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P53064 (RTF1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 123. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
RNA polymerase-associated protein RTF1
Gene names
Name:RTF1
Synonyms:CSL3
Ordered Locus Names:YGL244W
ORF Names:HRA458
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length558 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

The PAF1 complex is a multifunctional complex. Involved in transcription initiation via genetic interactions with TATA-binding proteins. Involved in elongation. It regulates 3'-end formation of snR47 by modulating the recruitment or stable association of NRD1 and NAB3 with RNA polymerase II. Also has a role in transcription-coupled histone modification. Required for activation of RAD6 ubiquitin conjugate and the BRE1 ubiquitin ligase which ubiquitinate 'Lys-126' histone H2B. Activates the SET1 histone methyltransferase complex for methylation of 'Lys-4' of histone H3 and for methylation of 'Lys-73' of histone H3 by DOT1 and 'Lys-36' of histone H3 by SET2. Important for TATA site selection by TBP. Directly or indirectly regulates the DNA-binding properties of SPT15, the TATA box-binding protein, and the relative activities of different TATA elements. Ref.8 Ref.9

Subunit structure

Component of the PAF1 complex which consists of at least CDC73, CTR9, LEO1, PAF1 and RTF1. Ref.5

Subcellular location

Nucleusnucleoplasm Ref.6 Ref.8.

Miscellaneous

Present with 6510 molecules/cell in log phase SD medium.

Sequence similarities

Contains 1 Plus3 domain.

Sequence caution

The sequence CAA89011.1 differs from that shown. Reason: Erroneous initiation.

Ontologies

Keywords
   Biological processTranscription
Transcription regulation
   Cellular componentNucleus
   Molecular functionActivator
   PTMPhosphoprotein
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processDNA-templated transcription, initiation

Inferred from electronic annotation. Source: InterPro

DNA-templated transcription, termination

Inferred from mutant phenotype PubMed 23109428. Source: SGD

global genome nucleotide-excision repair

Inferred from mutant phenotype PubMed 21737840. Source: SGD

histone modification

Inferred from electronic annotation. Source: InterPro

mRNA 3'-end processing

Inferred from mutant phenotype PubMed 15149594. Source: SGD

negative regulation of transcription from RNA polymerase II promoter

Inferred from mutant phenotype PubMed 15180994. Source: SGD

positive regulation of phosphorylation of RNA polymerase II C-terminal domain serine 2 residues

Inferred from mutant phenotype PubMed 18469135. Source: SGD

positive regulation of transcription elongation from RNA polymerase I promoter

Inferred from direct assay PubMed 20299458. Source: SGD

positive regulation of transcription elongation from RNA polymerase II promoter

Inferred from mutant phenotype PubMed 14710186. Source: SGD

recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex

Inferred from mutant phenotype PubMed 18469135. Source: SGD

regulation of chromatin silencing at telomere

Inferred from mutant phenotype PubMed 12667454PubMed 12876293. Source: SGD

regulation of histone H2B conserved C-terminal lysine ubiquitination

Inferred from direct assay PubMed 19531475. Source: SGD

regulation of histone H2B ubiquitination

Inferred from mutant phenotype PubMed 12876293PubMed 12876294. Source: SGD

regulation of histone H3-K4 methylation

Inferred from mutant phenotype PubMed 12667454PubMed 12876293PubMed 12876294PubMed 15180994. Source: SGD

regulation of histone H3-K79 methylation

Inferred from mutant phenotype PubMed 12876293. Source: SGD

regulation of phosphorylation of RNA polymerase II C-terminal domain serine 2 residues

Inferred from mutant phenotype PubMed 15149594. Source: SGD

regulation of transcription from RNA polymerase II promoter

Inferred from genetic interaction Ref.5. Source: SGD

regulation of transcription-coupled nucleotide-excision repair

Inferred from genetic interaction PubMed 21737840. Source: SGD

snoRNA 3'-end processing

Inferred from mutant phenotype Ref.9. Source: SGD

snoRNA transcription from an RNA polymerase II promoter

Inferred from mutant phenotype Ref.9. Source: SGD

transcription elongation from RNA polymerase II promoter

Inferred from mutant phenotype PubMed 11927560. Source: SGD

   Cellular_componentCdc73/Paf1 complex

Inferred from physical interaction Ref.5PubMed 11927560. Source: SGD

nucleus

Inferred from direct assay Ref.8. Source: SGD

transcriptionally active chromatin

Inferred from direct assay PubMed 12682017. Source: SGD

   Molecular_functionDNA binding

Inferred from electronic annotation. Source: InterPro

RNA binding

Inferred from direct assay PubMed 20732871. Source: SGD

RNA polymerase II C-terminal domain phosphoserine binding

Inferred from direct assay PubMed 22796944. Source: SGD

RNA polymerase II transcription factor binding transcription factor activity

Inferred from physical interaction PubMed 11927560. Source: SGD

protein binding

Inferred from physical interaction PubMed 11805826PubMed 11927560PubMed 12242279PubMed 16429126PubMed 19531475PubMed 21376235PubMed 22796944. Source: IntAct

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 558558RNA polymerase-associated protein RTF1
PRO_0000097512

Regions

Domain238 – 370133Plus3
Compositional bias72 – 765Poly-Glu

Amino acid modifications

Modified residue171Phosphoserine Ref.11
Modified residue691Phosphotyrosine Ref.12
Modified residue711Phosphoserine Ref.11 Ref.12
Modified residue4771Phosphoserine Ref.11

Sequences

Sequence LengthMass (Da)Tools
P53064 [UniParc].

Last modified November 1, 1997. Version 2.
Checksum: 13AECCEC6D63CED4

FASTA55865,869
        10         20         30         40         50         60 
MSDLDEDLLA LAGADESEEE DQVLTTTSAK RAKNNDQSLS KKRRIEVGSV EDDDEEDDYN 

        70         80         90        100        110        120 
PYSVGNADYG SEEEEEANPF PLEGKYKDES DREHLESLPE MERETLLFER SQIMQKYQER 

       130        140        150        160        170        180 
KLFRARGRDM KEQQQRAKND EDSRKTRAST RSTHATGHSD IKASKLSQLK KQRARKNRHY 

       190        200        210        220        230        240 
SDNEDEDDEE DYREEDYKDD EGSEYGDDEE YNPFDRRDTY DKREEVEWAE EEDEQDREPE 

       250        260        270        280        290        300 
ISDFNKLRIG RSFVAKFCFY PGFEDAVKGC YGRVNVGTDK RTGKTSYRMV RIERVFLQKP 

       310        320        330        340        350        360 
YNMGKFYTNQ YFGVTQGKDR KVFQMNYFSD GLFAEDEYQR YLRALDNSQM IKPSLHSLSN 

       370        380        390        400        410        420 
KTKEVMDFVN TPLTDKTTDE VVRHRMQFNK KLSGTNAVLE KTVLREKLQY AKETNNEKDI 

       430        440        450        460        470        480 
AKYSAQLRNF EKRMSVYEKH HENDQSDIKK LGELTSKNRK LNMSNIRNAE HVKKEDSNNF 

       490        500        510        520        530        540 
DSKSDPFSRL KTRTKVYYQE IQKEENAKAK EIAQQEKLQE DKDAKDKREK ELLVAQFRRL 

       550 
GGLERMVGEL DIKFDLKF 

« Hide

References

« Hide 'large scale' references
[1]"Identification of RTF1, a novel gene important for TATA site selection by TATA box-binding protein in Saccharomyces cerevisiae."
Stolinski L.A., Eisenmann D.M., Arndt K.M.
Mol. Cell. Biol. 17:4490-4500(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]"The sequence of an 11.1 kb DNA fragment between ADH4 and ADE5 on the left arm of chromosome VII, reveals the presence of eight open reading frames."
Vandenbol M., Durand P., Portetelle D., Hilger F.
Yeast 11:1519-1523(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[3]"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. expand/collapse author list , 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] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[4]"The reference genome sequence of Saccharomyces cerevisiae: Then and now."
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.
G3 (Bethesda) 4:389-398(2014) [PubMed] [Europe PMC] [Abstract]
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[5]"Ctr9, Rtf1, and Leo1 are components of the Paf1/RNA polymerase II complex."
Mueller C.L., Jaehning J.A.
Mol. Cell. Biol. 22:1971-1980(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION IN THE PAF1 COMPLEX.
[6]"Global analysis of protein localization in budding yeast."
Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., O'Shea E.K.
Nature 425:686-691(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
[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] [Europe PMC] [Abstract]
Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[8]"Separation of the Saccharomyces cerevisiae Paf1 complex from RNA polymerase II results in changes in its subnuclear localization."
Porter S.E., Penheiter K.L., Jaehning J.A.
Eukaryot. Cell 4:209-220(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, SUBCELLULAR LOCATION.
[9]"A requirement for the Saccharomyces cerevisiae Paf1 complex in snoRNA 3' end formation."
Sheldon K.E., Mauger D.M., Arndt K.M.
Mol. Cell 20:225-236(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[10]"Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry."
Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L., Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F.
Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[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] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-17; SER-71 AND SER-477, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[12]"Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT TYR-69 AND SER-71, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
U86702 Genomic DNA. Translation: AAB47535.1.
Z49149 Genomic DNA. Translation: CAA89011.1. Different initiation.
Z72766 Genomic DNA. Translation: CAA96963.1.
Z72767 Genomic DNA. Translation: CAA96965.1.
BK006941 Genomic DNA. Translation: DAA07875.1.
PIRS53936.
RefSeqNP_011270.1. NM_001181110.1.

3D structure databases

ProteinModelPortalP53064.
SMRP53064. Positions 243-361.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid32996. 323 interactions.
DIPDIP-4065N.
IntActP53064. 15 interactions.
MINTMINT-502955.
STRING4932.YGL244W.

Proteomic databases

MaxQBP53064.
PaxDbP53064.
PeptideAtlasP53064.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYGL244W; YGL244W; YGL244W.
GeneID852607.
KEGGsce:YGL244W.

Organism-specific databases

CYGDYGL244w.
SGDS000003213. RTF1.

Phylogenomic databases

eggNOGCOG5296.
GeneTreeENSGT00390000012493.
HOGENOMHOG000065976.
KOK15178.
OMASEMKPVN.
OrthoDBEOG7PVWZJ.

Enzyme and pathway databases

BioCycYEAST:G3O-30715-MONOMER.

Gene expression databases

GenevestigatorP53064.

Family and domain databases

InterProIPR004343. Plus-3.
IPR018144. Plus3-dom_subgr.
[Graphical view]
PfamPF03126. Plus-3. 1 hit.
[Graphical view]
SMARTSM00719. Plus3. 1 hit.
[Graphical view]
PROSITEPS51360. PLUS3. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

NextBio971796.
PROP53064.

Entry information

Entry nameRTF1_YEAST
AccessionPrimary (citable) accession number: P53064
Secondary accession number(s): D6VV91, P89115
Entry history
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: November 1, 1997
Last modified: June 11, 2014
This is version 123 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome VII

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

Yeast

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

SIMILARITY comments

Index of protein domains and families