RAT1-interacting protein - Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

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P53063 (DOM3Z_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified December 14, 2011. Version 91. History...

Clusters with 100%, 90%, 50% identity |

Documents (3) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
RAT1-interacting protein

Gene names

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

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)

Taxonomic identifier

559292 [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	Possesses pyrophosphohydrolase activity towards 5' triphosphorylated RNA By similarity. Stimulates exoribonuclease activity of RAT1, allowing it to degrade RNAs with stable secondary structure more effectively. Required for the processing of nuclear mRNA and rRNA precursors. May promote termination of transcription by RNA polymerase II. Ref.5 Ref.6 Ref.7 Ref.9 Ref.11
Subunit structure	Interacts with RAT1, RTT103 and pre-60S ribosomal subunits. Ref.5 Ref.6
Subcellular location	Nucleus Ref.6.
Miscellaneous	Present with 4030 molecules/cell in log phase SD medium. Ref.8
Sequence similarities	Belongs to the Dom3Z family.

Ontologies

Keywords
Biological process	Transcription Transcription regulation Transcription termination mRNA processing rRNA processing
Cellular component	Nucleus
Ligand	Metal-binding Nucleotide-binding
PTM	Phosphoprotein
Technical term	Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological process	deadenylation-dependent decapping of nuclear-transcribed mRNA Inferred from direct assay. Source: SGD mRNA processing Inferred from electronic annotation. Source: UniProtKB-KW maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Inferred from mutant phenotype Ref.5. Source: SGD maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Inferred from mutant phenotype Ref.5. Source: SGD regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW termination of RNA polymerase II transcription, poly(A)-coupled Inferred from mutant phenotype Ref.9. Source: SGD
Cellular component	nucleus Inferred from direct assay Ref.6. Source: SGD
Molecular function	enzyme regulator activity Inferred from direct assay Ref.5. Source: SGD m7G(5')pppN diphosphatase activity Inferred from direct assay. Source: SGD metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW nucleotide binding Inferred from electronic annotation. Source: UniProtKB-KW protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
RAT1	Q02792	5	EBI-24206,EBI-14845

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

Removed Ref.5

Chain

2 – 387

386

RAT1-interacting protein

PRO_0000202708

Regions

Region

273 – 387

115

Interaction with RAT1

Sites

Metal binding

172

Divalent metal cation By similarity

Metal binding

223

Divalent metal cation By similarity

Metal binding

241

Divalent metal cation By similarity

Metal binding

242

Divalent metal cation; via carbonyl oxygen By similarity

Binding site

105

GDP By similarity

Binding site

221

GDP By similarity

Binding site

267

GDP By similarity

Amino acid modifications

Modified residue

198

Phosphoserine Ref.12

Experimental info

Sequence conflict

F → S AA sequence Ref.5

Sequences

Sequence

Length

Mass (Da)

Tools

P53063 [UniParc].

Last modified January 23, 2007. Version 3.
Checksum: E4A6565AF690A3E1
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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

« Hide

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. Kleine K. Nature 387:81-84(1997) [PubMed: 9169869] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 96604 / S288c / FY1679.
[3]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[4]	"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. LaBaer J. Genome Res. 17:536-543(2007) [PubMed: 17322287] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[5]	"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.
[6]	"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.
[7]	"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.
[8]	"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].
[9]	"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.
[10]	Erratum Kim M., Krogan N.J., Vasiljeva L., Rando O.J., Nedea E., Greenblatt J.F., Buratowski S. Nature 433:661-661(2005)
[11]	"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.
[12]	"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
EMBL GenBank DDBJ	X94357 Genomic DNA. Translation: CAA64141.1. Z72768 Genomic DNA. Translation: CAA96966.1. AY693165 Genomic DNA. Translation: AAT93184.1. BK006941 Genomic DNA. Translation: DAA07873.1.
PIR	S61615.
RefSeq	NP_011268.1. NM_001181112.1.
3D structure databases
ProteinModelPortal	P53063.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-6807N.
IntAct	P53063. 13 interactions.
MINT	MINT-616869.
STRING	P53063.
Proteomic databases
PeptideAtlas	P53063.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YGL246C; YGL246C; YGL246C.
GeneID	852646.
KEGG	sce:YGL246C.
NMPDR	fig\|4932.3.peg.2371.
Organism-specific databases
SGD	S000003215. RAI1.
Phylogenomic databases
eggNOG	fuNOG07875.
GeneTree	EFGT00050000006376.
HOGENOM	HBG395893.
OMA	CIFDFKE.
OrthoDB	EOG4D82FD.
Gene expression databases
ArrayExpress	P53063.
Genevestigator	P53063.
GermOnline	YGL246C. Saccharomyces cerevisiae.
Family and domain databases
InterPro	IPR013961. RAI1. [Graphical view]
KO	K14845.
Pfam	PF08652. RAI1. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	971909.

Entry information

Entry name

DOM3Z_YEAST

Accession

Primary (citable) accession number: P53063
Secondary accession number(s): D6VV89

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1996
Last sequence update:	January 23, 2007
Last modified:	December 14, 2011
This is version 91 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program

Relevant documents

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

Yeast chromosome VII

Yeast (Saccharomyces cerevisiae) chromosome VII: entries and gene names

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Regions

Sites

Amino acid modifications

Experimental info

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Gene expression databases

Family and domain databases

Other

Entry information

Relevant documents