ID   RNT1_YEAST              Reviewed;         471 AA.
AC   Q02555; D6W065; Q04008; Q05038;
DT   01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT   01-NOV-1997, sequence version 1.
DT   27-MAR-2024, entry version 183.
DE   RecName: Full=Ribonuclease 3;
DE            EC=3.1.26.3;
DE   AltName: Full=Ribonuclease III;
DE            Short=RNase III;
GN   Name=RNT1; OrderedLocusNames=YMR239C; ORFNames=YM9408.01C, YM9959.21;
OS   Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
OC   Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC   Saccharomycetales; Saccharomycetaceae; Saccharomyces.
OX   NCBI_TaxID=559292;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX   PubMed=8620530; DOI=10.1016/s0092-8674(00)81087-9;
RA   Elela S.A., Igel H., Ares M. Jr.;
RT   "RNase III cleaves eukaryotic preribosomal RNA at a U3 snoRNP-dependent
RT   site.";
RL   Cell 85:115-124(1996).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=9169872;
RA   Bowman S., Churcher C.M., Badcock K., Brown D., Chillingworth T.,
RA   Connor R., Dedman K., Devlin K., Gentles S., Hamlin N., Hunt S., Jagels K.,
RA   Lye G., Moule S., Odell C., Pearson D., Rajandream M.A., Rice P.,
RA   Skelton J., Walsh S.V., Whitehead S., Barrell B.G.;
RT   "The nucleotide sequence of Saccharomyces cerevisiae chromosome XIII.";
RL   Nature 387:90-93(1997).
RN   [3]
RP   GENOME REANNOTATION.
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=24374639; DOI=10.1534/g3.113.008995;
RA   Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
RA   Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
RA   Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.;
RT   "The reference genome sequence of Saccharomyces cerevisiae: Then and now.";
RL   G3 (Bethesda) 4:389-398(2014).
RN   [4]
RP   LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
RX   PubMed=14562106; DOI=10.1038/nature02046;
RA   Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N.,
RA   O'Shea E.K., Weissman J.S.;
RT   "Global analysis of protein expression in yeast.";
RL   Nature 425:737-741(2003).
CC   -!- FUNCTION: DsRNA-specific nuclease that cleaves eukaryotic pre-ribosomal
CC       RNA at the U3 snoRNP-dependent A0 site in the 5'-external transcribed
CC       spacer (ETS) and in the 3'-ETS. In vitro, cleaves synthetic 5'-ETS RNA
CC       A0 site in the absence of snoRNA or other factors. Has an essential
CC       growth function in addition to pre-rRNA processing.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=Endonucleolytic cleavage to 5'-phosphomonoester.; EC=3.1.26.3;
CC   -!- INTERACTION:
CC       Q02555; Q00416: SEN1; NbExp=2; IntAct=EBI-15673, EBI-16945;
CC   -!- MISCELLANEOUS: Present with 4970 molecules/cell in log phase SD medium.
CC       {ECO:0000269|PubMed:14562106}.
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DR   EMBL; U27016; AAB04172.1; -; Genomic_DNA.
DR   EMBL; Z48756; CAA88649.1; -; Genomic_DNA.
DR   EMBL; Z49939; CAA90210.1; -; Genomic_DNA.
DR   EMBL; BK006946; DAA10139.1; -; Genomic_DNA.
DR   PIR; S56053; S56053.
DR   RefSeq; NP_013966.1; NM_001182746.1.
DR   PDB; 1T4L; NMR; -; B=366-453.
DR   PDB; 1T4N; NMR; -; A=364-447.
DR   PDB; 1T4O; X-ray; 2.50 A; A/B=362-471.
DR   PDB; 2LBS; NMR; -; B=366-453.
DR   PDB; 2LUP; NMR; -; B=366-453.
DR   PDB; 2LUQ; NMR; -; A=366-453.
DR   PDB; 4OOG; X-ray; 2.50 A; A/B=42-151, C=197-457.
DR   PDB; 5T16; X-ray; 2.78 A; A/B/I/J=184-459, C/D/E/F/K/L/M/N=41-159.
DR   PDBsum; 1T4L; -.
DR   PDBsum; 1T4N; -.
DR   PDBsum; 1T4O; -.
DR   PDBsum; 2LBS; -.
DR   PDBsum; 2LUP; -.
DR   PDBsum; 2LUQ; -.
DR   PDBsum; 4OOG; -.
DR   PDBsum; 5T16; -.
DR   AlphaFoldDB; Q02555; -.
DR   BMRB; Q02555; -.
DR   SMR; Q02555; -.
DR   BioGRID; 35418; 365.
DR   DIP; DIP-4298N; -.
DR   IntAct; Q02555; 8.
DR   MINT; Q02555; -.
DR   STRING; 4932.YMR239C; -.
DR   iPTMnet; Q02555; -.
DR   MaxQB; Q02555; -.
DR   PaxDb; 4932-YMR239C; -.
DR   PeptideAtlas; Q02555; -.
DR   EnsemblFungi; YMR239C_mRNA; YMR239C; YMR239C.
DR   GeneID; 855280; -.
DR   KEGG; sce:YMR239C; -.
DR   AGR; SGD:S000004852; -.
DR   SGD; S000004852; RNT1.
DR   VEuPathDB; FungiDB:YMR239C; -.
DR   eggNOG; KOG1817; Eukaryota.
DR   HOGENOM; CLU_026251_0_0_1; -.
DR   InParanoid; Q02555; -.
DR   OMA; MIIYNKF; -.
DR   OrthoDB; 5475137at2759; -.
DR   BioCyc; YEAST:YMR239C-MONOMER; -.
DR   BRENDA; 3.1.26.3; 984.
DR   BioGRID-ORCS; 855280; 3 hits in 10 CRISPR screens.
DR   EvolutionaryTrace; Q02555; -.
DR   PRO; PR:Q02555; -.
DR   Proteomes; UP000002311; Chromosome XIII.
DR   RNAct; Q02555; Protein.
DR   GO; GO:0005730; C:nucleolus; IDA:SGD.
DR   GO; GO:0005654; C:nucleoplasm; IDA:SGD.
DR   GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR   GO; GO:0003725; F:double-stranded RNA binding; IEA:InterPro.
DR   GO; GO:0004525; F:ribonuclease III activity; IDA:SGD.
DR   GO; GO:0034963; P:box C/D RNA processing; IMP:SGD.
DR   GO; GO:0034964; P:box H/ACA RNA processing; IMP:SGD.
DR   GO; GO:0006325; P:chromatin organization; IMP:SGD.
DR   GO; GO:0060237; P:regulation of fungal-type cell wall organization; IMP:SGD.
DR   GO; GO:0006364; P:rRNA processing; IMP:SGD.
DR   GO; GO:0009303; P:rRNA transcription; IMP:SGD.
DR   GO; GO:0006369; P:termination of RNA polymerase II transcription; IBA:GO_Central.
DR   GO; GO:0030847; P:termination of RNA polymerase II transcription, exosome-dependent; IDA:SGD.
DR   GO; GO:0034473; P:U1 snRNA 3'-end processing; IMP:SGD.
DR   GO; GO:0034475; P:U4 snRNA 3'-end processing; IMP:SGD.
DR   GO; GO:0034476; P:U5 snRNA 3'-end processing; IDA:SGD.
DR   CDD; cd19876; DSRM_RNT1p-like; 1.
DR   CDD; cd00593; RIBOc; 1.
DR   Gene3D; 3.30.160.20; -; 1.
DR   Gene3D; 1.10.1520.10; Ribonuclease III domain; 1.
DR   InterPro; IPR014720; dsRBD_dom.
DR   InterPro; IPR040540; RNase_3_N.
DR   InterPro; IPR000999; RNase_III_dom.
DR   InterPro; IPR036389; RNase_III_sf.
DR   InterPro; IPR044449; Rnt1/Pac1_DSRM_fungi.
DR   PANTHER; PTHR14950; DICER-RELATED; 1.
DR   PANTHER; PTHR14950:SF37; ENDORIBONUCLEASE DICER; 1.
DR   Pfam; PF00035; dsrm; 1.
DR   Pfam; PF00636; Ribonuclease_3; 1.
DR   Pfam; PF18497; RNase_3_N; 1.
DR   SMART; SM00358; DSRM; 1.
DR   SMART; SM00535; RIBOc; 1.
DR   SUPFAM; SSF54768; dsRNA-binding domain-like; 1.
DR   SUPFAM; SSF69065; RNase III domain-like; 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; Endonuclease; Hydrolase; Nuclease; Reference proteome;
KW   RNA-binding.
FT   CHAIN           1..471
FT                   /note="Ribonuclease 3"
FT                   /id="PRO_0000180466"
FT   DOMAIN          227..331
FT                   /note="RNase III"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00177"
FT   DOMAIN          369..437
FT                   /note="DRBM"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00266"
FT   REGION          1..29
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          168..189
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          451..471
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        169..184
FT                   /note="Acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        456..471
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   HELIX           46..69
FT                   /evidence="ECO:0007829|PDB:4OOG"
FT   HELIX           73..81
FT                   /evidence="ECO:0007829|PDB:4OOG"
FT   STRAND          84..86
FT                   /evidence="ECO:0007829|PDB:4OOG"
FT   HELIX           88..95
FT                   /evidence="ECO:0007829|PDB:4OOG"
FT   HELIX           97..110
FT                   /evidence="ECO:0007829|PDB:4OOG"
FT   HELIX           116..126
FT                   /evidence="ECO:0007829|PDB:4OOG"
FT   STRAND          136..138
FT                   /evidence="ECO:0007829|PDB:4OOG"
FT   HELIX           140..149
FT                   /evidence="ECO:0007829|PDB:4OOG"
FT   HELIX           208..213
FT                   /evidence="ECO:0007829|PDB:4OOG"
FT   HELIX           218..221
FT                   /evidence="ECO:0007829|PDB:4OOG"
FT   HELIX           229..233
FT                   /evidence="ECO:0007829|PDB:4OOG"
FT   HELIX           238..259
FT                   /evidence="ECO:0007829|PDB:4OOG"
FT   HELIX           265..276
FT                   /evidence="ECO:0007829|PDB:4OOG"
FT   HELIX           278..287
FT                   /evidence="ECO:0007829|PDB:4OOG"
FT   HELIX           290..293
FT                   /evidence="ECO:0007829|PDB:4OOG"
FT   STRAND          303..305
FT                   /evidence="ECO:0007829|PDB:5T16"
FT   TURN            306..309
FT                   /evidence="ECO:0007829|PDB:4OOG"
FT   HELIX           313..329
FT                   /evidence="ECO:0007829|PDB:4OOG"
FT   HELIX           331..356
FT                   /evidence="ECO:0007829|PDB:4OOG"
FT   HELIX           358..360
FT                   /evidence="ECO:0007829|PDB:4OOG"
FT   HELIX           370..378
FT                   /evidence="ECO:0007829|PDB:1T4O"
FT   HELIX           381..383
FT                   /evidence="ECO:0007829|PDB:1T4O"
FT   STRAND          386..391
FT                   /evidence="ECO:0007829|PDB:1T4O"
FT   STRAND          394..396
FT                   /evidence="ECO:0007829|PDB:1T4N"
FT   STRAND          400..405
FT                   /evidence="ECO:0007829|PDB:1T4O"
FT   TURN            407..409
FT                   /evidence="ECO:0007829|PDB:1T4L"
FT   STRAND          411..419
FT                   /evidence="ECO:0007829|PDB:1T4O"
FT   HELIX           420..433
FT                   /evidence="ECO:0007829|PDB:1T4O"
FT   HELIX           435..441
FT                   /evidence="ECO:0007829|PDB:1T4O"
FT   HELIX           450..453
FT                   /evidence="ECO:0007829|PDB:4OOG"
FT   STRAND          455..457
FT                   /evidence="ECO:0007829|PDB:5T16"
SQ   SEQUENCE   471 AA;  54071 MW;  570294172E66A0DE CRC64;
     MGSKVAGKKK TQNDNKLDNE NGSQQRENIN TKTLLKGNLK ISNYKYLEVI QLEHAVTKLV
     ESYNKIIELS PNLVAYNEAV NNQDRVPVQI LPSLSRYQLK LAAELKTLHD LKKDAILTEI
     TDYENEFDTE QKQPILQEIS KADMEKLEKL EQVKREKREK IDVNVYENLN EKEDEEEDEG
     EDSYDPTKAG DIVKATKWPP KLPEIQDLAI RARVFIHKST IKDKVYLSGS EMINAHNERL
     EFLGDSILNS VMTLIIYNKF PDYSEGQLST LRMNLVSNEQ IKQWSIMYNF HEKLKTNFDL
     KDENSNFQNG KLKLYADVFE AYIGGLMEDD PRNNLPKIRK WLRKLAKPVI EEATRNQVAL
     EKTDKLDMNA KRQLYSLIGY ASLRLHYVTV KKPTAVDPNS IVECRVGDGT VLGTGVGRNI
     KIAGIRAAEN ALRDKKMLDF YAKQRAAIPR SESVLKDPSQ KNKKRKFSDT S
//