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5'-3' exoribonuclease 2 (EC 3.1.13.-) (Ribonucleic acid-trafficking protein 1) (p116)

 XRN2_YEAST              Reviewed;        1006 AA.
Q02792; D6W2B4;
01-OCT-1993, integrated into UniProtKB/Swiss-Prot.
23-JAN-2007, sequence version 3.
07-NOV-2018, entry version 164.
RecName: Full=5'-3' exoribonuclease 2;
EC=3.1.13.-;
AltName: Full=Ribonucleic acid-trafficking protein 1;
AltName: Full=p116;
Name=RAT1; Synonyms=HKE1, TAP1; OrderedLocusNames=YOR048C;
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].
PubMed=1628825; DOI=10.1101/gad.6.7.1173;
Amberg D.C., Goldstein A.L., Cole C.N.;
"Isolation and characterization of RAT1: an essential gene of
Saccharomyces cerevisiae required for the efficient nucleocytoplasmic
trafficking of mRNA.";
Genes Dev. 6:1173-1189(1992).
[2]
NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, COFACTOR, AND SUBCELLULAR
LOCATION.
PubMed=8417335; DOI=10.1128/MCB.13.1.341;
Kenna M., Stevens A., McCammon M., Douglas M.G.;
"An essential yeast gene with homology to the exonuclease-encoding
XRN1/KEM1 gene also encodes a protein with exoribonuclease activity.";
Mol. Cell. Biol. 13:341-350(1993).
[3]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
PubMed=8497260; DOI=10.1128/MCB.13.6.3434;
Aldrich T.L., di Segni G., McConaughy B.L., Keen N.J., Whelen S.,
Hall B.D.;
"Structure of the yeast TAP1 protein: dependence of transcription
activation on the DNA context of the target gene.";
Mol. Cell. Biol. 13:3434-3444(1993).
[4]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=9169874;
Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W.,
Arino J., Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R.,
Boyer J., Camasses A., Casamayor A., Casas C., Cheret G.,
Cziepluch C., Daignan-Fornier B., Dang V.-D., de Haan M., Delius H.,
Durand P., Fairhead C., Feldmann H., Gaillon L., Galisson F.,
Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E., Grivell L.A.,
Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U.,
Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B.,
Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A.,
Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J.,
Maarse A.C., Madania A., Mannhaupt G., Marck C., Martin R.P.,
Mewes H.-W., Michaux G., Paces V., Parle-McDermott A.G., Pearson B.M.,
Perrin A., Pettersson B., Poch O., Pohl T.M., Poirey R.,
Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rechmann S.,
Schwager C., Schweizer M., Sor F., Sterky F., Tarassov I.A.,
Teodoru C., Tettelin H., Thierry A., Tobiasch E., Tzermia M.,
Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I., Vlcek C.,
Voet M., Volckaert G., Voss H., Wambutt R., Wedler H., Wiemann S.,
Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K.;
"The nucleotide sequence of Saccharomyces cerevisiae chromosome XV.";
Nature 387:98-102(1997).
[5]
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).
[6]
NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 929-1006.
STRAIN=BJ1991;
PubMed=8497275; DOI=10.1128/MCB.13.6.3650;
Ganster R.W., Shen W., Schmidt M.C.;
"Isolation of STD1, a high-copy-number suppressor of a dominant
negative mutation in the yeast TATA-binding protein.";
Mol. Cell. Biol. 13:3650-3659(1993).
[7]
PROTEIN SEQUENCE OF 2-9, FUNCTION, COFACTOR, AND BIOPHYSICOCHEMICAL
PROPERTIES.
PubMed=7608167; DOI=10.1074/jbc.270.27.16063;
Stevens A., Poole T.L.;
"5'-exonuclease-2 of Saccharomyces cerevisiae. Purification and
features of ribonuclease activity with comparison to 5'-exonuclease-
1.";
J. Biol. Chem. 270:16063-16069(1995).
[8]
FUNCTION.
PubMed=9207242; DOI=10.1006/bbrc.1997.6877;
Poole T.L., Stevens A.;
"Structural modifications of RNA influence the 5' exoribonucleolytic
hydrolysis by XRN1 and HKE1 of Saccharomyces cerevisiae.";
Biochem. Biophys. Res. Commun. 235:799-805(1997).
[9]
FUNCTION, AND ACTIVITY REGULATION.
PubMed=9384595; DOI=10.1093/emboj/16.23.7184;
Dichtl B., Stevens A., Tollervey D.;
"Lithium toxicity in yeast is due to the inhibition of RNA processing
enzymes.";
EMBO J. 16:7184-7195(1997).
[10]
SUBCELLULAR LOCATION, AND MUTAGENESIS OF HIS-518; LEU-520; LYS-534;
LYS-535 AND LYS-537.
PubMed=9315672; DOI=10.1128/MCB.17.10.6122;
Johnson A.W.;
"Rat1p and Xrn1p are functionally interchangeable exoribonucleases
that are restricted to and required in the nucleus and cytoplasm,
respectively.";
Mol. Cell. Biol. 17:6122-6130(1997).
[11]
FUNCTION.
PubMed=9488433; DOI=10.1128/MCB.18.3.1181;
Petfalski E., Dandekar T., Henry Y., Tollervey D.;
"Processing of the precursors to small nucleolar RNAs and rRNAs
requires common components.";
Mol. Cell. Biol. 18:1181-1189(1998).
[12]
FUNCTION.
PubMed=9584178; DOI=10.1128/MCB.18.6.3376;
Villa T., Ceradini F., Presutti C., Bozzoni I.;
"Processing of the intron-encoded U18 small nucleolar RNA in the yeast
Saccharomyces cerevisiae relies on both exo- and endonucleolytic
activities.";
Mol. Cell. Biol. 18:3376-3383(1998).
[13]
FUNCTION.
PubMed=9891049; DOI=10.1128/MCB.19.2.1144;
Qu L.-H., Henras A., Lu Y.-J., Zhou H., Zhou W.-X., Zhu Y.-Q.,
Zhao J., Henry Y., Caizergues-Ferrer M., Bachellerie J.-P.;
"Seven novel methylation guide small nucleolar RNAs are processed from
a common polycistronic transcript by Rat1p and RNase III in yeast.";
Mol. Cell. Biol. 19:1144-1158(1999).
[14]
FUNCTION.
PubMed=11030620; DOI=10.1016/S0092-8674(00)00065-9;
Bousquet-Antonelli C., Presutti C., Tollervey D.;
"Identification of a regulated pathway for nuclear pre-mRNA
turnover.";
Cell 102:765-775(2000).
[15]
FUNCTION, AND INTERACTION WITH RAI1.
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).
[16]
FUNCTION.
PubMed=11142370; DOI=10.1017/S1355838200001540;
Geerlings T.H., Vos J.C., Raue H.A.;
"The final step in the formation of 25S rRNA in Saccharomyces
cerevisiae is performed by 5'->3' exonucleases.";
RNA 6:1698-1703(2000).
[17]
FUNCTION.
PubMed=11238889; DOI=10.1128/MCB.21.5.1515-1530.2001;
He F., Jacobson A.;
"Upf1p, Nmd2p, and Upf3p regulate the decapping and exonucleolytic
degradation of both nonsense-containing mRNAs and wild-type mRNAs.";
Mol. Cell. Biol. 21:1515-1530(2001).
[18]
FUNCTION.
PubMed=12769851; DOI=10.1016/S1097-2765(03)00137-0;
Danin-Kreiselman M., Lee C.Y., Chanfreau G.;
"RNase III-mediated degradation of unspliced pre-mRNAs and lariat
introns.";
Mol. Cell 11:1279-1289(2003).
[19]
IDENTIFICATION BY MASS SPECTROMETRY, INTERACTION WITH RAI1, 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).
[20]
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).
[21]
FUNCTION.
PubMed=14561886; DOI=10.1261/rna.5126203;
Lee C.Y., Lee A., Chanfreau G.;
"The roles of endonucleolytic cleavage and exonucleolytic digestion in
the 5'-end processing of S. cerevisiae box C/D snoRNAs.";
RNA 9:1362-1370(2003).
[22]
FUNCTION, IDENTIFICATION BY MASS SPECTROMETRY, IDENTIFICATION IN A
COMPLEX WITH RTT103, AND MUTAGENESIS OF ASP-235.
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).
[23]
ERRATUM.
Kim M., Krogan N.J., Vasiljeva L., Rando O.J., Nedea E.,
Greenblatt J.F., Buratowski S.;
Nature 433:661-661(2005).
[24]
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).
[25]
FUNCTION.
PubMed=16598041; DOI=10.1101/gad.1409106;
Luo W., Johnson A.W., Bentley D.L.;
"The role of Rat1 in coupling mRNA 3'-end processing to transcription
termination: implications for a unified allosteric-torpedo model.";
Genes Dev. 20:954-965(2006).
[26]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-574, AND IDENTIFICATION
BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=19779198; DOI=10.1126/science.1172867;
Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
"Global analysis of Cdk1 substrate phosphorylation sites provides
insights into evolution.";
Science 325:1682-1686(2009).
-!- FUNCTION: Possesses 5'->3' exoribonuclease activity. Required for
the processing of nuclear mRNA, rRNA and small nucleolar RNA
(snoRNA) precursors. May promote termination of transcription by
RNA polymerase II via the recruitment of 3'-end processing factors
to the poly(A) site and by the degradation of nascent RNA
downstream of the poly(A) site. {ECO:0000269|PubMed:10805743,
ECO:0000269|PubMed:11030620, ECO:0000269|PubMed:11142370,
ECO:0000269|PubMed:11238889, ECO:0000269|PubMed:12769851,
ECO:0000269|PubMed:14561886, ECO:0000269|PubMed:15565157,
ECO:0000269|PubMed:16131592, ECO:0000269|PubMed:16598041,
ECO:0000269|PubMed:7608167, ECO:0000269|PubMed:8417335,
ECO:0000269|PubMed:9207242, ECO:0000269|PubMed:9384595,
ECO:0000269|PubMed:9488433, ECO:0000269|PubMed:9584178,
ECO:0000269|PubMed:9891049}.
-!- CATALYTIC ACTIVITY: Exonucleolytic cleavage in the 5'- to 3'-
direction to yield nucleoside 5'-phosphates.
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
Evidence={ECO:0000269|PubMed:7608167,
ECO:0000269|PubMed:8417335};
Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
Evidence={ECO:0000269|PubMed:7608167,
ECO:0000269|PubMed:8417335};
-!- ACTIVITY REGULATION: Inhibited by nucleoside 3', 5'-bisphosphates.
{ECO:0000269|PubMed:9384595}.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
pH dependence:
Optimum pH is 8.0-8.8. {ECO:0000269|PubMed:7608167};
-!- SUBUNIT: Interacts with RAI1 and RTT103.
{ECO:0000269|PubMed:10805743, ECO:0000269|PubMed:12612077,
ECO:0000269|PubMed:15565157}.
-!- INTERACTION:
P53063:RAI1; NbExp=4; IntAct=EBI-14845, EBI-24206;
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:12612077,
ECO:0000269|PubMed:8417335, ECO:0000269|PubMed:9315672}.
-!- MISCELLANEOUS: Present with 623 molecules/cell in log phase SD
medium. {ECO:0000269|PubMed:14562106}.
-!- SIMILARITY: Belongs to the 5'-3' exonuclease family. XRN2/RAT1
subfamily. {ECO:0000305}.
-----------------------------------------------------------------------
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EMBL; M95626; AAA34960.1; -; Genomic_DNA.
EMBL; Z11746; -; NOT_ANNOTATED_CDS; Genomic_DNA.
EMBL; S61567; AAB26818.1; -; Genomic_DNA.
EMBL; Z74956; CAA99240.1; -; Genomic_DNA.
EMBL; L06011; AAA16950.1; -; Unassigned_DNA.
EMBL; BK006948; DAA10830.1; -; Genomic_DNA.
PIR; S20126; S20126.
RefSeq; NP_014691.1; NM_001183467.1.
ProteinModelPortal; Q02792; -.
SMR; Q02792; -.
BioGrid; 34449; 498.
ComplexPortal; CPX-1332; RAT1-RAI1 RNA polymerase II termination complex.
DIP; DIP-6692N; -.
IntAct; Q02792; 4.
MINT; Q02792; -.
STRING; 4932.YOR048C; -.
iPTMnet; Q02792; -.
MaxQB; Q02792; -.
PaxDb; Q02792; -.
PRIDE; Q02792; -.
EnsemblFungi; YOR048C; YOR048C; YOR048C.
GeneID; 854213; -.
KEGG; sce:YOR048C; -.
SGD; S000005574; RAT1.
GeneTree; ENSGT00670000098098; -.
HOGENOM; HOG000205514; -.
KO; K12619; -.
OMA; GEHFDSN; -.
OrthoDB; EOG092C068M; -.
BioCyc; YEAST:G3O-33592-MONOMER; -.
Reactome; R-SCE-6791226; Major pathway of rRNA processing in the nucleolus and cytosol.
PRO; PR:Q02792; -.
Proteomes; UP000002311; Chromosome XV.
GO; GO:0005634; C:nucleus; IDA:SGD.
GO; GO:0004534; F:5'-3' exoribonuclease activity; IDA:SGD.
GO; GO:0019843; F:rRNA binding; IDA:GO_Central.
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:0006397; P:mRNA processing; IEA:UniProtKB-KW.
GO; GO:1901408; P:negative regulation of phosphorylation of RNA polymerase II C-terminal domain; IMP:SGD.
GO; GO:0034244; P:negative regulation of transcription elongation from RNA polymerase II promoter; IMP:SGD.
GO; GO:0071028; P:nuclear mRNA surveillance; IMP:SGD.
GO; GO:0071035; P:nuclear polyadenylation-dependent rRNA catabolic process; IMP:SGD.
GO; GO:0006364; P:rRNA processing; IMP:SGD.
GO; GO:0043144; P:snoRNA processing; IMP:SGD.
GO; GO:0030847; P:termination of RNA polymerase II transcription, exosome-dependent; IMP:SGD.
GO; GO:0030846; P:termination of RNA polymerase II transcription, poly(A)-coupled; IMP:SGD.
InterPro; IPR027073; 5_3_exoribonuclease.
InterPro; IPR004859; Put_53exo.
InterPro; IPR017151; Xrn2/3/4.
PANTHER; PTHR12341; PTHR12341; 1.
Pfam; PF03159; XRN_N; 1.
PIRSF; PIRSF037239; Exonuclease_Xrn2; 1.
1: Evidence at protein level;
Coiled coil; Complete proteome; Direct protein sequencing;
Exonuclease; Hydrolase; mRNA processing; Nuclease; Nucleus;
Phosphoprotein; Reference proteome; Repeat; rRNA processing;
Transcription; Transcription regulation; Transcription termination.
INIT_MET 1 1 Removed. {ECO:0000269|PubMed:7608167}.
CHAIN 2 1006 5'-3' exoribonuclease 2.
/FTId=PRO_0000071399.
REPEAT 955 958 1-1.
REPEAT 961 964 2-1.
REPEAT 972 975 2-2.
REPEAT 975 978 3-1.
REPEAT 984 986 3-2.
REPEAT 996 999 1-2.
REGION 492 529 Required for retention in the nucleus.
REGION 955 999 2 X 4 AA repeats of S-R-Y-D, N-N-N-Y, Y-
S-G-N.
COILED 256 287 {ECO:0000255}.
COILED 453 544 {ECO:0000255}.
COMPBIAS 933 1004 Asn-rich.
MOD_RES 574 574 Phosphoserine.
{ECO:0000244|PubMed:19779198}.
MUTAGEN 235 235 D->A: Abrogates exonuclease activity and
impairs termination of transcription by
RNA polymerase II.
{ECO:0000269|PubMed:15565157}.
MUTAGEN 518 518 H->Y: Causes mislocalization to the
cytoplasm and suppresses the requirement
for XRN1 function.
{ECO:0000269|PubMed:9315672}.
MUTAGEN 520 520 L->P: Suppresses the requirement for XRN1
function. {ECO:0000269|PubMed:9315672}.
MUTAGEN 534 534 K->A: Causes mislocalization to the
cytoplasm; when associated with A-535 and
A-537. {ECO:0000269|PubMed:9315672}.
MUTAGEN 535 535 K->A: Causes mislocalization to the
cytoplasm; when associated with A-534 and
A-537. {ECO:0000269|PubMed:9315672}.
MUTAGEN 535 535 K->N: Causes mislocalization to the
cytoplasm and suppresses the requirement
for XRN1 function.
{ECO:0000269|PubMed:9315672}.
MUTAGEN 537 537 K->A: Causes mislocalization to the
cytoplasm; when associated with A-534 and
A-535. {ECO:0000269|PubMed:9315672}.
MUTAGEN 537 537 K->E: Causes mislocalization to the
cytoplasm and suppresses the requirement
for XRN1 function.
{ECO:0000269|PubMed:9315672}.
MUTAGEN 683 683 Y->H: In allele TAP1-1; activates
transcription of the promoter-defective
yeast SUP4 tRNA(Tyr) allele SUP4A53T61.
SEQUENCE 1006 AA; 115934 MW; 5DDD5B0245F3E12A CRC64;
MGVPSFFRWL SRKYPKIISP VLEEQPQIVD GVILPLDYSA SNPNGELDNL YLDMNGIVHP
CSHPENKPPP ETEDEMLLAV FEYTNRVLNM ARPRKVLVMA VDGVAPRAKM NQQRARRFRS
ARDAQIENEA REEIMRQREE VGEIIDDAVR NKKTWDSNAI TPGTPFMDKL AAALRYWTAF
KLATDPGWKN LQVIISDATV PGEGEHKIMN FIRSQRADPE YNPNTTHCIY GLDADLIFLG
LATHEPHFKI LREDVFAQDN RKRNNLKDTI NMTEEEKQFL QKQNSEQPFL WLHINVLREY
LSAELWVPGL PFTFDLERAI DDWVFMCFFC GNDFLPHLPC LDVRENSIDI LLDIWKVVLP
KLKTYMTCDG VLNLPSVETL LQHLGSREGD IFKTRHIQEA RKKEAFERRK AQKNMSKGQD
RHPTVATEQL QMYDTQGNLA KGSWNLTTSD MVRLKKELML ANEGNEEAIA KVKQQSDKNN
ELMKDISKEE IDDAVSKANK TNFNLAEVMK QKIINKKHRL EKDNEEEEIA KDSKKVKTEK
AESECDLDAE IKDEIVADVN DRENSETTEV SRDSPVHSTV NVSEGPKNGV FDTDEFVKLF
EPGYHERYYT AKFHVTPQDI EQLRKDMVKC YIEGVAWVLM YYYQGCASWN WFYPYHYAPL
ATDFHGFSHL EIKFEEGTPF LPYEQLMSVL PAASGHALPK IFRSLMSEPD SEIIDFYPEE
FPIDMNGKKM SWQGIALLPF IDQDRLLTAV RAQYPLLSDA ERARNIRGEP VLLISNKNAN
YERFSKKLYS KENNNNNVVV KFQHFKSGLS GIVSKDVEGF ELNGKIVCPI QGGSLPNLST
TLILKMSYRL IPLPSRNKSI ILNGFIPSEP VLTAYDLDSI MYKYNNQNYS RRWNFGNDLK
QNIVPVGPKG ITQYKPRTGG YRAFFYFAEL SRNNVQPAHN YGRNSYNSQP GFNNSRYDGG
NNNYRQNSNY RNNNYSGNRN SGQYSGNSYS RNNKQSRYDN SRANRR


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