RIX1_YEAST
ID RIX1_YEAST Reviewed; 763 AA.
AC P38883; D3DLE5;
DT 01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
DT 27-JUL-2011, sequence version 2.
DT 03-AUG-2022, entry version 157.
DE RecName: Full=Pre-rRNA-processing protein RIX1;
DE AltName: Full=Involved in processing IST2 protein 2;
DE AltName: Full=Ribosomal export protein 1;
GN Name=RIX1; Synonyms=IPI2; OrderedLocusNames=YHR197W;
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 [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 204508 / S288c;
RX PubMed=8091229; DOI=10.1126/science.8091229;
RA Johnston M., Andrews S., Brinkman R., Cooper J., Ding H., Dover J., Du Z.,
RA Favello A., Fulton L., Gattung S., Geisel C., Kirsten J., Kucaba T.,
RA Hillier L.W., Jier M., Johnston L., Langston Y., Latreille P., Louis E.J.,
RA Macri C., Mardis E., Menezes S., Mouser L., Nhan M., Rifkin L., Riles L.,
RA St Peter H., Trevaskis E., Vaughan K., Vignati D., Wilcox L., Wohldman P.,
RA Waterston R., Wilson R., Vaudin M.;
RT "Complete nucleotide sequence of Saccharomyces cerevisiae chromosome
RT VIII.";
RL Science 265:2077-2082(1994).
RN [2]
RP GENOME REANNOTATION, AND SEQUENCE REVISION TO 762.
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 [3]
RP INTERACTION WITH NUG1.
RX PubMed=11583615; DOI=10.1016/s1097-2765(01)00342-2;
RA Bassler J., Grandi P., Gadal O., Lessmann T., Petfalski E., Tollervey D.,
RA Lechner J., Hurt E.;
RT "Identification of a 60S preribosomal particle that is closely linked to
RT nuclear export.";
RL Mol. Cell 8:517-529(2001).
RN [4]
RP FUNCTION.
RX PubMed=11313466; DOI=10.1128/mcb.21.10.3405-3415.2001;
RA Gadal O., Strauss D., Kessl J., Trumpower B., Tollervey D., Hurt E.;
RT "Nuclear export of 60s ribosomal subunits depends on Xpo1p and requires a
RT nuclear export sequence-containing factor, Nmd3p, that associates with the
RT large subunit protein Rpl10p.";
RL Mol. Cell. Biol. 21:3405-3415(2001).
RN [5]
RP IDENTIFICATION IN THE RIX1 COMPLEX, IDENTIFICATION BY MASS SPECTROMETRY,
RP AND INTERACTION WITH IPI3.
RX PubMed=14690591; DOI=10.1016/s1097-2765(03)00476-3;
RA Hazbun T.R., Malmstroem L., Anderson S., Graczyk B.J., Fox B., Riffle M.,
RA Sundin B.A., Aranda J.D., McDonald W.H., Chiu C.-H., Snydsman B.E.,
RA Bradley P., Muller E.G.D., Fields S., Baker D., Yates J.R. III, Davis T.N.;
RT "Assigning function to yeast proteins by integration of technologies.";
RL Mol. Cell 12:1353-1365(2003).
RN [6]
RP SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX PubMed=14562095; DOI=10.1038/nature02026;
RA Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA Weissman J.S., O'Shea E.K.;
RT "Global analysis of protein localization in budding yeast.";
RL Nature 425:686-691(2003).
RN [7]
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 [8]
RP IDENTIFICATION IN THE RIX1 COMPLEX, SUBCELLULAR LOCATION, FUNCTION OF THE
RP RIX1 COMPLEX, AND IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=15528184; DOI=10.1074/jbc.m406876200;
RA Galani K., Nissan T.A., Petfalski E., Tollervey D., Hurt E.;
RT "Rea1, a dynein-related nuclear AAA-ATPase, is involved in late rRNA
RT processing and nuclear export of 60 S subunits.";
RL J. Biol. Chem. 279:55411-55418(2004).
RN [9]
RP IDENTIFICATION IN THE RIX1 COMPLEX, INTERACTION WITH MDN1 AND PRE-60S
RP RIBOSOMAL PARTICLES, AND IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=15260980; DOI=10.1016/j.molcel.2004.06.033;
RA Nissan T.A., Galani K., Maco B., Tollervey D., Aebi U., Hurt E.;
RT "A pre-ribosome with a tadpole-like structure functions in ATP-dependent
RT maturation of 60S subunits.";
RL Mol. Cell 15:295-301(2004).
RN [10]
RP IDENTIFICATION IN THE RIX1 COMPLEX, AND FUNCTION OF THE RIX1 COMPLEX.
RX PubMed=14759368; DOI=10.1016/s1097-2765(04)00003-6;
RA Krogan N.J., Peng W.-T., Cagney G., Robinson M.D., Haw R., Zhong G.,
RA Guo X., Zhang X., Canadien V., Richards D.P., Beattie B.K., Lalev A.,
RA Zhang W., Davierwala A.P., Mnaimneh S., Starostine A., Tikuisis A.P.,
RA Grigull J., Datta N., Bray J.E., Hughes T.R., Emili A., Greenblatt J.F.;
RT "High-definition macromolecular composition of yeast RNA-processing
RT complexes.";
RL Mol. Cell 13:225-239(2004).
RN [11]
RP SUMOYLATION.
RX PubMed=16978391; DOI=10.1111/j.1600-0854.2006.00471.x;
RA Panse V.G., Kressler D., Pauli A., Petfalski E., Gnaedig M., Tollervey D.,
RA Hurt E.;
RT "Formation and nuclear export of preribosomes are functionally linked to
RT the small-ubiquitin-related modifier pathway.";
RL Traffic 7:1311-1321(2006).
RN [12]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT SER-2, CLEAVAGE OF INITIATOR
RP METHIONINE [LARGE SCALE ANALYSIS], AND IDENTIFICATION BY MASS SPECTROMETRY
RP [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 [13]
RP IDENTIFICATION IN THE RIX1 COMPLEX, AND INTERACTION WITH MDN1 AND IPI3.
RX PubMed=26619264; DOI=10.1038/nsmb.3132;
RA Barrio-Garcia C., Thoms M., Flemming D., Kater L., Berninghausen O.,
RA Bassler J., Beckmann R., Hurt E.;
RT "Architecture of the Rix1-Rea1 checkpoint machinery during pre-60S-ribosome
RT remodeling.";
RL Nat. Struct. Mol. Biol. 23:37-44(2016).
CC -!- FUNCTION: Component of the RIX1 complex required for processing of ITS2
CC sequences from 35S pre-rRNA and the nucleoplasmic transit of the pre-
CC 60S ribosomal subunits (PubMed:11313466, PubMed:14759368,
CC PubMed:15528184, PubMed:26619264). Regulates pre-60S association of the
CC critical remodeling factor MDN1 (PubMed:26619264).
CC {ECO:0000269|PubMed:11313466, ECO:0000269|PubMed:14759368,
CC ECO:0000269|PubMed:15528184, ECO:0000269|PubMed:26619264}.
CC -!- SUBUNIT: Component of the RIX1 complex, composed of IPI1, RIX1/IPI2 and
CC IPI3 in a 1:2:2 stoichiometry. The complex interacts (via RIX1) with
CC MDN1 (via its hexameric AAA ATPase ring) and the pre-60S ribosome
CC particles (PubMed:14690591, PubMed:14759368, PubMed:15260980,
CC PubMed:15528184, PubMed:26619264). Interacts with NUG1
CC (PubMed:11583615). Interacts with IPI3 (PubMed:14690591).
CC {ECO:0000269|PubMed:11583615, ECO:0000269|PubMed:14690591,
CC ECO:0000269|PubMed:14759368, ECO:0000269|PubMed:15260980,
CC ECO:0000269|PubMed:15528184, ECO:0000269|PubMed:26619264}.
CC -!- INTERACTION:
CC P38883; P53877: IPI3; NbExp=8; IntAct=EBI-24899, EBI-29063;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:14562095,
CC ECO:0000269|PubMed:15528184}.
CC -!- PTM: Sumoylated. {ECO:0000269|PubMed:16978391}.
CC -!- MISCELLANEOUS: Present with 7820 molecules/cell in log phase SD medium.
CC {ECO:0000269|PubMed:14562106}.
CC -!- SIMILARITY: Belongs to the RIX1/PELP1 family. {ECO:0000305}.
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DR EMBL; U00030; AAB68356.1; -; Genomic_DNA.
DR EMBL; BK006934; DAA06889.2; -; Genomic_DNA.
DR PIR; S46678; S46678.
DR RefSeq; NP_012067.4; NM_001179328.4.
DR PDB; 6YLE; EM; 3.30 A; C/D=1-763.
DR PDB; 6YLH; EM; 3.10 A; 6/7=1-763.
DR PDBsum; 6YLE; -.
DR PDBsum; 6YLH; -.
DR AlphaFoldDB; P38883; -.
DR SMR; P38883; -.
DR BioGRID; 36631; 259.
DR ComplexPortal; CPX-1711; RIX1 complex.
DR DIP; DIP-804N; -.
DR IntAct; P38883; 57.
DR MINT; P38883; -.
DR STRING; 4932.YHR197W; -.
DR iPTMnet; P38883; -.
DR MaxQB; P38883; -.
DR PaxDb; P38883; -.
DR PRIDE; P38883; -.
DR EnsemblFungi; YHR197W_mRNA; YHR197W; YHR197W.
DR GeneID; 856604; -.
DR KEGG; sce:YHR197W; -.
DR SGD; S000001240; RIX1.
DR VEuPathDB; FungiDB:YHR197W; -.
DR eggNOG; ENOG502R65X; Eukaryota.
DR HOGENOM; CLU_020084_0_0_1; -.
DR InParanoid; P38883; -.
DR OMA; WCGINLI; -.
DR BioCyc; YEAST:G3O-31225-MON; -.
DR Reactome; R-SCE-6791226; Major pathway of rRNA processing in the nucleolus and cytosol.
DR PRO; PR:P38883; -.
DR Proteomes; UP000002311; Chromosome VIII.
DR RNAct; P38883; protein.
DR GO; GO:0005829; C:cytosol; IDA:SGD.
DR GO; GO:0005654; C:nucleoplasm; IDA:SGD.
DR GO; GO:0005634; C:nucleus; IDA:SGD.
DR GO; GO:0097344; C:Rix1 complex; IDA:SGD.
DR GO; GO:0003682; F:chromatin binding; IDA:SGD.
DR GO; GO:0006267; P:pre-replicative complex assembly involved in nuclear cell cycle DNA replication; IMP:SGD.
DR GO; GO:0030174; P:regulation of DNA-templated DNA replication initiation; IMP:SGD.
DR GO; GO:0000027; P:ribosomal large subunit assembly; IMP:SGD.
DR GO; GO:0006364; P:rRNA processing; IMP:SGD.
DR InterPro; IPR012583; RIX1_N.
DR Pfam; PF08167; RIX1; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Nucleus; Reference proteome;
KW Ribosome biogenesis; rRNA processing; Ubl conjugation.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0007744|PubMed:22814378"
FT CHAIN 2..763
FT /note="Pre-rRNA-processing protein RIX1"
FT /id="PRO_0000202938"
FT REGION 2..233
FT /note="Interaction with IPI3"
FT /evidence="ECO:0000269|PubMed:26619264"
FT REGION 663..763
FT /note="Interaction with MDN1"
FT /evidence="ECO:0000269|PubMed:26619264"
FT REGION 722..763
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 733..763
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 2
FT /note="N-acetylserine"
FT /evidence="ECO:0007744|PubMed:22814378"
FT CONFLICT 762
FT /note="E -> G (in Ref. 1; AAB68356)"
FT /evidence="ECO:0000305"
FT HELIX 8..13
FT /evidence="ECO:0007829|PDB:6YLE"
FT HELIX 20..29
FT /evidence="ECO:0007829|PDB:6YLE"
FT HELIX 33..35
FT /evidence="ECO:0007829|PDB:6YLE"
FT TURN 41..44
FT /evidence="ECO:0007829|PDB:6YLE"
FT HELIX 45..57
FT /evidence="ECO:0007829|PDB:6YLE"
FT STRAND 60..62
FT /evidence="ECO:0007829|PDB:6YLE"
FT HELIX 63..77
FT /evidence="ECO:0007829|PDB:6YLE"
FT HELIX 79..102
FT /evidence="ECO:0007829|PDB:6YLE"
FT TURN 105..107
FT /evidence="ECO:0007829|PDB:6YLE"
FT STRAND 108..112
FT /evidence="ECO:0007829|PDB:6YLE"
FT HELIX 113..128
FT /evidence="ECO:0007829|PDB:6YLE"
FT TURN 129..132
FT /evidence="ECO:0007829|PDB:6YLE"
FT HELIX 135..138
FT /evidence="ECO:0007829|PDB:6YLE"
FT TURN 139..142
FT /evidence="ECO:0007829|PDB:6YLE"
FT HELIX 143..157
FT /evidence="ECO:0007829|PDB:6YLE"
FT HELIX 161..174
FT /evidence="ECO:0007829|PDB:6YLE"
FT STRAND 176..179
FT /evidence="ECO:0007829|PDB:6YLE"
FT HELIX 180..182
FT /evidence="ECO:0007829|PDB:6YLE"
FT HELIX 183..194
FT /evidence="ECO:0007829|PDB:6YLE"
FT STRAND 198..201
FT /evidence="ECO:0007829|PDB:6YLE"
FT HELIX 203..215
FT /evidence="ECO:0007829|PDB:6YLE"
FT HELIX 216..218
FT /evidence="ECO:0007829|PDB:6YLE"
FT HELIX 242..252
FT /evidence="ECO:0007829|PDB:6YLE"
FT HELIX 255..265
FT /evidence="ECO:0007829|PDB:6YLE"
FT STRAND 268..270
FT /evidence="ECO:0007829|PDB:6YLE"
FT HELIX 271..277
FT /evidence="ECO:0007829|PDB:6YLE"
FT STRAND 288..290
FT /evidence="ECO:0007829|PDB:6YLE"
FT STRAND 300..302
FT /evidence="ECO:0007829|PDB:6YLE"
FT HELIX 303..308
FT /evidence="ECO:0007829|PDB:6YLE"
FT HELIX 310..325
FT /evidence="ECO:0007829|PDB:6YLE"
FT STRAND 332..335
FT /evidence="ECO:0007829|PDB:6YLE"
FT HELIX 336..346
FT /evidence="ECO:0007829|PDB:6YLE"
FT STRAND 352..354
FT /evidence="ECO:0007829|PDB:6YLE"
FT STRAND 358..360
FT /evidence="ECO:0007829|PDB:6YLE"
FT HELIX 365..390
FT /evidence="ECO:0007829|PDB:6YLE"
FT TURN 391..396
FT /evidence="ECO:0007829|PDB:6YLE"
FT HELIX 397..399
FT /evidence="ECO:0007829|PDB:6YLE"
FT HELIX 402..410
FT /evidence="ECO:0007829|PDB:6YLE"
FT STRAND 415..417
FT /evidence="ECO:0007829|PDB:6YLE"
FT HELIX 423..426
FT /evidence="ECO:0007829|PDB:6YLE"
FT HELIX 431..447
FT /evidence="ECO:0007829|PDB:6YLE"
FT HELIX 455..467
FT /evidence="ECO:0007829|PDB:6YLE"
FT STRAND 471..473
FT /evidence="ECO:0007829|PDB:6YLE"
FT STRAND 511..516
FT /evidence="ECO:0007829|PDB:6YLE"
FT HELIX 520..535
FT /evidence="ECO:0007829|PDB:6YLE"
FT HELIX 542..561
FT /evidence="ECO:0007829|PDB:6YLE"
FT STRAND 562..564
FT /evidence="ECO:0007829|PDB:6YLE"
FT HELIX 567..578
FT /evidence="ECO:0007829|PDB:6YLE"
FT HELIX 588..594
FT /evidence="ECO:0007829|PDB:6YLE"
FT STRAND 595..598
FT /evidence="ECO:0007829|PDB:6YLE"
FT HELIX 602..607
FT /evidence="ECO:0007829|PDB:6YLE"
SQ 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
