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Decapping nuclease RAI1 (EC 3.6.1.-) (RAT1-interacting protein)

 DXO_YEAST               Reviewed;         387 AA.
P53063; D6VV89;
01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
23-JAN-2007, sequence version 3.
05-DEC-2018, entry version 151.
RecName: Full=Decapping nuclease RAI1;
EC=3.6.1.-;
AltName: Full=RAT1-interacting protein;
Name=RAI1; OrderedLocusNames=YGL246C; ORFNames=NRE387;
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
NCBI_TaxID=559292;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=ATCC 96604 / S288c / FY1679;
PubMed=8972578;
DOI=10.1002/(SICI)1097-0061(199612)12:15<1555::AID-YEA43>3.0.CO;2-Q;
Coissac E., Maillier E., Robineau S., Netter P.;
"Sequence of a 39,411 bp DNA fragment covering the left end of
chromosome VII of Saccharomyces cerevisiae.";
Yeast 12:1555-1562(1996).
[2]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=9169869;
Tettelin H., Agostoni-Carbone M.L., Albermann K., Albers M.,
Arroyo J., Backes U., Barreiros T., Bertani I., Bjourson A.J.,
Brueckner M., Bruschi C.V., Carignani G., Castagnoli L., Cerdan E.,
Clemente M.L., Coblenz A., Coglievina M., Coissac E., Defoor E.,
Del Bino S., Delius H., Delneri D., de Wergifosse P., Dujon B.,
Durand P., Entian K.-D., Eraso P., Escribano V., Fabiani L.,
Fartmann B., Feroli F., Feuermann M., Frontali L., Garcia-Gonzalez M.,
Garcia-Saez M.I., Goffeau A., Guerreiro P., Hani J., Hansen M.,
Hebling U., Hernandez K., Heumann K., Hilger F., Hofmann B.,
Indge K.J., James C.M., Klima R., Koetter P., Kramer B., Kramer W.,
Lauquin G., Leuther H., Louis E.J., Maillier E., Marconi A.,
Martegani E., Mazon M.J., Mazzoni C., McReynolds A.D.K.,
Melchioretto P., Mewes H.-W., Minenkova O., Mueller-Auer S.,
Nawrocki A., Netter P., Neu R., Nombela C., Oliver S.G., Panzeri L.,
Paoluzi S., Plevani P., Portetelle D., Portillo F., Potier S.,
Purnelle B., Rieger M., Riles L., Rinaldi T., Robben J.,
Rodrigues-Pousada C., Rodriguez-Belmonte E., Rodriguez-Torres A.M.,
Rose M., Ruzzi M., Saliola M., Sanchez-Perez M., Schaefer B.,
Schaefer M., Scharfe M., Schmidheini T., Schreer A., Skala J.,
Souciet J.-L., Steensma H.Y., Talla E., Thierry A., Vandenbol M.,
van der Aart Q.J.M., Van Dyck L., Vanoni M., Verhasselt P., Voet M.,
Volckaert G., Wambutt R., Watson M.D., Weber N., Wedler E., Wedler H.,
Wipfli P., Wolf K., Wright L.F., Zaccaria P., Zimmermann M.,
Zollner A., Kleine K.;
"The nucleotide sequence of Saccharomyces cerevisiae chromosome VII.";
Nature 387:81-84(1997).
[3]
GENOME REANNOTATION.
STRAIN=ATCC 204508 / S288c;
PubMed=24374639; DOI=10.1534/g3.113.008995;
Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R.,
Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S.,
Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M.,
Cherry J.M.;
"The reference genome sequence of Saccharomyces cerevisiae: Then and
now.";
G3 (Bethesda) 4:389-398(2014).
[4]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=17322287; DOI=10.1101/gr.6037607;
Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F.,
Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A.,
Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F.,
Williamson J., Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G.,
Kolodner R.D., LaBaer J.;
"Approaching a complete repository of sequence-verified protein-
encoding clones for Saccharomyces cerevisiae.";
Genome Res. 17:536-543(2007).
[5]
PROTEIN SEQUENCE OF 2-17, FUNCTION, AND INTERACTION WITH RAT1.
PubMed=10805743; DOI=10.1128/MCB.20.11.4006-4015.2000;
Xue Y., Bai X., Lee I., Kallstrom G., Ho J., Brown J., Stevens A.,
Johnson A.W.;
"Saccharomyces cerevisiae RAI1 (YGL246c) is homologous to human DOM3Z
and encodes a protein that binds the nuclear exoribonuclease Rat1p.";
Mol. Cell. Biol. 20:4006-4015(2000).
[6]
FUNCTION, INTERACTION WITH RAT1 AND PRE-60S RIBOSOMAL SUBUNITS, AND
SUBCELLULAR LOCATION.
PubMed=12612077; DOI=10.1128/MCB.23.6.2042-2054.2003;
Sydorskyy Y., Dilworth D.J., Yi E.C., Goodlett D.R., Wozniak R.W.,
Aitchison J.D.;
"Intersection of the Kap123p-mediated nuclear import and ribosome
export pathways.";
Mol. Cell. Biol. 23:2042-2054(2003).
[7]
FUNCTION.
PubMed=12897126; DOI=10.1128/MCB.23.16.5502-5515.2003;
Das B., Butler J.S., Sherman F.;
"Degradation of normal mRNA in the nucleus of Saccharomyces
cerevisiae.";
Mol. Cell. Biol. 23:5502-5515(2003).
[8]
LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
PubMed=14562106; DOI=10.1038/nature02046;
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A.,
Dephoure N., O'Shea E.K., Weissman J.S.;
"Global analysis of protein expression in yeast.";
Nature 425:737-741(2003).
[9]
FUNCTION, IDENTIFICATION BY MASS SPECTROMETRY, AND IDENTIFICATION IN A
COMPLEX WITH RTT103.
PubMed=15565157; DOI=10.1038/nature03041;
Kim M., Krogan N.J., Vasiljeva L., Rando O.J., Nedea E.,
Greenblatt J.F., Buratowski S.;
"The yeast Rat1 exonuclease promotes transcription termination by RNA
polymerase II.";
Nature 432:517-522(2004).
[10]
ERRATUM.
Kim M., Krogan N.J., Vasiljeva L., Rando O.J., Nedea E.,
Greenblatt J.F., Buratowski S.;
Nature 433:661-661(2005).
[11]
FUNCTION.
PubMed=16131592; DOI=10.1261/rna.2900205;
Fang F., Phillips S., Butler J.S.;
"Rat1p and Rai1p function with the nuclear exosome in the processing
and degradation of rRNA precursors.";
RNA 11:1571-1578(2005).
[12]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-198, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=18407956; DOI=10.1074/mcp.M700468-MCP200;
Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
"A multidimensional chromatography technology for in-depth
phosphoproteome analysis.";
Mol. Cell. Proteomics 7:1389-1396(2008).
[13]
FUNCTION, CATALYTIC ACTIVITY, INTERACTION WITH RAT1, AND MUTAGENESIS
OF GLU-221 AND ASP-223.
PubMed=20802481; DOI=10.1038/nature09338;
Jiao X., Xiang S., Oh C., Martin C.E., Tong L., Kiledjian M.;
"Identification of a quality-control mechanism for mRNA 5'-end
capping.";
Nature 467:608-611(2010).
[14]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=22814378; DOI=10.1073/pnas.1210303109;
Van Damme P., Lasa M., Polevoda B., Gazquez C., Elosegui-Artola A.,
Kim D.S., De Juan-Pardo E., Demeyer K., Hole K., Larrea E.,
Timmerman E., Prieto J., Arnesen T., Sherman F., Gevaert K.,
Aldabe R.;
"N-terminal acetylome analyses and functional insights of the N-
terminal acetyltransferase NatB.";
Proc. Natl. Acad. Sci. U.S.A. 109:12449-12454(2012).
-!- FUNCTION: Ribonuclease that specifically degrades pre-mRNAs with a
defective 5' end cap and is part of a pre-mRNA capping quality
control. Has decapping and pyrophosphohydrolase activities. Has
decapping activity toward incomplete 5' end cap mRNAs such as
unmethylated 5' end-capped RNA to release GpppN and 5' end
monophosphate RNA. Also possesses RNA 5'-pyrophosphohydrolase
activity by hydrolyzing the 5' end triphosphate to release
pyrophosphates. Stimulates exoribonuclease activity of RAT1,
allowing it to degrade RNAs with stable secondary structure more
effectively. Required for the processing of nuclear mRNA and rRNA
precursors. May promote termination of transcription by RNA
polymerase II. {ECO:0000269|PubMed:10805743,
ECO:0000269|PubMed:12612077, ECO:0000269|PubMed:12897126,
ECO:0000269|PubMed:15565157, ECO:0000269|PubMed:16131592,
ECO:0000269|PubMed:20802481}.
-!- COFACTOR:
Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
Evidence={ECO:0000250};
Note=Divalent metal cation. {ECO:0000250};
-!- SUBUNIT: Interacts with RAT1, RTT103 and pre-60S ribosomal
subunits. {ECO:0000269|PubMed:10805743,
ECO:0000269|PubMed:12612077, ECO:0000269|PubMed:15565157,
ECO:0000269|PubMed:20802481}.
-!- INTERACTION:
Q02792:RAT1; NbExp=4; IntAct=EBI-24206, EBI-14845;
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:12612077}.
-!- MISCELLANEOUS: Present with 4030 molecules/cell in log phase SD
medium. {ECO:0000269|PubMed:14562106}.
-!- SIMILARITY: Belongs to the DXO/Dom3Z family. {ECO:0000305}.
-!- CAUTION: In contrast to canonical decapping enzymes, which release
m(7)pppG (m(7)GDP), the decapping activity releases the entire cap
structure GpppN and a 5' end monophosphate RNA.
{ECO:0000305|PubMed:20802481}.
-----------------------------------------------------------------------
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-----------------------------------------------------------------------
EMBL; X94357; CAA64141.1; -; Genomic_DNA.
EMBL; Z72768; CAA96966.1; -; Genomic_DNA.
EMBL; AY693165; AAT93184.1; -; Genomic_DNA.
EMBL; BK006941; DAA07873.1; -; Genomic_DNA.
PIR; S61615; S61615.
RefSeq; NP_011268.1; NM_001181112.1.
ProteinModelPortal; P53063; -.
SMR; P53063; -.
BioGrid; 33033; 71.
ComplexPortal; CPX-1332; RAT1-RAI1 RNA polymerase II termination complex.
DIP; DIP-6807N; -.
IntAct; P53063; 13.
MINT; P53063; -.
STRING; 4932.YGL246C; -.
iPTMnet; P53063; -.
MaxQB; P53063; -.
PaxDb; P53063; -.
PRIDE; P53063; -.
EnsemblFungi; YGL246C_mRNA; YGL246C_mRNA; YGL246C.
GeneID; 852646; -.
KEGG; sce:YGL246C; -.
SGD; S000003215; RAI1.
GeneTree; ENSGT00390000006425; -.
HOGENOM; HOG000200647; -.
InParanoid; P53063; -.
KO; K14845; -.
OMA; MAYWGYK; -.
OrthoDB; EOG092C2WHY; -.
BioCyc; YEAST:G3O-30717-MONOMER; -.
PRO; PR:P53063; -.
Proteomes; UP000002311; Chromosome VII.
GO; GO:0005829; C:cytosol; IDA:SGD.
GO; GO:0005634; C:nucleus; IDA:SGD.
GO; GO:0030234; F:enzyme regulator activity; IDA:SGD.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0000166; F:nucleotide binding; IEA:UniProtKB-KW.
GO; GO:1990174; F:phosphodiesterase decapping endonuclease activity; IDA:SGD.
GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
GO; GO:0034353; F:RNA pyrophosphohydrolase activity; IDA:SGD.
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.
GO; GO:0031087; P:deadenylation-independent decapping of nuclear-transcribed mRNA; IDA:SGD.
GO; GO:0000466; P:maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA); IMP:SGD.
GO; GO:0000463; P:maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA); IMP:SGD.
GO; GO:0006397; P:mRNA processing; IEA:UniProtKB-KW.
GO; GO:0071035; P:nuclear polyadenylation-dependent rRNA catabolic process; IMP:SGD.
GO; GO:0000956; P:nuclear-transcribed mRNA catabolic process; IMP:SGD.
GO; GO:0030846; P:termination of RNA polymerase II transcription, poly(A)-coupled; IMP:SGD.
InterPro; IPR013961; RAI1.
InterPro; IPR039039; RAI1-like_fam.
PANTHER; PTHR12395; PTHR12395; 1.
Pfam; PF08652; RAI1; 1.
1: Evidence at protein level;
Complete proteome; Direct protein sequencing; Hydrolase;
Metal-binding; mRNA processing; Nuclease; Nucleotide-binding; Nucleus;
Phosphoprotein; Reference proteome; RNA-binding; rRNA processing;
Transcription; Transcription regulation; Transcription termination.
INIT_MET 1 1 Removed. {ECO:0000269|PubMed:10805743}.
CHAIN 2 387 Decapping nuclease RAI1.
/FTId=PRO_0000202708.
REGION 273 387 Interaction with RAT1.
METAL 172 172 Divalent metal cation. {ECO:0000250}.
METAL 223 223 Divalent metal cation. {ECO:0000250}.
METAL 241 241 Divalent metal cation. {ECO:0000250}.
METAL 242 242 Divalent metal cation; via carbonyl
oxygen. {ECO:0000250}.
BINDING 105 105 Substrate. {ECO:0000250}.
BINDING 221 221 Substrate. {ECO:0000250}.
BINDING 267 267 Substrate. {ECO:0000250}.
MOD_RES 198 198 Phosphoserine.
{ECO:0000244|PubMed:18407956}.
MUTAGEN 221 221 E->A: Abolishes the decapping activity.
{ECO:0000269|PubMed:20802481}.
MUTAGEN 223 223 D->A: Abolishes the decapping activity.
{ECO:0000269|PubMed:20802481}.
CONFLICT 8 8 F -> S (in Ref. 5; AA sequence).
{ECO:0000305}.
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


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