ID A0A0Q6JXF0_9SPHN Unreviewed; 938 AA.
AC A0A0Q6JXF0;
DT 20-JAN-2016, integrated into UniProtKB/TrEMBL.
DT 20-JAN-2016, sequence version 1.
DT 27-MAR-2024, entry version 32.
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=ASG67_12745 {ECO:0000313|EMBL:KQU48196.1};
OS Sphingomonas sp. Leaf339.
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Sphingomonadales;
OC Sphingomonadaceae; Sphingomonas.
OX NCBI_TaxID=1736343 {ECO:0000313|EMBL:KQU48196.1, ECO:0000313|Proteomes:UP000051371};
RN [1] {ECO:0000313|EMBL:KQU48196.1, ECO:0000313|Proteomes:UP000051371}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Leaf339 {ECO:0000313|EMBL:KQU48196.1,
RC ECO:0000313|Proteomes:UP000051371};
RA Gilbert D.G.;
RL Submitted (OCT-2015) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|EMBL:KQU48196.1, ECO:0000313|Proteomes:UP000051371}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Leaf339 {ECO:0000313|EMBL:KQU48196.1,
RC ECO:0000313|Proteomes:UP000051371};
RA Schulze-Lefert P.;
RT "Functional overlap of the Arabidopsis leaf and root microbiotas.";
RL Submitted (NOV-2015) 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 -!- SIMILARITY: Belongs to the RNase E/G family. RNase G subfamily.
CC {ECO:0000256|ARBA:ARBA00005663}.
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:KQU48196.1}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; LMRS01000045; KQU48196.1; -; Genomic_DNA.
DR RefSeq; WP_056531686.1; NZ_LMRS01000045.1.
DR AlphaFoldDB; A0A0Q6JXF0; -.
DR STRING; 1736343.ASG67_12745; -.
DR OrthoDB; 9804278at2; -.
DR Proteomes; UP000051371; 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 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 SMART; SM00316; S1; 1.
DR SUPFAM; SSF50249; Nucleic acid-binding proteins; 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:UP000051371};
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 34..203
FT /note="S1 motif"
FT /evidence="ECO:0000259|SMART:SM00316"
FT REGION 97..159
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 488..491
FT /note="Required for zinc-mediated homotetramerization and
FT catalytic activity"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00970"
FT REGION 561..580
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 591..759
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 774..938
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 100..114
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 125..139
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 140..159
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 591..608
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 609..637
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 663..692
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 777..791
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 814..830
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 847..862
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 387
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00970"
FT BINDING 430
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00970"
FT BINDING 488
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 491
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 938 AA; 102909 MW; 49655F88BECAE786 CRC64;
MLIDARHREE TRVAVVQNNR IEEFDFESAE RKQLKGNIYL AKVTRVEPSL QAAFVEYGGN
RHGFLAFSEI HPDYYQIPKE DREALLAEEA EHAAEEAALR AELDDDEDHD DDDHDGRGDF
DGDHDDDDHE HDDDGAEGES GEDAPRRPRK GGANDDQVEA LRQRRQNLRR RYKIQDVIRR
RQVLLVQVVK EERGNKGAAL TTYLSLAGRY CVLMPNTSHG GGISRKISNA GDRKRLKTIM
ADLALPQSMG CIVRTAGLQR TKVEIKRDFD YLARLWDEIR EKTLTSAAPA LVYGDSDLMK
RAIRDIYNKD IDEVIVEGEE GYRQAKDFMR LLMPSHAKKV KQYADAVPLF QRAHVEDQLA
AMYNPVVQLK SGGYLVINPT EALVSIDINS GRSTREHNIE QTATATNLEA AQEIARQLRL
RDMAGLVVID FIDMDHSSNV RKVEKAMKDA LKNDRARIQV GRISSFGLME MSRQRLRTGV
LEASTRACPH CEGTGLVRTA SSAGLSALRL LEEEAARGRG SLLTLRASHE ATIYVLNRKR
ADIAEVEDRY GVTIEIVPDR EEEGAHMTVE ASGPPPAHAP KIDELVMDEE EDDYIEEPEV
EEEEIEEEVA QATVRAPREP REPREARSDD DGEGRGKRRR RRRGRRGRPH PEGGSAEGEQ
PELAEGEQGE NDQADIDTAD QTDGDDDTVE TGEFAGEQPA EGETGGRRRR GRRGRRGGRR
GDTMADAPVA NDDDQAVVET PAEAADASDA GPVADPLALP TPAPVAVIVQ PAVEAEEAAP
KTRRRPRARA AAPETVAEAP APVTAPAVED VAEPAPAKPR RSRRKAADAT VEAPAEVAAE
PATPTEEEAA PKPRRGRRKA SETETVAAPA AKPKARTPRA AKPAAAAAAV AVAEATPAAE
PEPEPMTAAD PALTGGEGEP DDQSGGPRRG WWQRTFGA
//
