DXO_YEAST
ID DXO_YEAST Reviewed; 387 AA.
AC P53063; D6VV89;
DT 01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 03-AUG-2022, entry version 170.
DE RecName: Full=Decapping nuclease RAI1 {ECO:0000305};
DE Short=ScRai1 {ECO:0000303|PubMed:26101253};
DE EC=3.6.1.- {ECO:0000269|PubMed:20802481, ECO:0000269|PubMed:26101253};
DE AltName: Full=NAD-capped RNA hydrolase RAI1 {ECO:0000305};
DE Short=DeNADding enzyme RAI1 {ECO:0000305};
DE EC=3.6.1.- {ECO:0000250|UniProtKB:O13836};
DE AltName: Full=RAT1-interacting protein {ECO:0000303|PubMed:10805743};
GN Name=RAI1 {ECO:0000303|PubMed:10805743}; OrderedLocusNames=YGL246C;
GN ORFNames=NRE387;
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].
RC STRAIN=ATCC 96604 / S288c / FY1679;
RX PubMed=8972578;
RX DOI=10.1002/(sici)1097-0061(199612)12:15<1555::aid-yea43>3.0.co;2-q;
RA Coissac E., Maillier E., Robineau S., Netter P.;
RT "Sequence of a 39,411 bp DNA fragment covering the left end of chromosome
RT VII of Saccharomyces cerevisiae.";
RL Yeast 12:1555-1562(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=9169869;
RA Tettelin H., Agostoni-Carbone M.L., Albermann K., Albers M., Arroyo J.,
RA Backes U., Barreiros T., Bertani I., Bjourson A.J., Brueckner M.,
RA Bruschi C.V., Carignani G., Castagnoli L., Cerdan E., Clemente M.L.,
RA Coblenz A., Coglievina M., Coissac E., Defoor E., Del Bino S., Delius H.,
RA Delneri D., de Wergifosse P., Dujon B., Durand P., Entian K.-D., Eraso P.,
RA Escribano V., Fabiani L., Fartmann B., Feroli F., Feuermann M.,
RA Frontali L., Garcia-Gonzalez M., Garcia-Saez M.I., Goffeau A.,
RA Guerreiro P., Hani J., Hansen M., Hebling U., Hernandez K., Heumann K.,
RA Hilger F., Hofmann B., Indge K.J., James C.M., Klima R., Koetter P.,
RA Kramer B., Kramer W., Lauquin G., Leuther H., Louis E.J., Maillier E.,
RA Marconi A., Martegani E., Mazon M.J., Mazzoni C., McReynolds A.D.K.,
RA Melchioretto P., Mewes H.-W., Minenkova O., Mueller-Auer S., Nawrocki A.,
RA Netter P., Neu R., Nombela C., Oliver S.G., Panzeri L., Paoluzi S.,
RA Plevani P., Portetelle D., Portillo F., Potier S., Purnelle B., Rieger M.,
RA Riles L., Rinaldi T., Robben J., Rodrigues-Pousada C.,
RA Rodriguez-Belmonte E., Rodriguez-Torres A.M., Rose M., Ruzzi M.,
RA Saliola M., Sanchez-Perez M., Schaefer B., Schaefer M., Scharfe M.,
RA Schmidheini T., Schreer A., Skala J., Souciet J.-L., Steensma H.Y.,
RA Talla E., Thierry A., Vandenbol M., van der Aart Q.J.M., Van Dyck L.,
RA Vanoni M., Verhasselt P., Voet M., Volckaert G., Wambutt R., Watson M.D.,
RA Weber N., Wedler E., Wedler H., Wipfli P., Wolf K., Wright L.F.,
RA Zaccaria P., Zimmermann M., Zollner A., Kleine K.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome VII.";
RL Nature 387:81-84(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 NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=17322287; DOI=10.1101/gr.6037607;
RA Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F.,
RA Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J.,
RA Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J.,
RA Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D.,
RA LaBaer J.;
RT "Approaching a complete repository of sequence-verified protein-encoding
RT clones for Saccharomyces cerevisiae.";
RL Genome Res. 17:536-543(2007).
RN [5]
RP PROTEIN SEQUENCE OF 2-17, FUNCTION, AND INTERACTION WITH RAT1.
RX PubMed=10805743; DOI=10.1128/mcb.20.11.4006-4015.2000;
RA Xue Y., Bai X., Lee I., Kallstrom G., Ho J., Brown J., Stevens A.,
RA Johnson A.W.;
RT "Saccharomyces cerevisiae RAI1 (YGL246c) is homologous to human DOM3Z and
RT encodes a protein that binds the nuclear exoribonuclease Rat1p.";
RL Mol. Cell. Biol. 20:4006-4015(2000).
RN [6]
RP FUNCTION, INTERACTION WITH RAT1 AND PRE-60S RIBOSOMAL SUBUNITS, AND
RP SUBCELLULAR LOCATION.
RX PubMed=12612077; DOI=10.1128/mcb.23.6.2042-2054.2003;
RA Sydorskyy Y., Dilworth D.J., Yi E.C., Goodlett D.R., Wozniak R.W.,
RA Aitchison J.D.;
RT "Intersection of the Kap123p-mediated nuclear import and ribosome export
RT pathways.";
RL Mol. Cell. Biol. 23:2042-2054(2003).
RN [7]
RP FUNCTION.
RX PubMed=12897126; DOI=10.1128/mcb.23.16.5502-5515.2003;
RA Das B., Butler J.S., Sherman F.;
RT "Degradation of normal mRNA in the nucleus of Saccharomyces cerevisiae.";
RL Mol. Cell. Biol. 23:5502-5515(2003).
RN [8]
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).
RN [9]
RP FUNCTION, IDENTIFICATION BY MASS SPECTROMETRY, AND IDENTIFICATION IN A
RP COMPLEX WITH RTT103.
RX PubMed=15565157; DOI=10.1038/nature03041;
RA Kim M., Krogan N.J., Vasiljeva L., Rando O.J., Nedea E., Greenblatt J.F.,
RA Buratowski S.;
RT "The yeast Rat1 exonuclease promotes transcription termination by RNA
RT polymerase II.";
RL Nature 432:517-522(2004).
RN [10]
RP ERRATUM OF PUBMED:15565157.
RA Kim M., Krogan N.J., Vasiljeva L., Rando O.J., Nedea E., Greenblatt J.F.,
RA Buratowski S.;
RL Nature 433:661-661(2005).
RN [11]
RP FUNCTION.
RX PubMed=16131592; DOI=10.1261/rna.2900205;
RA Fang F., Phillips S., Butler J.S.;
RT "Rat1p and Rai1p function with the nuclear exosome in the processing and
RT degradation of rRNA precursors.";
RL RNA 11:1571-1578(2005).
RN [12]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-198, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200;
RA Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
RT "A multidimensional chromatography technology for in-depth phosphoproteome
RT analysis.";
RL Mol. Cell. Proteomics 7:1389-1396(2008).
RN [13]
RP FUNCTION, CATALYTIC ACTIVITY, INTERACTION WITH RAT1, AND MUTAGENESIS OF
RP GLU-221 AND ASP-223.
RX PubMed=20802481; DOI=10.1038/nature09338;
RA Jiao X., Xiang S., Oh C., Martin C.E., Tong L., Kiledjian M.;
RT "Identification of a quality-control mechanism for mRNA 5'-end capping.";
RL Nature 467:608-611(2010).
RN [14]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22814378; DOI=10.1073/pnas.1210303109;
RA Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
RA Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E., Timmerman E.,
RA Prieto J., Arnesen T., Sherman F., Gevaert K., Aldabe R.;
RT "N-terminal acetylome analyses and functional insights of the N-terminal
RT acetyltransferase NatB.";
RL Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
RN [15]
RP FUNCTION.
RX PubMed=26101253; DOI=10.1093/nar/gkv620;
RA Wang V.Y., Jiao X., Kiledjian M., Tong L.;
RT "Structural and biochemical studies of the distinct activity profiles of
RT Rai1 enzymes.";
RL Nucleic Acids Res. 43:6596-6606(2015).
CC -!- FUNCTION: Decapping enzyme for NAD-capped RNAs: specifically hydrolyzes
CC the nicotinamide adenine dinucleotide (NAD) cap from a subset of RNAs
CC by removing the entire NAD moiety from the 5'-end of an NAD-capped RNA
CC (By similarity). The NAD-cap is present at the 5'-end of some RNAs and
CC snoRNAs. In contrast to the canonical 5'-end N7 methylguanosine (m7G)
CC cap, the NAD cap promotes mRNA decay (By similarity). Also acts as a
CC non-canonical decapping enzyme that removes the entire cap structure of
CC m7G capped or incompletely capped RNAs (PubMed:12897126,
CC PubMed:20802481, PubMed:26101253). Has decapping activity toward
CC incomplete 5'-end m7G cap mRNAs such as unmethylated 5'-end-capped RNA
CC (cap0), while it has no activity toward 2'-O-ribose methylated m7G cap
CC (cap1) (PubMed:12897126, PubMed:20802481). Also possesses RNA 5'-
CC pyrophosphohydrolase activity by hydrolyzing the 5'-end triphosphate to
CC release pyrophosphates (PubMed:20802481). Stimulates exoribonuclease
CC activity of RAT1, allowing it to degrade RNAs with stable secondary
CC structure more effectively (PubMed:20802481). Required for the
CC processing of nuclear mRNA and rRNA precursors (PubMed:10805743,
CC PubMed:12612077, PubMed:16131592). May promote termination of
CC transcription by RNA polymerase II (PubMed:15565157).
CC {ECO:0000250|UniProtKB:O13836, ECO:0000250|UniProtKB:O70348,
CC ECO:0000269|PubMed:10805743, ECO:0000269|PubMed:12612077,
CC ECO:0000269|PubMed:12897126, ECO:0000269|PubMed:15565157,
CC ECO:0000269|PubMed:16131592, ECO:0000269|PubMed:20802481,
CC ECO:0000269|PubMed:26101253}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 5'-end NAD(+)-phospho-ribonucleoside in mRNA + H2O = a 5'-
CC end phospho-ribonucleoside in mRNA + H(+) + NAD(+);
CC Xref=Rhea:RHEA:60880, Rhea:RHEA-COMP:15692, Rhea:RHEA-COMP:15698,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:57540,
CC ChEBI:CHEBI:138282, ChEBI:CHEBI:144029;
CC Evidence={ECO:0000250|UniProtKB:O13836};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:60881;
CC Evidence={ECO:0000250|UniProtKB:O13836};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 5'-end (N(7)-methyl 5'-triphosphoguanosine)-ribonucleoside-
CC ribonucleotide in mRNA + H2O = a (N(7)-methyl 5'-triphospho-
CC guanosine)-nucleoside + a 5'-end phospho-ribonucleoside in mRNA +
CC H(+); Xref=Rhea:RHEA:66928, Rhea:RHEA-COMP:15692, Rhea:RHEA-
CC COMP:17313, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:138282,
CC ChEBI:CHEBI:172876, ChEBI:CHEBI:172877;
CC Evidence={ECO:0000269|PubMed:20802481};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:66929;
CC Evidence={ECO:0000269|PubMed:20802481};
CC -!- COFACTOR:
CC Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
CC Evidence={ECO:0000250|UniProtKB:Q5AAT0};
CC Note=Divalent metal cation. {ECO:0000250|UniProtKB:Q5AAT0};
CC -!- SUBUNIT: Interacts with RAT1, RTT103 and pre-60S ribosomal subunits.
CC {ECO:0000269|PubMed:10805743, ECO:0000269|PubMed:12612077,
CC ECO:0000269|PubMed:15565157, ECO:0000269|PubMed:20802481}.
CC -!- INTERACTION:
CC P53063; Q02792: RAT1; NbExp=4; IntAct=EBI-24206, EBI-14845;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:12612077}.
CC -!- MISCELLANEOUS: Present with 4030 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the DXO/Dom3Z family. {ECO:0000305}.
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; X94357; CAA64141.1; -; Genomic_DNA.
DR EMBL; Z72768; CAA96966.1; -; Genomic_DNA.
DR EMBL; AY693165; AAT93184.1; -; Genomic_DNA.
DR EMBL; BK006941; DAA07873.1; -; Genomic_DNA.
DR PIR; S61615; S61615.
DR RefSeq; NP_011268.1; NM_001181112.1.
DR AlphaFoldDB; P53063; -.
DR SMR; P53063; -.
DR BioGRID; 33033; 93.
DR ComplexPortal; CPX-1332; RAT1-RAI1 RNA polymerase II termination complex.
DR DIP; DIP-6807N; -.
DR IntAct; P53063; 13.
DR MINT; P53063; -.
DR STRING; 4932.YGL246C; -.
DR iPTMnet; P53063; -.
DR MaxQB; P53063; -.
DR PaxDb; P53063; -.
DR PRIDE; P53063; -.
DR EnsemblFungi; YGL246C_mRNA; YGL246C; YGL246C.
DR GeneID; 852646; -.
DR KEGG; sce:YGL246C; -.
DR SGD; S000003215; RAI1.
DR VEuPathDB; FungiDB:YGL246C; -.
DR eggNOG; KOG1982; Eukaryota.
DR GeneTree; ENSGT00390000006425; -.
DR HOGENOM; CLU_024877_4_1_1; -.
DR InParanoid; P53063; -.
DR OMA; MAYWGYK; -.
DR BioCyc; YEAST:G3O-30717-MON; -.
DR PRO; PR:P53063; -.
DR Proteomes; UP000002311; Chromosome VII.
DR RNAct; P53063; protein.
DR GO; GO:0005829; C:cytosol; IDA:SGD.
DR GO; GO:0090730; C:Las1 complex; IPI:ComplexPortal.
DR GO; GO:0005634; C:nucleus; IDA:SGD.
DR GO; GO:0110103; C:RNA polymerase II termination complex; IPI:ComplexPortal.
DR GO; GO:0030234; F:enzyme regulator activity; IDA:SGD.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
DR GO; GO:1990174; F:phosphodiesterase decapping endonuclease activity; IDA:SGD.
DR GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR GO; GO:0110152; F:RNA NAD-cap (NAD-forming) hydrolase activity; IEA:RHEA.
DR GO; GO:0034353; F:RNA pyrophosphohydrolase activity; IDA:SGD.
DR GO; GO:0000448; P:cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA); IDA:SGD.
DR GO; GO:0031087; P:deadenylation-independent decapping of nuclear-transcribed mRNA; IDA:SGD.
DR GO; GO:0000466; P:maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA); IMP:SGD.
DR GO; GO:0000463; P:maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA); IMP:SGD.
DR GO; GO:0006397; P:mRNA processing; IEA:UniProtKB-KW.
DR GO; GO:0110155; P:NAD-cap decapping; IBA:GO_Central.
DR GO; GO:0071035; P:nuclear polyadenylation-dependent rRNA catabolic process; IMP:SGD.
DR GO; GO:0000956; P:nuclear-transcribed mRNA catabolic process; IMP:SGD.
DR GO; GO:0090305; P:nucleic acid phosphodiester bond hydrolysis; IBA:GO_Central.
DR GO; GO:1904595; P:positive regulation of termination of RNA polymerase II transcription; IDA:ComplexPortal.
DR GO; GO:0030846; P:termination of RNA polymerase II transcription, poly(A)-coupled; IMP:SGD.
DR InterPro; IPR013961; RAI1.
DR InterPro; IPR039039; RAI1-like_fam.
DR PANTHER; PTHR12395; PTHR12395; 1.
DR Pfam; PF08652; RAI1; 1.
PE 1: Evidence at protein level;
KW Direct protein sequencing; Hydrolase; Metal-binding; mRNA processing;
KW Nuclease; Nucleotide-binding; Nucleus; Phosphoprotein; Reference proteome;
KW RNA-binding; rRNA processing; Transcription; Transcription regulation;
KW Transcription termination.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:10805743"
FT CHAIN 2..387
FT /note="Decapping nuclease RAI1"
FT /id="PRO_0000202708"
FT REGION 273..387
FT /note="Interaction with RAT1"
FT BINDING 172
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000250|UniProtKB:O13836"
FT BINDING 221
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 223
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000250|UniProtKB:O13836"
FT BINDING 241
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000250|UniProtKB:O13836"
FT BINDING 242
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000250|UniProtKB:O13836"
FT BINDING 243
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT BINDING 267
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:O70348"
FT MOD_RES 198
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18407956"
FT MUTAGEN 221
FT /note="E->A: Abolishes the decapping activity."
FT /evidence="ECO:0000269|PubMed:20802481"
FT MUTAGEN 223
FT /note="D->A: Abolishes the decapping activity."
FT /evidence="ECO:0000269|PubMed:20802481"
FT CONFLICT 8
FT /note="F -> S (in Ref. 5; AA sequence)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 387 AA; 44510 MW; E4A6565AF690A3E1 CRC64;
MGVSANLFVK QRGSTTALKQ PKEIGFYSRT KDEEYLISDD TNLNYYYLPD AELDRKLDLS
SGFQKFKDYY KDFEDRCSLR GLLETIESSE RHKGKKINAD IITFRGIARK LISCAFDSPS
FNTVDLRIVS FNGQLFIKEV PEAVNAAKAS SATEAGRNIN QDLNVFTGYK FETLATLSNP
LQYTPREVIE KRTKRIVSHG DEYISVVRTG VGNCKLILGA EVDCIFDFKE NGRDNLKHYA
ELKCTQQVAN ISDTHKFERK LFRTWLQCFL VGIPRIIYGF KDDHYVLKTV EEFSTEEVPV
LLKNNNPQVG SACLEAIKWY GLLTEWLLKM IPRDEDPHSQ IRAFKLVFEN NHLRLSEIEE
SDEEYSGLID GEHILSNGFK EWRKSLK
