAV28_18585; -.
DR EnsemblBacteria; BAC49570; BAC49570; BAC49570.
DR KEGG; bja:bll4305; -.
DR PATRIC; fig|224911.44.peg.4046; -.
DR eggNOG; COG1530; Bacteria.
DR HOGENOM; CLU_003468_5_0_5; -.
DR InParanoid; Q89M88; -.
DR OrthoDB; 9804278at2; -.
DR PhylomeDB; Q89M88; -.
DR Proteomes; UP000002526; Chromosome.
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: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:0004540; F:RNA nuclease 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: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; IBA:GO_Central.
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 Reference proteome {ECO:0000313|Proteomes:UP000002526};
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 648..728
FT /note="RNase E/G thioredoxin-like"
FT /evidence="ECO:0000259|Pfam:PF20833"
FT REGION 93..137
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 171..228
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 277..316
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 649..652
FT /note="Required for zinc-mediated homotetramerization and
FT catalytic activity"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00970"
FT REGION 751..1032
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 93..109
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 171..227
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 291..316
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 760..786
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 835..849
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 850..865
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 957..974
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 975..989
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 993..1011
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 548
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00970"
FT BINDING 591
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00970"
FT BINDING 649
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 652
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 1032 AA; 113459 MW; 59A3CEC3037F1DE7 CRC64;
MPNKMLIDAT HPEETRVVVV RGNRVEEFDF ETAQRKQLRG NIYLAKVTRV EPSLQAAFVE
YGGNRHGFLA FSEIHPDYYQ IPVADRQALI EAEEQAHREA EEESENRSHG RRRSRHRNAR
RRGHGERVRS DIVEGLDASA DPAAQPVEGQ ILPEHAEGAP QEGEHLHADA EHHGEHDAHD
HHEHDHHDHD HHEHAHDDHH PDHAHDHDDH GHDGGHDHHD HDHADETPAP VAAFGAEPVV
ATEAVAEPQE ATSEAHAEAL AEAVTAAAEP ADAVYAAGES TEAPHHDADA AAEDDDDEDD
DGEEAEEEVV ESVGGDDVME EVPERTFRPR RQYKIQEVIK RRQVMLVQVV KEERGNKGAA
LTTYLSLAGR YAVLMPNTAR GGGISRKITS AQDRSRLKEV VQDLDVPEGM GIILRTAGAA
RTKPEIKRDF EYLIRMWETV RDLTLKSQAP TLVYEEGSLI KRSLRDLYNK EIDEISVAGE
SGYREARDFM KMLMPANVSA VKQYRDGQPL FSRMGVESQL DAMFSPTVQL RSGGYIVINQ
TEALVSIDVN SGRSTREHHI EDTALKTNLE AAEEVARQLR LRDLAGLIVI DFIDMDEKRN
NRAVERKLSD CLRQDRARIQ VGRISHFGLL EMSRQRIRAS VLESSTDPCP HCGGTGHVRS
VSSVALQLLR GLEEILMKGA THNLVVRTRT DVALYVLNHK RGHLRDLENG FKVTLAVIAD
PSVSGPQAYL IDRGEQVHTL EAAKALLAAQ AAASPPPVVE EAYDDEEFDP ELESEIESEE
TEGLTEEQAA GEAAPEQDGQ RRKRRRRRRG RGGQRDGELR EDSAPTLPEP AMVAGESEED
AESEQDGEEG EEQAARGEQQ GGGERRRRRG RRGGRRRRGG GEEGLAGSIG DELGTQSPSE
ATEAVADFDG FGGEAAPSIA QAEHTAEPQI APPEPRAEVQ AEVPAQPEPA PAVVTAEEEP
ADEKAARRRS TVREKVSFLS SSPSEPATPV AQASEPVAPP APAPAPAPEA ASETPAAPRR
AGWWSRRFGG GE
//
