RNC_AQUAE
ID RNC_AQUAE Reviewed; 221 AA.
AC O67082;
DT 30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1998, sequence version 1.
DT 03-AUG-2022, entry version 148.
DE RecName: Full=Ribonuclease 3;
DE EC=3.1.26.3;
DE AltName: Full=Ribonuclease III;
DE Short=RNase III;
GN Name=rnc; OrderedLocusNames=aq_946;
OS Aquifex aeolicus (strain VF5).
OC Bacteria; Aquificae; Aquificales; Aquificaceae; Aquifex.
OX NCBI_TaxID=224324;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=VF5;
RX PubMed=9537320; DOI=10.1038/32831;
RA Deckert G., Warren P.V., Gaasterland T., Young W.G., Lenox A.L.,
RA Graham D.E., Overbeek R., Snead M.A., Keller M., Aujay M., Huber R.,
RA Feldman R.A., Short J.M., Olsen G.J., Swanson R.V.;
RT "The complete genome of the hyperthermophilic bacterium Aquifex aeolicus.";
RL Nature 392:353-358(1998).
RN [2]
RP BIOPHYSICOCHEMICAL PROPERTIES, FUNCTION AS AN ENDORIBONUCLEASE, FUNCTION IN
RP RRNA PRECURSOR PROCESSING, COFACTOR, RNA-BINDING, AND MUTAGENESIS OF
RP GLN-157.
RX PubMed=21138964; DOI=10.1093/nar/gkq1030;
RA Shi Z., Nicholson R.H., Jaggi R., Nicholson A.W.;
RT "Characterization of Aquifex aeolicus ribonuclease III and the reactivity
RT epitopes of its pre-ribosomal RNA substrates.";
RL Nucleic Acids Res. 39:2756-2768(2011).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) OF 1-147 WITH AND WITHOUT MANGANESE,
RP COFACTOR, AND SUBUNIT.
RC STRAIN=VF5;
RX PubMed=11738048; DOI=10.1016/s0969-2126(01)00685-2;
RA Blaszczyk J., Tropea J.E., Bubunenko M., Routzahn K.M., Waugh D.S.,
RA Court D.L., Ji X.;
RT "Crystallographic and modeling studies of RNase III suggest a mechanism for
RT double-stranded RNA cleavage.";
RL Structure 9:1225-1236(2001).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 1-147 WITH MAGNESIUM, X-RAY
RP CRYSTALLOGRAPHY (2.15 ANGSTROMS) OF 1-220 WITH DS-RNA, RNA-BINDING,
RP COFACTOR, SUBUNIT, AND MUTAGENESIS OF GLU-110.
RC STRAIN=VF5;
RX PubMed=15016361; DOI=10.1016/j.str.2004.02.004;
RA Blaszczyk J., Gan J., Tropea J.E., Court D.L., Waugh D.S., Ji X.;
RT "Noncatalytic assembly of ribonuclease III with double-stranded RNA.";
RL Structure 12:457-466(2004).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) IN COMPLEX WITH DS-RNA.
RX PubMed=16216575; DOI=10.1016/j.str.2005.06.014;
RA Gan J., Tropea J.E., Austin B.P., Court D.L., Waugh D.S., Ji X.;
RT "Intermediate states of ribonuclease III in complex with double-stranded
RT RNA.";
RL Structure 13:1435-1442(2005).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (2.05 ANGSTROMS) IN COMPLEX WITH PRODUCT, FUNCTION AS
RP AN RNASE, COFACTOR, SUBUNIT, RNA-BINDING, AND MUTAGENESIS OF ASP-44.
RX PubMed=16439209; DOI=10.1016/j.cell.2005.11.034;
RA Gan J., Tropea J.E., Austin B.P., Court D.L., Waugh D.S., Ji X.;
RT "Structural insight into the mechanism of double-stranded RNA processing by
RT ribonuclease III.";
RL Cell 124:355-366(2006).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) IN COMPLEX WITH PRODUCT AND
RP MAGNESIUM, COFACTOR, AND MUTAGENESIS OF GLU-110.
RX PubMed=18047582; DOI=10.1111/j.1365-2958.2007.06032.x;
RA Gan J., Shaw G., Tropea J.E., Waugh D.S., Court D.L., Ji X.;
RT "A stepwise model for double-stranded RNA processing by ribonuclease III.";
RL Mol. Microbiol. 67:143-154(2008).
CC -!- FUNCTION: Digests double-stranded RNA. Involved in the processing of
CC primary rRNA transcript to yield the immediate precursors to the large
CC and small rRNAs (23S and 16S). Also processes some mRNAs, and tRNAs
CC when they are encoded in the rRNA operon. Probably processes pre-crRNA
CC and tracrRNA of type II CRISPR loci if present in the organism.
CC {ECO:0000269|PubMed:16439209, ECO:0000269|PubMed:21138964}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Endonucleolytic cleavage to 5'-phosphomonoester.; EC=3.1.26.3;
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:11738048, ECO:0000269|PubMed:15016361,
CC ECO:0000269|PubMed:16439209, ECO:0000269|PubMed:18047582,
CC ECO:0000269|PubMed:21138964};
CC Note=Binds 2 Mg(2+) per subunit. Mn(2+) also supports catalytic
CC activity. {ECO:0000269|PubMed:11738048, ECO:0000269|PubMed:15016361,
CC ECO:0000269|PubMed:16439209, ECO:0000269|PubMed:18047582,
CC ECO:0000269|PubMed:21138964};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=98 nM for 16S-u-hp RNA {ECO:0000269|PubMed:21138964};
CC pH dependence:
CC Optimum pH is 8-9. {ECO:0000269|PubMed:21138964};
CC Temperature dependence:
CC Optimum temperature is 70-85 degrees Celsius.
CC {ECO:0000269|PubMed:21138964};
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:11738048,
CC ECO:0000269|PubMed:15016361, ECO:0000269|PubMed:16216575,
CC ECO:0000269|PubMed:16439209, ECO:0000269|PubMed:18047582}.
CC -!- INTERACTION:
CC O67082; O67082: rnc; NbExp=2; IntAct=EBI-15529943, EBI-15529943;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the ribonuclease III family. {ECO:0000305}.
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DR EMBL; AE000657; AAC07049.1; -; Genomic_DNA.
DR PIR; G70381; G70381.
DR RefSeq; NP_213645.1; NC_000918.1.
DR RefSeq; WP_010880583.1; NC_000918.1.
DR PDB; 1I4S; X-ray; 2.15 A; A/B=1-147.
DR PDB; 1JFZ; X-ray; 2.10 A; A/B/C/D=1-147.
DR PDB; 1RC5; X-ray; 2.30 A; A/B/C/D=1-147.
DR PDB; 1RC7; X-ray; 2.15 A; A=1-220.
DR PDB; 1YYK; X-ray; 2.50 A; A/B=1-221.
DR PDB; 1YYO; X-ray; 2.90 A; A/B=1-221.
DR PDB; 1YYW; X-ray; 2.80 A; A/B/C/D=1-221.
DR PDB; 1YZ9; X-ray; 2.10 A; A/B=1-221.
DR PDB; 2EZ6; X-ray; 2.05 A; A/B=1-221.
DR PDB; 2NUE; X-ray; 2.90 A; A/B=1-221.
DR PDB; 2NUF; X-ray; 2.50 A; A/B=1-221.
DR PDB; 2NUG; X-ray; 1.70 A; A/B=1-221.
DR PDB; 4M2Z; X-ray; 2.85 A; A/B=1-221.
DR PDB; 4M30; X-ray; 2.50 A; A/B=1-221.
DR PDBsum; 1I4S; -.
DR PDBsum; 1JFZ; -.
DR PDBsum; 1RC5; -.
DR PDBsum; 1RC7; -.
DR PDBsum; 1YYK; -.
DR PDBsum; 1YYO; -.
DR PDBsum; 1YYW; -.
DR PDBsum; 1YZ9; -.
DR PDBsum; 2EZ6; -.
DR PDBsum; 2NUE; -.
DR PDBsum; 2NUF; -.
DR PDBsum; 2NUG; -.
DR PDBsum; 4M2Z; -.
DR PDBsum; 4M30; -.
DR AlphaFoldDB; O67082; -.
DR SMR; O67082; -.
DR DIP; DIP-48455N; -.
DR STRING; 224324.aq_946; -.
DR EnsemblBacteria; AAC07049; AAC07049; aq_946.
DR KEGG; aae:aq_946; -.
DR PATRIC; fig|224324.8.peg.743; -.
DR eggNOG; COG0571; Bacteria.
DR HOGENOM; CLU_000907_1_3_0; -.
DR InParanoid; O67082; -.
DR OMA; LTHKSCK; -.
DR OrthoDB; 1890943at2; -.
DR BRENDA; 3.1.26.3; 396.
DR EvolutionaryTrace; O67082; -.
DR Proteomes; UP000000798; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0003725; F:double-stranded RNA binding; IBA:GO_Central.
DR GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004525; F:ribonuclease III activity; IBA:GO_Central.
DR GO; GO:0006397; P:mRNA processing; IEA:UniProtKB-UniRule.
DR GO; GO:0010468; P:regulation of gene expression; IBA:GO_Central.
DR GO; GO:0006396; P:RNA processing; IBA:GO_Central.
DR GO; GO:0006364; P:rRNA processing; IEA:UniProtKB-UniRule.
DR GO; GO:0008033; P:tRNA processing; IEA:UniProtKB-KW.
DR CDD; cd00593; RIBOc; 1.
DR Gene3D; 1.10.1520.10; -; 1.
DR HAMAP; MF_00104; RNase_III; 1.
DR InterPro; IPR014720; dsRBD_dom.
DR InterPro; IPR011907; RNase_III.
DR InterPro; IPR000999; RNase_III_dom.
DR InterPro; IPR036389; RNase_III_sf.
DR Pfam; PF00035; dsrm; 1.
DR Pfam; PF14622; Ribonucleas_3_3; 1.
DR SMART; SM00358; DSRM; 1.
DR SMART; SM00535; RIBOc; 1.
DR SUPFAM; SSF69065; SSF69065; 1.
DR TIGRFAMs; TIGR02191; RNaseIII; 1.
DR PROSITE; PS50137; DS_RBD; 1.
DR PROSITE; PS00517; RNASE_3_1; 1.
DR PROSITE; PS50142; RNASE_3_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Endonuclease; Hydrolase; Magnesium; Metal-binding;
KW mRNA processing; Nuclease; Reference proteome; RNA-binding;
KW rRNA processing; tRNA processing.
FT CHAIN 1..221
FT /note="Ribonuclease 3"
FT /id="PRO_0000180371"
FT DOMAIN 4..121
FT /note="RNase III"
FT DOMAIN 151..219
FT /note="DRBM"
FT ACT_SITE 44
FT /evidence="ECO:0000255"
FT ACT_SITE 110
FT /evidence="ECO:0000305"
FT BINDING 40
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:15016361,
FT ECO:0000269|PubMed:18047582, ECO:0000305|PubMed:11738048,
FT ECO:0007744|PDB:1JFZ, ECO:0007744|PDB:1RC5"
FT BINDING 107
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:15016361,
FT ECO:0000269|PubMed:18047582, ECO:0000305|PubMed:11738048,
FT ECO:0007744|PDB:1JFZ, ECO:0007744|PDB:1RC5"
FT BINDING 110
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000269|PubMed:15016361,
FT ECO:0000269|PubMed:18047582, ECO:0000305|PubMed:11738048,
FT ECO:0007744|PDB:1JFZ, ECO:0007744|PDB:1RC5"
FT MUTAGEN 44
FT /note="D->N: Very low catalytic activity, binds RNA
FT normally."
FT /evidence="ECO:0000269|PubMed:16439209"
FT MUTAGEN 110
FT /note="E->K: Loss of magnesium, alters ds-RNA binding, loss
FT of activity."
FT /evidence="ECO:0000269|PubMed:15016361,
FT ECO:0000269|PubMed:18047582"
FT MUTAGEN 157
FT /note="Q->A: No RNase activity, no RNA binding."
FT /evidence="ECO:0000269|PubMed:21138964"
FT TURN 1..3
FT /evidence="ECO:0007829|PDB:1JFZ"
FT HELIX 4..11
FT /evidence="ECO:0007829|PDB:2NUG"
FT HELIX 18..25
FT /evidence="ECO:0007829|PDB:2NUG"
FT TURN 28..30
FT /evidence="ECO:0007829|PDB:2NUG"
FT STRAND 32..34
FT /evidence="ECO:0007829|PDB:2NUG"
FT HELIX 37..57
FT /evidence="ECO:0007829|PDB:2NUG"
FT HELIX 64..74
FT /evidence="ECO:0007829|PDB:2NUG"
FT HELIX 77..85
FT /evidence="ECO:0007829|PDB:2NUG"
FT TURN 86..88
FT /evidence="ECO:0007829|PDB:2NUG"
FT HELIX 89..91
FT /evidence="ECO:0007829|PDB:2NUG"
FT STRAND 96..98
FT /evidence="ECO:0007829|PDB:2EZ6"
FT HELIX 102..119
FT /evidence="ECO:0007829|PDB:2NUG"
FT HELIX 124..144
FT /evidence="ECO:0007829|PDB:2NUG"
FT HELIX 152..164
FT /evidence="ECO:0007829|PDB:2NUG"
FT STRAND 169..177
FT /evidence="ECO:0007829|PDB:2NUG"
FT HELIX 179..181
FT /evidence="ECO:0007829|PDB:2NUG"
FT STRAND 183..190
FT /evidence="ECO:0007829|PDB:2NUG"
FT STRAND 193..201
FT /evidence="ECO:0007829|PDB:2NUG"
FT HELIX 202..217
FT /evidence="ECO:0007829|PDB:2NUG"
SQ SEQUENCE 221 AA; 26100 MW; ACB69735DB49641D CRC64;
MKMLEQLEKK LGYTFKDKSL LEKALTHVSY SKKEHYETLE FLGDALVNFF IVDLLVQYSP
NKREGFLSPL KAYLISEEFF NLLAQKLELH KFIRIKRGKI NETIIGDVFE ALWAAVYIDS
GRDANFTREL FYKLFKEDIL SAIKEGRVKK DYKTILQEIT QKRWKERPEY RLISVEGPHH
KKKFIVEAKI KEYRTLGEGK SKKEAEQRAA EELIKLLEES E
