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Pre-rRNA-processing protein RIX1 (Involved in processing IST2 protein 2) (Ribosomal export protein 1)

 RIX1_YEAST              Reviewed;         763 AA.
P38883; D3DLE5;
01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
27-JUL-2011, sequence version 2.
12-SEP-2018, entry version 135.
RecName: Full=Pre-rRNA-processing protein RIX1;
AltName: Full=Involved in processing IST2 protein 2;
AltName: Full=Ribosomal export protein 1;
Name=RIX1; Synonyms=IPI2; OrderedLocusNames=YHR197W;
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
NCBI_TaxID=559292;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=8091229; DOI=10.1126/science.8091229;
Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Dover J.,
Du Z., Favello A., Fulton L., Gattung S., Geisel C., Kirsten J.,
Kucaba T., Hillier L.W., Jier M., Johnston L., Langston Y.,
Latreille P., Louis E.J., Macri C., Mardis E., Menezes S., Mouser L.,
Nhan M., Rifkin L., Riles L., St Peter H., Trevaskis E., Vaughan K.,
Vignati D., Wilcox L., Wohldman P., Waterston R., Wilson R.,
Vaudin M.;
"Complete nucleotide sequence of Saccharomyces cerevisiae chromosome
VIII.";
Science 265:2077-2082(1994).
[2]
GENOME REANNOTATION, AND SEQUENCE REVISION TO 762.
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).
[3]
INTERACTION WITH NUG1.
PubMed=11583615; DOI=10.1016/S1097-2765(01)00342-2;
Bassler J., Grandi P., Gadal O., Lessmann T., Petfalski E.,
Tollervey D., Lechner J., Hurt E.;
"Identification of a 60S preribosomal particle that is closely linked
to nuclear export.";
Mol. Cell 8:517-529(2001).
[4]
FUNCTION.
PubMed=11313466; DOI=10.1128/MCB.21.10.3405-3415.2001;
Gadal O., Strauss D., Kessl J., Trumpower B., Tollervey D., Hurt E.;
"Nuclear export of 60s ribosomal subunits depends on Xpo1p and
requires a nuclear export sequence-containing factor, Nmd3p, that
associates with the large subunit protein Rpl10p.";
Mol. Cell. Biol. 21:3405-3415(2001).
[5]
IDENTIFICATION IN THE RIX1 COMPLEX, IDENTIFICATION BY MASS
SPECTROMETRY, AND INTERACTION WITH IPI3.
PubMed=14690591; DOI=10.1016/S1097-2765(03)00476-3;
Hazbun T.R., Malmstroem L., Anderson S., Graczyk B.J., Fox B.,
Riffle M., Sundin B.A., Aranda J.D., McDonald W.H., Chiu C.-H.,
Snydsman B.E., Bradley P., Muller E.G.D., Fields S., Baker D.,
Yates J.R. III, Davis T.N.;
"Assigning function to yeast proteins by integration of
technologies.";
Mol. Cell 12:1353-1365(2003).
[6]
SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
PubMed=14562095; DOI=10.1038/nature02026;
Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
Weissman J.S., O'Shea E.K.;
"Global analysis of protein localization in budding yeast.";
Nature 425:686-691(2003).
[7]
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).
[8]
IDENTIFICATION IN THE RIX1 COMPLEX, SUBCELLULAR LOCATION, FUNCTION OF
THE RIX1 COMPLEX, AND IDENTIFICATION BY MASS SPECTROMETRY.
PubMed=15528184; DOI=10.1074/jbc.M406876200;
Galani K., Nissan T.A., Petfalski E., Tollervey D., Hurt E.;
"Rea1, a dynein-related nuclear AAA-ATPase, is involved in late rRNA
processing and nuclear export of 60 S subunits.";
J. Biol. Chem. 279:55411-55418(2004).
[9]
IDENTIFICATION IN THE RIX1 COMPLEX, INTERACTION WITH MDN1 AND PRE-60S
RIBOSOMAL PARTICLES, AND IDENTIFICATION BY MASS SPECTROMETRY.
PubMed=15260980; DOI=10.1016/j.molcel.2004.06.033;
Nissan T.A., Galani K., Maco B., Tollervey D., Aebi U., Hurt E.;
"A pre-ribosome with a tadpole-like structure functions in ATP-
dependent maturation of 60S subunits.";
Mol. Cell 15:295-301(2004).
[10]
IDENTIFICATION IN THE RIX1 COMPLEX, AND FUNCTION OF THE RIX1 COMPLEX.
PubMed=14759368; DOI=10.1016/S1097-2765(04)00003-6;
Krogan N.J., Peng W.-T., Cagney G., Robinson M.D., Haw R., Zhong G.,
Guo X., Zhang X., Canadien V., Richards D.P., Beattie B.K., Lalev A.,
Zhang W., Davierwala A.P., Mnaimneh S., Starostine A., Tikuisis A.P.,
Grigull J., Datta N., Bray J.E., Hughes T.R., Emili A.,
Greenblatt J.F.;
"High-definition macromolecular composition of yeast RNA-processing
complexes.";
Mol. Cell 13:225-239(2004).
[11]
SUMOYLATION.
PubMed=16978391; DOI=10.1111/j.1600-0854.2006.00471.x;
Panse V.G., Kressler D., Pauli A., Petfalski E., Gnaedig M.,
Tollervey D., Hurt E.;
"Formation and nuclear export of preribosomes are functionally linked
to the small-ubiquitin-related modifier pathway.";
Traffic 7:1311-1321(2006).
[12]
ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, CLEAVAGE OF INITIATOR
METHIONINE [LARGE SCALE ANALYSIS], AND 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).
[13]
IDENTIFICATION IN THE RIX1 COMPLEX, AND INTERACTION WITH MDN1 AND
IPI3.
PubMed=26619264; DOI=10.1038/nsmb.3132;
Barrio-Garcia C., Thoms M., Flemming D., Kater L., Berninghausen O.,
Bassler J., Beckmann R., Hurt E.;
"Architecture of the Rix1-Rea1 checkpoint machinery during pre-60S-
ribosome remodeling.";
Nat. Struct. Mol. Biol. 23:37-44(2016).
-!- FUNCTION: Component of the RIX1 complex required for processing of
ITS2 sequences from 35S pre-rRNA and the nucleoplasmic transit of
the pre-60S ribosomal subunits (PubMed:11313466, PubMed:14759368,
PubMed:15528184, PubMed:26619264). Regulates pre-60S association
of the critical remodeling factor MDN1 (PubMed:26619264).
{ECO:0000269|PubMed:11313466, ECO:0000269|PubMed:14759368,
ECO:0000269|PubMed:15528184, ECO:0000269|PubMed:26619264}.
-!- SUBUNIT: Component of the RIX1 complex, composed of IPI1,
RIX1/IPI2 and IPI3 in a 1:2:2 stoichiometry. The complex interacts
(via RIX1) with MDN1 (via its hexameric AAA ATPase ring) and the
pre-60S ribosome particles (PubMed:14690591, PubMed:14759368,
PubMed:15260980, PubMed:15528184, PubMed:26619264). Interacts with
NUG1 (PubMed:11583615). Interacts with IPI3 (PubMed:14690591).
{ECO:0000269|PubMed:11583615, ECO:0000269|PubMed:14690591,
ECO:0000269|PubMed:14759368, ECO:0000269|PubMed:15260980,
ECO:0000269|PubMed:15528184, ECO:0000269|PubMed:26619264}.
-!- INTERACTION:
P53877:IPI3; NbExp=8; IntAct=EBI-24899, EBI-29063;
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:14562095,
ECO:0000269|PubMed:15528184}.
-!- PTM: Sumoylated. {ECO:0000269|PubMed:16978391}.
-!- MISCELLANEOUS: Present with 7820 molecules/cell in log phase SD
medium. {ECO:0000269|PubMed:14562106}.
-!- SIMILARITY: Belongs to the RIX1/PELP1 family. {ECO:0000305}.
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EMBL; U00030; AAB68356.1; -; Genomic_DNA.
EMBL; BK006934; DAA06889.2; -; Genomic_DNA.
PIR; S46678; S46678.
RefSeq; NP_012067.4; NM_001179328.4.
BioGrid; 36631; 226.
ComplexPortal; CPX-1711; RIX1 complex.
DIP; DIP-804N; -.
IntAct; P38883; 57.
MINT; P38883; -.
STRING; 4932.YHR197W; -.
iPTMnet; P38883; -.
MaxQB; P38883; -.
PaxDb; P38883; -.
PRIDE; P38883; -.
EnsemblFungi; YHR197W; YHR197W; YHR197W.
GeneID; 856604; -.
KEGG; sce:YHR197W; -.
EuPathDB; FungiDB:YHR197W; -.
SGD; S000001240; RIX1.
HOGENOM; HOG000154134; -.
InParanoid; P38883; -.
KO; K14828; -.
OMA; WCGINLI; -.
OrthoDB; EOG092C0SY4; -.
BioCyc; YEAST:G3O-31225-MONOMER; -.
PRO; PR:P38883; -.
Proteomes; UP000002311; Chromosome VIII.
GO; GO:0005829; C:cytosol; IDA:SGD.
GO; GO:0005654; C:nucleoplasm; IDA:SGD.
GO; GO:0005634; C:nucleus; IDA:SGD.
GO; GO:0097344; C:Rix1 complex; IDA:SGD.
GO; GO:0003682; F:chromatin binding; IDA:SGD.
GO; GO:0006267; P:pre-replicative complex assembly involved in nuclear cell cycle DNA replication; IMP:SGD.
GO; GO:0030174; P:regulation of DNA-dependent DNA replication initiation; IMP:SGD.
GO; GO:0000027; P:ribosomal large subunit assembly; IMP:SGD.
GO; GO:0000054; P:ribosomal subunit export from nucleus; IMP:SGD.
GO; GO:0006364; P:rRNA processing; IMP:SGD.
InterPro; IPR012583; RIX1_N.
Pfam; PF08167; RIX1; 1.
1: Evidence at protein level;
Acetylation; Complete proteome; Nucleus; Reference proteome;
Ribosome biogenesis; rRNA processing; Ubl conjugation.
INIT_MET 1 1 Removed. {ECO:0000244|PubMed:22814378}.
CHAIN 2 763 Pre-rRNA-processing protein RIX1.
/FTId=PRO_0000202938.
REGION 2 233 Interaction with IPI3.
{ECO:0000269|PubMed:26619264}.
REGION 663 763 Interaction with MDN1.
{ECO:0000269|PubMed:26619264}.
COMPBIAS 690 763 Glu-rich.
MOD_RES 2 2 N-acetylserine.
{ECO:0000244|PubMed:22814378}.
CONFLICT 762 762 E -> G (in Ref. 1; AAB68356).
{ECO:0000305}.
SEQUENCE 763 AA; 86739 MW; 14A0CE9A21F11711 CRC64;
MSEEFIAVST LARNLEIAKG NEFHTILATL RSPVYINEQL LKSELSFLVT KILKLIRSGN
DFDLWKGCHT SVVTCAYNPL VLSTHGGQLL AAIYSRLEQK TGFYSSVISS SHGKQLFNTL
ISSVAIIIDL MKNKPTLSRE ALVPKLKAII PTLITLSQYE PELVLPVLQR ILKRNTTTFK
PFTNKFRTVL INLIISDYAS LGTKTQRLVC ENFAYLHLLK IQVSDTSDDE TQAHHKIYAD
SNWRTGLMSI LSQFKPIIQL CGEILDFEQD NELYKLIKSL PVIDESNNKE EFLPSLKLDF
NAPLTLWEIP QRLSLLADML VAFISLPTPF PIRVPLGGIN SLCEVLLGVS NKYLPLKKEL
RHDNELNGVI NTILPQIQFQ GIRLWEIMVS KYGKCGLSFF EGILSSIELF IPLKKKSNNE
IDFNVVGSLK FEFATVFRLV NMILSHLGHQ LNIISVISQL IEVALFLSHD KTLIDSLFKN
RKSIMKQQTK TKQSKRSKSA EGAFSDIYTH PELFVCKNSM NWFNEINDFF ITALNNWILP
STPHIQILKY SITQSLRLKE RFGYIPESFV NLLRCEVLHP GSERVSILPI AISLLKNIND
DMFELLCHPK VPVGMVYQLH KPLDLGEDGE VRDDINKKEV ETNESSSNAN TGLETLKALE
NLENVTIPEP KHEVPKVVDD TAIFKKRSVE EVIERESTSS HKKVKFVEET TVDNGEELIV
KKAVSQTKEE EKPMEDSEDE EQEEFEIPAI ELSDDEEEEE EEE


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