ID A0A2N4WZP4_9SPHN Unreviewed; 916 AA.
AC A0A2N4WZP4;
DT 25-APR-2018, integrated into UniProtKB/TrEMBL.
DT 25-APR-2018, sequence version 1.
DT 27-MAR-2024, entry version 24.
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=C0V78_01905 {ECO:0000313|EMBL:PLK25784.1};
OS Novosphingobium sp. TH158.
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Sphingomonadales;
OC Sphingomonadaceae; Novosphingobium.
OX NCBI_TaxID=2067455 {ECO:0000313|EMBL:PLK25784.1, ECO:0000313|Proteomes:UP000234499};
RN [1] {ECO:0000313|EMBL:PLK25784.1, ECO:0000313|Proteomes:UP000234499}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=TH158 {ECO:0000313|EMBL:PLK25784.1,
RC ECO:0000313|Proteomes:UP000234499};
RA Cai h.;
RT "genomes of bacteria within cyanobacterial aggregates.";
RL Submitted (DEC-2017) 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;
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}.
CC -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:PLK25784.1}.
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DR EMBL; PKRT01000001; PLK25784.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A2N4WZP4; -.
DR OrthoDB; 9804278at2; -.
DR Proteomes; UP000234499; Unassembled WGS sequence.
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 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:UP000234499};
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 539..620
FT /note="RNase E/G thioredoxin-like"
FT /evidence="ECO:0000259|Pfam:PF20833"
FT REGION 158..212
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 539..542
FT /note="Required for zinc-mediated homotetramerization and
FT catalytic activity"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00970"
FT REGION 616..916
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 639..661
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 693..717
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 777..797
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 813..833
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 848..867
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 438
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00970"
FT BINDING 481
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00970"
FT BINDING 539
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 542
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 916 AA; 100965 MW; C80C77BBD183D7F8 CRC64;
MTTRMLIDAR HQEETRVAVL KGNRIEEFDF ESAEHKQIKG NIYLAKVTRV EPSLQAAFVD
FGGNRHGFLA FSEIHPDYYQ IPKEDRERLL AEEAAHAEEE AALRAKAEGE EDFVGDDELG
ETLADELAGT THDHHHDDEF SGVMEVDTAE KDEVATIEDG HVENGFDHEG EEADEAGESE
GEGEGGEDRR GRRGRRRQGG GNRGHAKEAD ELRAKRMALR RRYKIQDVIQ RRQVLLVQVV
KEERGNKGAA LTTYLSLAGR YCVLMPNSSH GGGISRKISS AADRKRLKGI IAELDLPKSM
GCIVRTAGLQ RTKTEIKRDF DYLARLWDEI RETTLKSSAP APIHSDSDLI KRAIRDIYNK
EIEEVVVEGE QGYRAARDFM KLLMPSHAKR VKAYSDPVPL FQRYGAEDQL TAMFEPVVQL
KSGGYLVINP TEALVSIDIN SGRSTKEHGI EATALSTNLE AAREIARQLR LRDMAGLVVI
DFIDMEYGSN VRKVEKAMKE ALKNDRARIQ VGRISSFGLM EMSRQRLRTG VLEASTRSCP
HCDGTGLVRT ASSAGLAALR LIEDEAAKGK GTIITLYAST EASIYLLNTK RADLHEIEQR
YGVQVQVIPE GENEGAKMRV ASSGPRPTSL PRFEPIIEPE DDDIVEEDFD DGEDEEEDRE
ERGDDRDGRG RKRRRRRRGG KGRSRDGDRE DDRADGEEAE ADEGEEAGDE AEGGDETGED
GESPRKRRRR GRRRRGGRGR GEGEGADGES EAGAEGAEPK VAGDVAEPGA EASEEAPAEE
PAPKKRTRRK KADVTAEAEA AAEAASSEEA PAAEPVAEEK PKRTRRKKAE PAPEAETAPA
AEAPAEEPVV AEKPKRTRKK KAEPAPEAEA MAEPAPEAEP AAEAIAEASA DAAVETAAEE
ENGPKRRGWW QRTFGE
//
