Reviewed, UniProtKB/Swiss-Prot P53063 (DOM3Z_YEAST)

Names and origin

Protein names

Recommended name:
    RAT1-interacting protein

Gene names

Name:	RAI1
Ordered Locus Names:	YGL246C
ORF Names:	NRE387

Organism

Saccharomyces cerevisiae (Baker's yeast) [Complete proteome]

Taxonomic identifier

4932 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

Protein attributes

Sequence length	387 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Binds to and enhances the exonuclease activity of RAT1. Required for the processing of nuclear mRNA and rRNA precursors. May promote termination of transcription by RNA polymerase II.
Subunit structure	Interacts with RAT1, RTT103 and pre-60S ribosomal subunits.
Subcellular location	Nucleus.
Miscellaneous	Present with 4030 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the Dom3Z family.

Ontologies

Keywords
Biological process	Transcription Transcription regulation Transcription termination mRNA processing rRNA processing
Cellular component	Nucleus
PTM	Phosphoprotein
Technical term	Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Ref.4 Inferred from mutant phenotype. Source: SGD maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Ref.4 Inferred from mutant phenotype. Source: SGD termination of RNA polymerase II transcription, poly(A)-coupled Ref.8 Inferred from mutant phenotype. Source: SGD
Cellular component	nucleus Ref.4 Ref.5 Inferred from direct assay. Source: SGD
Molecular function	enzyme regulator activity Ref.4 Inferred from direct assay. Source: SGD protein binding Ref.4 Inferred from physical interaction. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
RAT1	Q02792	1	EBI-24206,EBI-14845

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view
Molecule processing
	Initiator methionine	1	1	Removed
	Chain	2 – 387	386	RAT1-interacting protein
Regions
	Region	273 – 387	115	Interaction with RAT1
Amino acid modifications
	Modified residue	198	1	Phosphoserine
Experimental info
	Sequence conflict	8	1	F → S AA sequence Ref.4

Sequences

	Sequence		Length	Mass (Da)
	P53063-1 [UniParc]. Last modified January 23, 2007. Version 3. Checksum: E4A6565AF690A3E1	FASTA	387	44,510
	10 20 30 40 50 60 MGVSANLFVK QRGSTTALKQ PKEIGFYSRT KDEEYLISDD TNLNYYYLPD AELDRKLDLS 70 80 90 100 110 120 SGFQKFKDYY KDFEDRCSLR GLLETIESSE RHKGKKINAD IITFRGIARK LISCAFDSPS 130 140 150 160 170 180 FNTVDLRIVS FNGQLFIKEV PEAVNAAKAS SATEAGRNIN QDLNVFTGYK FETLATLSNP 190 200 210 220 230 240 LQYTPREVIE KRTKRIVSHG DEYISVVRTG VGNCKLILGA EVDCIFDFKE NGRDNLKHYA 250 260 270 280 290 300 ELKCTQQVAN ISDTHKFERK LFRTWLQCFL VGIPRIIYGF KDDHYVLKTV EEFSTEEVPV 310 320 330 340 350 360 LLKNNNPQVG SACLEAIKWY GLLTEWLLKM IPRDEDPHSQ IRAFKLVFEN NHLRLSEIEE 370 380 SDEEYSGLID GEHILSNGFK EWRKSLK

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Sequence of a 39,411 bp DNA fragment covering the left end of chromosome VII of Saccharomyces cerevisiae." Coissac E., Maillier E., Robineau S., Netter P. Yeast 12:1555-1562(1996) [PubMed: 8972578] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[2]	"The nucleotide sequence of Saccharomyces cerevisiae chromosome VII." Tettelin H., Agostoni-Carbone M.L., Albermann K., Albers M., Arroyo J., Backes U., Barreiros T., Bertani I., Bjourson A.J., Brueckner M., Bruschi C.V., Carignani G., Castagnoli L., Cerdan E., Clemente M.L., Coblenz A., Coglievina M., Coissac E. , Defoor E., Del Bino S., Delius H., Delneri D., de Wergifosse P., Dujon B., Durand P., Entian K.-D., Eraso P., Escribano V., Fabiani L., Fartmann B., Feroli F., Feuermann M., Frontali L., Garcia-Gonzalez M., Garcia-Saez M.I., Goffeau A., Guerreiro P., Hani J., Hansen M., Hebling U., Hernandez K., Heumann K., Hilger F., Hofmann B., Indge K.J., James C.M., Klima R., Koetter P., Kramer B., Kramer W., Lauquin G., Leuther H., Louis E.J., Maillier E., Marconi A., Martegani E., Mazon M.J., Mazzoni C., McReynolds A.D.K., Melchioretto P., Mewes H.-W., Minenkova O., Mueller-Auer S., Nawrocki A., Netter P., Neu R., Nombela C., Oliver S.G., Panzeri L., Paoluzi S., Plevani P., Portetelle D., Portillo F., Potier S., Purnelle B., Rieger M., Riles L., Rinaldi T., Robben J., Rodrigues-Pousada C., Rodriguez-Belmonte E., Rodriguez-Torres A.M., Rose M., Ruzzi M., Saliola M., Sanchez-Perez M., Schaefer B., Schaefer M., Scharfe M., Schmidheini T., Schreer A., Skala J., Souciet J.-L., Steensma H.Y., Talla E., Thierry A., Vandenbol M., van der Aart Q.J.M., Van Dyck L., Vanoni M., Verhasselt P., Voet M., Volckaert G., Wambutt R., Watson M.D., Weber N., Wedler E., Wedler H., Wipfli P., Wolf K., Wright L.F., Zaccaria P., Zimmermann M., Zollner A., Kleine K. Nature 387:81-84(1997) [PubMed: 9169869] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[3]	"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae." Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F., Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J. , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J. Genome Res. 17:536-543(2007) [PubMed: 17322287] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[4]	"Saccharomyces cerevisiae RAI1 (YGL246c) is homologous to human DOM3Z and encodes a protein that binds the nuclear exoribonuclease Rat1p." Xue Y., Bai X., Lee I., Kallstrom G., Ho J., Brown J., Stevens A., Johnson A.W. Mol. Cell. Biol. 20:4006-4015(2000) [PubMed: 10805743] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-17, FUNCTION, INTERACTION WITH RAT1.
[5]	"Intersection of the Kap123p-mediated nuclear import and ribosome export pathways." Sydorskyy Y., Dilworth D.J., Yi E.C., Goodlett D.R., Wozniak R.W., Aitchison J.D. Mol. Cell. Biol. 23:2042-2054(2003) [PubMed: 12612077] [Abstract] Cited for: FUNCTION, INTERACTION WITH RAT1 AND PRE-60S RIBOSOMAL SUBUNITS, SUBCELLULAR LOCATION.
[6]	"Degradation of normal mRNA in the nucleus of Saccharomyces cerevisiae." Das B., Butler J.S., Sherman F. Mol. Cell. Biol. 23:5502-5515(2003) [PubMed: 12897126] [Abstract] Cited for: FUNCTION.
[7]	"Global analysis of protein expression in yeast." Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S. Nature 425:737-741(2003) [PubMed: 14562106] [Abstract] Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[8]	"The yeast Rat1 exonuclease promotes transcription termination by RNA polymerase II." Kim M., Krogan N.J., Vasiljeva L., Rando O.J., Nedea E., Greenblatt J.F., Buratowski S. Nature 432:517-522(2004) [PubMed: 15565157] [Abstract] Cited for: FUNCTION, IDENTIFICATION BY MASS SPECTROMETRY, IDENTIFICATION IN A COMPLEX WITH RTT103.
[9]	Erratum Kim M., Krogan N.J., Vasiljeva L., Rando O.J., Nedea E., Greenblatt J.F., Buratowski S. Nature 433:661-661(2005)
[10]	"Rat1p and Rai1p function with the nuclear exosome in the processing and degradation of rRNA precursors." Fang F., Phillips S., Butler J.S. RNA 11:1571-1578(2005) [PubMed: 16131592] [Abstract] Cited for: FUNCTION.
[11]	"A multidimensional chromatography technology for in-depth phosphoproteome analysis." Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H. Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed: 18407956] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-198, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBLGenBankDDBJ	X94357 Genomic DNA. Translation: CAA64141.1. Z72768 Genomic DNA. Translation: CAA96966.1. AY693165 Genomic DNA. Translation: AAT93184.1.
PIR	S61615.
RefSeq	NP_011268.1.
3D structure databases
ModBase	Search...
Protein-protein interaction databases
DIP	DIP:6807N.
IntAct	P53063.
Proteomic databases
PeptideAtlas	P53063.
Genome annotation databases
Ensembl	YGL246C. Saccharomyces cerevisiae. [Contig view]
GeneID	852646.
GenomeReviews	Gene locus YGL246C in contig Y13135_GR.
KEGG	sce:YGL246C.
NMPDR	fig|4932.3.peg.2371.
Organism-specific databases
CYGD	YGL246c.
SGD	S000003215. RAI1.
Yeast-GFP	Search...
Phylogenomic databases
HOGENOM	P53063.
Gene expression databases
ArrayExpress	P53063.
GermOnline	YGL246C. Saccharomyces cerevisiae.
Family and domain databases
InterPro	IPR013961. RAI1. [Graphical view]
Pfam	PF08652. RAI1. 1 hit. [Graphical view]
ProDom	P53063. [Graphical view] [Entries sharing at least one domain]
BLOCKS	Search...
Other Resources
LinkHub	P53063.
ProtoNet	Search...

Entry information

Entry name

DOM3Z_YEAST

Accession

Primary (citable) accession number: P53063

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1996
Last sequence update:	January 23, 2007
Last modified:	September 2, 2008
This is version 62 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

FPAP (Fungal Proteome Annotation Project)