ID Q9A749_CAUVC Unreviewed; 898 AA.
AC Q9A749;
DT 01-JUN-2001, integrated into UniProtKB/TrEMBL.
DT 01-JUN-2001, sequence version 1.
DT 27-MAR-2024, entry version 125.
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=CC_1877 {ECO:0000313|EMBL:AAK23852.1};
OS Caulobacter vibrioides (strain ATCC 19089 / CB15) (Caulobacter crescentus).
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Caulobacterales;
OC Caulobacteraceae; Caulobacter.
OX NCBI_TaxID=190650 {ECO:0000313|EMBL:AAK23852.1, ECO:0000313|Proteomes:UP000001816};
RN [1] {ECO:0000313|EMBL:AAK23852.1, ECO:0000313|Proteomes:UP000001816}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 19089 / CB15 {ECO:0000313|Proteomes:UP000001816};
RX PubMed=11259647; DOI=10.1073/pnas.061029298;
RA Nierman W.C., Feldblyum T.V., Laub M.T., Paulsen I.T., Nelson K.E.,
RA Eisen J.A., Heidelberg J.F., Alley M.R., Ohta N., Maddock J.R., Potocka I.,
RA Nelson W.C., Newton A., Stephens C., Phadke N.D., Ely B., DeBoy R.T.,
RA Dodson R.J., Durkin A.S., Gwinn M.L., Haft D.H., Kolonay J.F., Smit J.,
RA Craven M.B., Khouri H., Shetty J., Berry K., Utterback T., Tran K.,
RA Wolf A., Vamathevan J., Ermolaeva M., White O., Salzberg S.L., Venter J.C.,
RA Shapiro L., Fraser C.M.;
RT "Complete genome sequence of Caulobacter crescentus.";
RL Proc. Natl. Acad. Sci. U.S.A. 98:4136-4141(2001).
RN [2] {ECO:0007829|PDB:4AID, ECO:0007829|PDB:4AIM}
RP X-RAY CRYSTALLOGRAPHY (2.60 ANGSTROMS) OF 885-898.
RX PubMed=22724061; DOI=10.1098/RSOB.120028;
RA Hardwick S.W., Gubbey T., Hug I., Jenal U., Luisi B.F.;
RT "Crystal structure of Caulobacter crescentus polynucleotide phosphorylase
RT reveals a mechanism of RNA substrate channelling and RNA degradosome
RT assembly.";
RL Open Biol. 2:120028-120028(2012).
RN [3] {ECO:0007829|PDB:4OXP}
RP X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) OF 1-270.
RX PubMed=25389270; DOI=10.1093/nar/gku1134;
RA Voss J.E., Luisi B.F., Hardwick S.W.;
RT "Molecular recognition of RhlB and RNase D in the Caulobacter crescentus
RT RNA degradosome.";
RL Nucleic Acids Res. 42:13294-13305(2014).
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; AE005673; AAK23852.1; -; Genomic_DNA.
DR PIR; H87481; H87481.
DR RefSeq; NP_420684.1; NC_002696.2.
DR RefSeq; WP_010919743.1; NC_002696.2.
DR PDB; 4AID; X-ray; 2.60 A; F/G/H=885-898.
DR PDB; 4AIM; X-ray; 3.30 A; C=885-898.
DR PDB; 4OXP; X-ray; 2.10 A; A=1-270.
DR PDBsum; 4AID; -.
DR PDBsum; 4AIM; -.
DR PDBsum; 4OXP; -.
DR AlphaFoldDB; Q9A749; -.
DR SMR; Q9A749; -.
DR STRING; 190650.CC_1877; -.
DR EnsemblBacteria; AAK23852; AAK23852; CC_1877.
DR KEGG; ccr:CC_1877; -.
DR PATRIC; fig|190650.5.peg.1894; -.
DR eggNOG; COG1530; Bacteria.
DR eggNOG; COG3266; Bacteria.
DR HOGENOM; CLU_003468_5_0_5; -.
DR BioCyc; CAULO:CC1877-MONOMER; -.
DR Proteomes; UP000001816; 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 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 1: Evidence at protein level;
KW 3D-structure {ECO:0007829|PDB:4AID, ECO:0007829|PDB:4AIM};
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:UP000001816};
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 460..543
FT /note="RNase E/G thioredoxin-like"
FT /evidence="ECO:0000259|Pfam:PF20833"
FT REGION 91..131
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 461..464
FT /note="Required for zinc-mediated homotetramerization and
FT catalytic activity"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00970"
FT REGION 545..686
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 706..774
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 802..828
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 856..898
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 98..116
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 117..131
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 558..592
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 593..613
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 632..653
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 716..762
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 802..823
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 360
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00970"
FT BINDING 403
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00970"
FT BINDING 461
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 464
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 898 AA; 100693 MW; 52035FBF1F9710E4 CRC64;
MSKKMLIDAA HAEETRVVVV DGTRVEEFDF ESQTRKQLRG NIYLAKVTRV EPSLQAAFIE
YGGNRHGFLA FNEIHPDYYQ IPVADREALM RDDSGDDEDD TPISRRASGG DDEDDVNGGD
RAVDDDDDDV EEELARRKRR LMRKYKIQEV IRRRQIMLVQ VVKEERGNKG AALTTYLSLA
GRYGVLMPNT ARGGGISRKI TAVTDRKRLK SVVQSLDVPQ GMGLIVRTAG AKRTKAEIKR
DYEYLLRLWE NIRENTLHSI APALIYEEED LVKRAIRDMY DKDLDGIWVE GDAGYKEARD
FMRMLMPSQA KKVFNYRDPT PLFVKNKIED HLAQIYSPVV PLRSGGYLVI NQTEALVAID
VNSGKATRER NIEATALKTN CEAAEEAARQ LRLRDLAGLI VIDFIDMDEA KNNRTVEKVL
KDALKDDRAR IQMGKISGFG LMEISRQRRR TGVLEGTTHV CEHCEGTGRV RSVESSALAA
LRAVEAEALK GSGSVILKVS RSVGLYILNE KRDYLQRLLT THGLFVSVVV DDSLHAGDQE
IERTELGERI AVAPPPFVEE DDDFDPNAYD DEEEEDDVIL DDEDDTDRED TDDDDATTRK
SARDDERGDR KGRRGRRDRN RGRGRRDERD GETESEDEDV VAEGADEDRG EFGDDDEGGR
RRRRRGRRGG RRGGREDGDR PTDAFVWIRP RVPFGENVFT WHDPAALVGG GESRRQAPEP
RVDAATEAAP RPERAEREER PGRERGRRGR DRGRRQRDEA PVAEMTSVES ATVEAAEPFE
APILAPPVIA GPPADVWVEL PEVEEAPKKP KRSRARGKKA TETSVEAIDT VTEVAAEAPA
PETAEPEAVE VAPPAPTVEA APEPGPVVEA VEEAQPAEPD PNEITAPPEK PRRGWWRR
//
