IPI3_YEAST
ID IPI3_YEAST Reviewed; 555 AA.
AC P53877; D6W104;
DT 01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1996, sequence version 1.
DT 03-AUG-2022, entry version 171.
DE RecName: Full=Pre-rRNA-processing protein IPI3;
DE AltName: Full=Involved in processing IST2 protein 3;
GN Name=IPI3; OrderedLocusNames=YNL182C; ORFNames=N1636;
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=9169873;
RA Philippsen P., Kleine K., Poehlmann R., Duesterhoeft A., Hamberg K.,
RA Hegemann J.H., Obermaier B., Urrestarazu L.A., Aert R., Albermann K.,
RA Altmann R., Andre B., Baladron V., Ballesta J.P.G., Becam A.-M.,
RA Beinhauer J.D., Boskovic J., Buitrago M.J., Bussereau F., Coster F.,
RA Crouzet M., D'Angelo M., Dal Pero F., De Antoni A., del Rey F., Doignon F.,
RA Domdey H., Dubois E., Fiedler T.A., Fleig U., Floeth M., Fritz C.,
RA Gaillardin C., Garcia-Cantalejo J.M., Glansdorff N., Goffeau A.,
RA Gueldener U., Herbert C.J., Heumann K., Heuss-Neitzel D., Hilbert H.,
RA Hinni K., Iraqui Houssaini I., Jacquet M., Jimenez A., Jonniaux J.-L.,
RA Karpfinger-Hartl L., Lanfranchi G., Lepingle A., Levesque H., Lyck R.,
RA Maftahi M., Mallet L., Maurer C.T.C., Messenguy F., Mewes H.-W., Moestl D.,
RA Nasr F., Nicaud J.-M., Niedenthal R.K., Pandolfo D., Pierard A.,
RA Piravandi E., Planta R.J., Pohl T.M., Purnelle B., Rebischung C.,
RA Remacha M.A., Revuelta J.L., Rinke M., Saiz J.E., Sartorello F.,
RA Scherens B., Sen-Gupta M., Soler-Mira A., Urbanus J.H.M., Valle G.,
RA Van Dyck L., Verhasselt P., Vierendeels F., Vissers S., Voet M.,
RA Volckaert G., Wach A., Wambutt R., Wedler H., Zollner A., Hani J.;
RT "The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its
RT evolutionary implications.";
RL Nature 387:93-98(1997).
RN [2]
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 [3]
RP IDENTIFICATION IN THE RIX1 COMPLEX, IDENTIFICATION BY MASS SPECTROMETRY,
RP AND INTERACTION WITH RIX1.
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 [4]
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 [5]
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 [6]
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 [7]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-388, 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 [8]
RP IDENTIFICATION IN THE RIX1 COMPLEX.
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. {ECO:0000269|PubMed:14759368,
CC ECO:0000269|PubMed:15528184}.
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. Interacts with RIX1. {ECO:0000269|PubMed:14690591,
CC ECO:0000269|PubMed:14759368, ECO:0000269|PubMed:15260980,
CC ECO:0000269|PubMed:15528184}.
CC -!- INTERACTION:
CC P53877; P38883: RIX1; NbExp=8; IntAct=EBI-29063, EBI-24899;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:15528184}.
CC -!- DOMAIN: The coiled-coil motif forms a homodimeric contact and
CC facilitates RIX1 complex oligomerization.
CC {ECO:0000305|PubMed:26619264}.
CC -!- SIMILARITY: Belongs to the WD repeat IPI3/WDR18 family. {ECO:0000305}.
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DR EMBL; Z71458; CAA96075.1; -; Genomic_DNA.
DR EMBL; BK006947; DAA10370.1; -; Genomic_DNA.
DR PIR; S63137; S63137.
DR RefSeq; NP_014217.1; NM_001183020.1.
DR PDB; 6YLE; EM; 3.30 A; A/B=1-555.
DR PDB; 6YLH; EM; 3.10 A; 0/w=1-555.
DR PDBsum; 6YLE; -.
DR PDBsum; 6YLH; -.
DR AlphaFoldDB; P53877; -.
DR SMR; P53877; -.
DR BioGRID; 35650; 131.
DR ComplexPortal; CPX-1711; RIX1 complex.
DR DIP; DIP-4297N; -.
DR IntAct; P53877; 31.
DR MINT; P53877; -.
DR STRING; 4932.YNL182C; -.
DR iPTMnet; P53877; -.
DR MaxQB; P53877; -.
DR PaxDb; P53877; -.
DR PRIDE; P53877; -.
DR EnsemblFungi; YNL182C_mRNA; YNL182C; YNL182C.
DR GeneID; 855539; -.
DR KEGG; sce:YNL182C; -.
DR SGD; S000005126; IPI3.
DR VEuPathDB; FungiDB:YNL182C; -.
DR eggNOG; KOG0646; Eukaryota.
DR GeneTree; ENSGT00390000000289; -.
DR HOGENOM; CLU_029749_4_0_1; -.
DR InParanoid; P53877; -.
DR OMA; YVWELNS; -.
DR BioCyc; YEAST:G3O-33193-MON; -.
DR Reactome; R-SCE-6791226; Major pathway of rRNA processing in the nucleolus and cytosol.
DR PRO; PR:P53877; -.
DR Proteomes; UP000002311; Chromosome XIV.
DR RNAct; P53877; protein.
DR GO; GO:0005656; C:nuclear pre-replicative complex; IDA:SGD.
DR GO; GO:0005654; C:nucleoplasm; IDA:SGD.
DR GO; GO:0005634; C:nucleus; HDA:SGD.
DR GO; GO:0097344; C:Rix1 complex; IDA:SGD.
DR GO; GO:0003682; F:chromatin binding; IDA:SGD.
DR GO; GO:0006261; P:DNA-templated DNA replication; IBA:GO_Central.
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 Gene3D; 2.130.10.10; -; 1.
DR InterPro; IPR015943; WD40/YVTN_repeat-like_dom_sf.
DR InterPro; IPR001680; WD40_repeat.
DR InterPro; IPR036322; WD40_repeat_dom_sf.
DR InterPro; IPR045227; WDR18/Ipi3/RID3.
DR PANTHER; PTHR18763; PTHR18763; 1.
DR SMART; SM00320; WD40; 3.
DR SUPFAM; SSF50978; SSF50978; 1.
DR PROSITE; PS50082; WD_REPEATS_2; 1.
DR PROSITE; PS50294; WD_REPEATS_REGION; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Coiled coil; Nucleus; Phosphoprotein; Reference proteome;
KW Repeat; Ribosome biogenesis; rRNA processing; WD repeat.
FT CHAIN 1..555
FT /note="Pre-rRNA-processing protein IPI3"
FT /id="PRO_0000051484"
FT REPEAT 29..68
FT /note="WD 1"
FT /evidence="ECO:0000255"
FT REPEAT 90..133
FT /note="WD 2"
FT /evidence="ECO:0000255"
FT REPEAT 137..176
FT /note="WD 3"
FT /evidence="ECO:0000255"
FT REPEAT 187..234
FT /note="WD 4"
FT /evidence="ECO:0000255"
FT REPEAT 255..296
FT /note="WD 5"
FT /evidence="ECO:0000255"
FT REPEAT 342..383
FT /note="WD 6"
FT /evidence="ECO:0000255"
FT REGION 460..504
FT /note="Interaction with RIX1"
FT /evidence="ECO:0000269|PubMed:26619264"
FT COILED 513..554
FT /evidence="ECO:0000255"
FT MOD_RES 388
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:18407956"
FT STRAND 4..11
FT /evidence="ECO:0007829|PDB:6YLE"
FT STRAND 13..19
FT /evidence="ECO:0007829|PDB:6YLE"
FT STRAND 23..28
FT /evidence="ECO:0007829|PDB:6YLE"
FT STRAND 37..40
FT /evidence="ECO:0007829|PDB:6YLE"
FT TURN 41..43
FT /evidence="ECO:0007829|PDB:6YLE"
FT STRAND 44..48
FT /evidence="ECO:0007829|PDB:6YLE"
FT TURN 50..52
FT /evidence="ECO:0007829|PDB:6YLE"
FT STRAND 53..59
FT /evidence="ECO:0007829|PDB:6YLE"
FT STRAND 62..64
FT /evidence="ECO:0007829|PDB:6YLE"
FT STRAND 71..74
FT /evidence="ECO:0007829|PDB:6YLE"
FT STRAND 81..85
FT /evidence="ECO:0007829|PDB:6YLE"
FT TURN 94..96
FT /evidence="ECO:0007829|PDB:6YLE"
FT STRAND 109..114
FT /evidence="ECO:0007829|PDB:6YLE"
FT HELIX 116..118
FT /evidence="ECO:0007829|PDB:6YLE"
FT STRAND 120..124
FT /evidence="ECO:0007829|PDB:6YLE"
FT TURN 125..128
FT /evidence="ECO:0007829|PDB:6YLE"
FT STRAND 129..135
FT /evidence="ECO:0007829|PDB:6YLE"
FT STRAND 137..140
FT /evidence="ECO:0007829|PDB:6YLE"
FT STRAND 142..158
FT /evidence="ECO:0007829|PDB:6YLE"
FT STRAND 163..168
FT /evidence="ECO:0007829|PDB:6YLE"
FT HELIX 169..171
FT /evidence="ECO:0007829|PDB:6YLE"
FT STRAND 182..185
FT /evidence="ECO:0007829|PDB:6YLE"
FT STRAND 192..198
FT /evidence="ECO:0007829|PDB:6YLE"
FT STRAND 208..216
FT /evidence="ECO:0007829|PDB:6YLE"
FT STRAND 219..228
FT /evidence="ECO:0007829|PDB:6YLE"
FT STRAND 249..255
FT /evidence="ECO:0007829|PDB:6YLE"
FT STRAND 260..265
FT /evidence="ECO:0007829|PDB:6YLE"
FT STRAND 271..278
FT /evidence="ECO:0007829|PDB:6YLE"
FT STRAND 280..288
FT /evidence="ECO:0007829|PDB:6YLE"
FT STRAND 294..297
FT /evidence="ECO:0007829|PDB:6YLE"
FT STRAND 311..315
FT /evidence="ECO:0007829|PDB:6YLE"
FT STRAND 335..338
FT /evidence="ECO:0007829|PDB:6YLE"
FT STRAND 347..352
FT /evidence="ECO:0007829|PDB:6YLE"
FT STRAND 359..363
FT /evidence="ECO:0007829|PDB:6YLE"
FT STRAND 366..372
FT /evidence="ECO:0007829|PDB:6YLE"
FT TURN 373..376
FT /evidence="ECO:0007829|PDB:6YLE"
FT STRAND 377..383
FT /evidence="ECO:0007829|PDB:6YLE"
FT STRAND 395..401
FT /evidence="ECO:0007829|PDB:6YLE"
FT STRAND 437..439
FT /evidence="ECO:0007829|PDB:6YLE"
FT STRAND 450..453
FT /evidence="ECO:0007829|PDB:6YLE"
FT HELIX 459..461
FT /evidence="ECO:0007829|PDB:6YLE"
FT HELIX 473..484
FT /evidence="ECO:0007829|PDB:6YLE"
SQ SEQUENCE 555 AA; 61773 MW; 8EED6854DF9405A6 CRC64;
MDEQVIFTTN TSGTIASVHS FEQINLRQCS TQSRNSCVQV GNKYLFIAQA QKALINVYNL
SGSFKRESVE QRLPLPEILK CLEVVENDGV QYDRIQGVNH NLPDFNLPYL LLGSTESGKL
YIWELNSGIL LNVKPMAHYQ SITKIKSILN GKYIITSGND SRVIIWQTVD LVSASNDDPK
PLCILHDHTL PVTDFQVSSS QGKFLSCTDT KLFTVSQDAT IRCYDLSLIG SKKKQKANEN
DVSIGKTPVL LATFTTPYSI KSIVLDPADR ACYIGTAEGC FSLNLFYKLK GNAIVNLLQS
AGVNTVQKGR VFSLVQRNSL TGGENEDLDA LYAMGQLVCE NVLNSNVSCL EISMDGTLLL
IGDTEGKVSI AEIYSKQIIR TIQTLTTSQD SVGEVTNLLT NPYRLERGNL LFEGESKGKQ
PSNNNGHNFM KIPNLQRVIF DGKNKGHLHD IWYQIGEPEA ETDPNLALPL NDFNAYLEQV
KTQESIFSHI GKVSSNVKVI DNKIDATSSL DSNAAKDEEI TELKTNIEAL THAYKELRDM
HEKLYEEHQQ MLDKQ
