RNT1_YEAST
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 03-AUG-2022, entry version 175.
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; 362.
DR DIP; DIP-4298N; -.
DR IntAct; Q02555; 8.
DR MINT; Q02555; -.
DR STRING; 4932.YMR239C; -.
DR iPTMnet; Q02555; -.
DR MaxQB; Q02555; -.
DR PaxDb; Q02555; -.
DR PRIDE; Q02555; -.
DR EnsemblFungi; YMR239C_mRNA; YMR239C; YMR239C.
DR GeneID; 855280; -.
DR KEGG; sce:YMR239C; -.
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 BioCyc; YEAST:YMR239C-MON; -.
DR BRENDA; 3.1.26.3; 984.
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; IBA:GO_Central.
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:0000294; P:nuclear-transcribed mRNA catabolic process, endonucleolytic cleavage-dependent decay; IDA:SGD.
DR GO; GO:0031053; P:primary miRNA processing; IBA:GO_Central.
DR GO; GO:0060237; P:regulation of fungal-type cell wall organization; IMP:SGD.
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; IMP:SGD.
DR GO; GO:0009303; P:rRNA transcription; IMP:SGD.
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; 1.10.1520.10; -; 1.
DR InterPro; IPR014720; dsRBD_dom.
DR InterPro; IPR040540; RNase_3_N.
DR InterPro; IPR011907; RNase_III.
DR InterPro; IPR000999; RNase_III_dom.
DR InterPro; IPR036389; RNase_III_sf.
DR InterPro; IPR044449; Rnt1/Pac1_DSRM_fungi.
DR PANTHER; PTHR11207; PTHR11207; 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; SSF69065; SSF69065; 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
