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Exosome complex protein LRP1 (Like an rRNA processing protein 1) (Yeast C1D domain-containing protein) (rRNA processing protein 47)

 LRP1_YEAST              Reviewed;         184 AA.
P38801; D3DL32;
01-FEB-1995, integrated into UniProtKB/Swiss-Prot.
01-FEB-1995, sequence version 1.
27-SEP-2017, entry version 120.
RecName: Full=Exosome complex protein LRP1;
AltName: Full=Like an rRNA processing protein 1;
AltName: Full=Yeast C1D domain-containing protein;
AltName: Full=rRNA processing protein 47;
Name=LRP1; Synonyms=RRP47, YC1D; OrderedLocusNames=YHR081W;
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.
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]
SUBCELLULAR LOCATION.
PubMed=11914276; DOI=10.1101/gad.970902;
Kumar A., Agarwal S., Heyman J.A., Matson S., Heidtman M.,
Piccirillo S., Umansky L., Drawid A., Jansen R., Liu Y., Cheung K.-H.,
Miller P., Gerstein M., Roeder G.S., Snyder M.;
"Subcellular localization of the yeast proteome.";
Genes Dev. 16:707-719(2002).
[4]
FUNCTION.
PubMed=12421302; DOI=10.1046/j.1365-2958.2002.03224.x;
Erdemir T., Bilican B., Cagatay T., Goding C.R., Yavuzer U.;
"Saccharomyces cerevisiae C1D is implicated in both non-homologous DNA
end joining and homologous recombination.";
Mol. Microbiol. 46:947-957(2002).
[5]
FUNCTION, AND INTERACTION WITH RRP45 AND RRP46.
PubMed=12837249; DOI=10.1016/S0092-8674(03)00466-5;
Peng W.-T., Robinson M.D., Mnaimneh S., Krogan N.J., Cagney G.,
Morris Q.D., Davierwala A.P., Grigull J., Yang X., Zhang W.,
Mitsakakis N., Ryan O.W., Datta N., Jojic V., Pal C., Canadien V.,
Richards D.P., Beattie B., Wu L.F., Altschuler S.J., Roweis S.,
Frey B.J., Emili A., Greenblatt J.F., Hughes T.R.;
"A panoramic view of yeast noncoding RNA processing.";
Cell 113:919-933(2003).
[6]
FUNCTION, INTERACTION WITH RRP4 AND RRP6, SUBCELLULAR LOCATION, AND
IDENTIFICATION BY MASS SPECTROMETRY.
PubMed=12972615; DOI=10.1128/MCB.23.19.6982-6992.2003;
Mitchell P., Petfalski E., Houalla R., Podtelejnikov A., Mann M.,
Tollervey D.;
"Rrp47p is an exosome-associated protein required for the 3'
processing of stable RNAs.";
Mol. Cell. Biol. 23:6982-6992(2003).
[7]
FUNCTION, INTERACTION RRP6, AND SUBCELLULAR LOCATION.
PubMed=15489286; DOI=10.1101/gad.1241204;
Hieronymus H., Yu M.C., Silver P.A.;
"Genome-wide mRNA surveillance is coupled to mRNA export.";
Genes Dev. 18:2652-2662(2004).
[8]
FUNCTION.
PubMed=15161972; DOI=10.1073/pnas.0401263101;
Askree S.H., Yehuda T., Smolikov S., Gurevich R., Hawk J., Coker C.,
Krauskopf A., Kupiec M., McEachern M.J.;
"A genome-wide screen for Saccharomyces cerevisiae deletion mutants
that affect telomere length.";
Proc. Natl. Acad. Sci. U.S.A. 101:8658-8663(2004).
[9]
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).
-!- FUNCTION: Required for exosome-dependent processing of pre-rRNA
and small nucleolar RNA (snRNA) precursors. Involved in processing
of 35S pre-rRNA at the A0, A1 and A2 sites. Required for activity
of RRP6 in 7S pre-rRNA processing. Also has a role in 3'-
processing of U4 and U5 small nuclear RNAs (snRNAs). Acts as a
mRNA export factor. Mediates mRNA degradation upon UV irradiation.
Maintains genome integrity where it is involved in both non-
homologous end joining (NHEJ) and homologous recombination pathway
repair of double strand DNA breaks. During NHEJ, required for
joining 3'-overhanging ends. Also involved in telomere length
regulation and maintenance. {ECO:0000269|PubMed:12421302,
ECO:0000269|PubMed:12837249, ECO:0000269|PubMed:12972615,
ECO:0000269|PubMed:15161972, ECO:0000269|PubMed:15489286}.
-!- SUBUNIT: Associated with nuclear form of the RNA exosome complex.
Interacts with RRP4, RRP6, RRP45 and RRP46.
{ECO:0000269|PubMed:12837249, ECO:0000269|PubMed:12972615,
ECO:0000269|PubMed:15489286}.
-!- INTERACTION:
P53859:CSL4; NbExp=3; IntAct=EBI-1909, EBI-1731;
Q08162:DIS3; NbExp=10; IntAct=EBI-1909, EBI-1740;
P38792:RRP4; NbExp=7; IntAct=EBI-1909, EBI-1757;
Q05636:RRP45; NbExp=4; IntAct=EBI-1909, EBI-1810;
Q12149:RRP6; NbExp=10; IntAct=EBI-1909, EBI-1782;
-!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:11914276,
ECO:0000269|PubMed:12972615, ECO:0000269|PubMed:15489286}.
-!- SIMILARITY: Belongs to the C1D family. {ECO:0000305}.
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EMBL; U10556; AAB68886.1; -; Genomic_DNA.
EMBL; BK006934; DAA06776.1; -; Genomic_DNA.
PIR; S46808; S46808.
RefSeq; NP_011949.1; NM_001179211.1.
PDB; 4WFC; X-ray; 2.35 A; B/D/F=1-133.
PDB; 4WFD; X-ray; 2.40 A; B/E/H=1-103.
PDB; 5C0W; X-ray; 4.60 A; L=1-184.
PDBsum; 4WFC; -.
PDBsum; 4WFD; -.
PDBsum; 5C0W; -.
DisProt; DP00788; -.
ProteinModelPortal; P38801; -.
SMR; P38801; -.
BioGrid; 36516; 434.
DIP; DIP-4359N; -.
IntAct; P38801; 14.
MINT; MINT-499454; -.
STRING; 4932.YHR081W; -.
MaxQB; P38801; -.
PRIDE; P38801; -.
EnsemblFungi; YHR081W; YHR081W; YHR081W.
GeneID; 856481; -.
KEGG; sce:YHR081W; -.
EuPathDB; FungiDB:YHR081W; -.
SGD; S000001123; LRP1.
HOGENOM; HOG000000879; -.
InParanoid; P38801; -.
KO; K12592; -.
OMA; NFQGKHT; -.
OrthoDB; EOG092C52FJ; -.
BioCyc; YEAST:G3O-31128-MONOMER; -.
PRO; PR:P38801; -.
Proteomes; UP000002311; Chromosome VIII.
GO; GO:0000178; C:exosome (RNase complex); IEA:UniProtKB-KW.
GO; GO:0005634; C:nucleus; IDA:SGD.
GO; GO:0003690; F:double-stranded DNA binding; IDA:SGD.
GO; GO:0003725; F:double-stranded RNA binding; IDA:SGD.
GO; GO:0030234; F:enzyme regulator activity; IDA:SGD.
GO; GO:0000467; P:exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA); IMP:SGD.
GO; GO:0071028; P:nuclear mRNA surveillance; IMP:SGD.
GO; GO:0071039; P:nuclear polyadenylation-dependent CUT catabolic process; IMP:SGD.
GO; GO:0071035; P:nuclear polyadenylation-dependent rRNA catabolic process; IMP:SGD.
GO; GO:0071033; P:nuclear retention of pre-mRNA at the site of transcription; IGI:SGD.
GO; GO:0071051; P:polyadenylation-dependent snoRNA 3'-end processing; IMP:SGD.
GO; GO:0000973; P:posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery; IMP:SGD.
GO; GO:1901917; P:regulation of exoribonuclease activity; IDA:SGD.
GO; GO:0034475; P:U4 snRNA 3'-end processing; IMP:SGD.
GO; GO:0034476; P:U5 snRNA 3'-end processing; IMP:SGD.
InterPro; IPR011082; Exosome-assoc_fac/DNA_repair.
InterPro; IPR007146; Sas10/Utp3/C1D.
PANTHER; PTHR15341; PTHR15341; 1.
Pfam; PF04000; Sas10_Utp3; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; Exosome; Nucleus; Reference proteome;
RNA-binding; rRNA processing.
CHAIN 1 184 Exosome complex protein LRP1.
/FTId=PRO_0000202902.
HELIX 4 6 {ECO:0000244|PDB:4WFC}.
HELIX 8 28 {ECO:0000244|PDB:4WFC}.
HELIX 33 39 {ECO:0000244|PDB:4WFC}.
HELIX 43 67 {ECO:0000244|PDB:4WFC}.
HELIX 74 119 {ECO:0000244|PDB:4WFC}.
SEQUENCE 184 AA; 21045 MW; 27D00668C296CC9A CRC64;
MEDIEKIKPY VRSFSKALDE LKPEIEKLTS KSLDEQLLLL SDERAKLELI NRYAYVLSSL
MFANMKVLGV KDMSPILGEL KRVKSYMDKA KQYDNRITKS NEKSQAEQEK AKNIISNVLD
GNKNQFEPSI SRSNFQGKHT KFENDELAES TTTKIIDSTD HIRKASSKKS KRLDKVGKKK
GGKK


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