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Pre-rRNA-processing protein IPI3 (Involved in processing IST2 protein 3)

 IPI3_YEAST              Reviewed;         555 AA.
P53877; D6W104;
01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
01-OCT-1996, sequence version 1.
16-JAN-2019, entry version 153.
RecName: Full=Pre-rRNA-processing protein IPI3;
AltName: Full=Involved in processing IST2 protein 3;
Name=IPI3; OrderedLocusNames=YNL182C; ORFNames=N1636;
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=9169873;
Philippsen P., Kleine K., Poehlmann R., Duesterhoeft A., Hamberg K.,
Hegemann J.H., Obermaier B., Urrestarazu L.A., Aert R., Albermann K.,
Altmann R., Andre B., Baladron V., Ballesta J.P.G., Becam A.-M.,
Beinhauer J.D., Boskovic J., Buitrago M.J., Bussereau F., Coster F.,
Crouzet M., D'Angelo M., Dal Pero F., De Antoni A., del Rey F.,
Doignon F., Domdey H., Dubois E., Fiedler T.A., Fleig U., Floeth M.,
Fritz C., Gaillardin C., Garcia-Cantalejo J.M., Glansdorff N.,
Goffeau A., Gueldener U., Herbert C.J., Heumann K., Heuss-Neitzel D.,
Hilbert H., Hinni K., Iraqui Houssaini I., Jacquet M., Jimenez A.,
Jonniaux J.-L., Karpfinger-Hartl L., Lanfranchi G., Lepingle A.,
Levesque H., Lyck R., Maftahi M., Mallet L., Maurer C.T.C.,
Messenguy F., Mewes H.-W., Moestl D., Nasr F., Nicaud J.-M.,
Niedenthal R.K., Pandolfo D., Pierard A., Piravandi E., Planta R.J.,
Pohl T.M., Purnelle B., Rebischung C., Remacha M.A., Revuelta J.L.,
Rinke M., Saiz J.E., Sartorello F., Scherens B., Sen-Gupta M.,
Soler-Mira A., Urbanus J.H.M., Valle G., Van Dyck L., Verhasselt P.,
Vierendeels F., Vissers S., Voet M., Volckaert G., Wach A.,
Wambutt R., Wedler H., Zollner A., Hani J.;
"The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV
and its evolutionary implications.";
Nature 387:93-98(1997).
[2]
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).
[3]
IDENTIFICATION IN THE RIX1 COMPLEX, IDENTIFICATION BY MASS
SPECTROMETRY, AND INTERACTION WITH RIX1.
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).
[4]
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).
[5]
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).
[6]
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).
[7]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-388, 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).
[8]
IDENTIFICATION IN THE RIX1 COMPLEX.
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. {ECO:0000269|PubMed:14759368,
ECO:0000269|PubMed:15528184}.
-!- 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. Interacts with RIX1.
{ECO:0000269|PubMed:14690591, ECO:0000269|PubMed:14759368,
ECO:0000269|PubMed:15260980, ECO:0000269|PubMed:15528184}.
-!- INTERACTION:
P38883:RIX1; NbExp=8; IntAct=EBI-29063, EBI-24899;
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:15528184}.
-!- DOMAIN: The coiled-coil motif forms a homodimeric contact and
facilitates RIX1 complex oligomerization.
{ECO:0000305|PubMed:26619264}.
-!- SIMILARITY: Belongs to the WD repeat IPI3/WDR18 family.
{ECO:0000305}.
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EMBL; Z71458; CAA96075.1; -; Genomic_DNA.
EMBL; BK006947; DAA10370.1; -; Genomic_DNA.
PIR; S63137; S63137.
RefSeq; NP_014217.1; NM_001183020.1.
ProteinModelPortal; P53877; -.
BioGrid; 35650; 106.
ComplexPortal; CPX-1711; RIX1 complex.
DIP; DIP-4297N; -.
IntAct; P53877; 31.
MINT; P53877; -.
STRING; 4932.YNL182C; -.
iPTMnet; P53877; -.
MaxQB; P53877; -.
PaxDb; P53877; -.
PRIDE; P53877; -.
EnsemblFungi; YNL182C_mRNA; YNL182C_mRNA; YNL182C.
GeneID; 855539; -.
KEGG; sce:YNL182C; -.
SGD; S000005126; IPI3.
GeneTree; ENSGT00390000000289; -.
HOGENOM; HOG000113091; -.
InParanoid; P53877; -.
KO; K14829; -.
OMA; HYQAITK; -.
BioCyc; YEAST:G3O-33193-MONOMER; -.
PRO; PR:P53877; -.
Proteomes; UP000002311; Chromosome XIV.
GO; GO:0005656; C:nuclear pre-replicative complex; IDA:SGD.
GO; GO:0005654; C:nucleoplasm; 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:0006364; P:rRNA processing; IMP:SGD.
Gene3D; 2.130.10.10; -; 1.
InterPro; IPR015943; WD40/YVTN_repeat-like_dom_sf.
InterPro; IPR001680; WD40_repeat.
InterPro; IPR017986; WD40_repeat_dom.
InterPro; IPR036322; WD40_repeat_dom_sf.
SMART; SM00320; WD40; 3.
SUPFAM; SSF50978; SSF50978; 1.
PROSITE; PS50082; WD_REPEATS_2; 1.
PROSITE; PS50294; WD_REPEATS_REGION; 1.
1: Evidence at protein level;
Coiled coil; Complete proteome; Nucleus; Phosphoprotein;
Reference proteome; Repeat; Ribosome biogenesis; rRNA processing;
WD repeat.
CHAIN 1 555 Pre-rRNA-processing protein IPI3.
/FTId=PRO_0000051484.
REPEAT 29 68 WD 1. {ECO:0000255}.
REPEAT 90 133 WD 2. {ECO:0000255}.
REPEAT 137 176 WD 3. {ECO:0000255}.
REPEAT 187 234 WD 4. {ECO:0000255}.
REPEAT 255 296 WD 5. {ECO:0000255}.
REPEAT 342 383 WD 6. {ECO:0000255}.
REGION 460 504 Interaction with RIX1.
{ECO:0000269|PubMed:26619264}.
COILED 513 554 {ECO:0000255}.
MOD_RES 388 388 Phosphoserine.
{ECO:0000244|PubMed:18407956}.
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


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