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P53064

- RTF1_YEAST

UniProt

P53064 - RTF1_YEAST

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Protein
RNA polymerase-associated protein RTF1
Gene
RTF1, CSL3, YGL244W, HRA458
Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

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.2 Publications

GO - Molecular functioni

  1. DNA binding Source: InterPro
  2. RNA binding Source: SGD
  3. RNA polymerase II C-terminal domain phosphoserine binding Source: SGD
  4. RNA polymerase II transcription factor binding transcription factor activity Source: SGD
  5. protein binding Source: IntAct

GO - Biological processi

  1. DNA-templated transcription, initiation Source: InterPro
  2. DNA-templated transcription, termination Source: SGD
  3. global genome nucleotide-excision repair Source: SGD
  4. histone modification Source: InterPro
  5. mRNA 3'-end processing Source: SGD
  6. negative regulation of transcription from RNA polymerase II promoter Source: SGD
  7. positive regulation of phosphorylation of RNA polymerase II C-terminal domain serine 2 residues Source: SGD
  8. positive regulation of transcription elongation from RNA polymerase I promoter Source: SGD
  9. positive regulation of transcription elongation from RNA polymerase II promoter Source: SGD
  10. recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex Source: SGD
  11. regulation of chromatin silencing at telomere Source: SGD
  12. regulation of histone H2B conserved C-terminal lysine ubiquitination Source: SGD
  13. regulation of histone H2B ubiquitination Source: SGD
  14. regulation of histone H3-K4 methylation Source: SGD
  15. regulation of histone H3-K79 methylation Source: SGD
  16. regulation of phosphorylation of RNA polymerase II C-terminal domain serine 2 residues Source: SGD
  17. regulation of transcription from RNA polymerase II promoter Source: SGD
  18. regulation of transcription-coupled nucleotide-excision repair Source: SGD
  19. snoRNA 3'-end processing Source: SGD
  20. snoRNA transcription from an RNA polymerase II promoter Source: SGD
  21. transcription elongation from RNA polymerase II promoter Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Activator

Keywords - Biological processi

Transcription, Transcription regulation

Enzyme and pathway databases

BioCyciYEAST:G3O-30715-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
RNA polymerase-associated protein RTF1
Gene namesi
Name:RTF1
Synonyms:CSL3
Ordered Locus Names:YGL244W
ORF Names:HRA458
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome VII

Organism-specific databases

CYGDiYGL244w.
SGDiS000003213. RTF1.

Subcellular locationi

Nucleusnucleoplasm 2 Publications

GO - Cellular componenti

  1. Cdc73/Paf1 complex Source: SGD
  2. nucleus Source: SGD
  3. transcriptionally active chromatin Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 558558RNA polymerase-associated protein RTF1
PRO_0000097512Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei17 – 171Phosphoserine1 Publication
Modified residuei69 – 691Phosphotyrosine1 Publication
Modified residuei71 – 711Phosphoserine2 Publications
Modified residuei477 – 4771Phosphoserine1 Publication

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP53064.
PaxDbiP53064.
PeptideAtlasiP53064.

Expressioni

Gene expression databases

GenevestigatoriP53064.

Interactioni

Subunit structurei

Component of the PAF1 complex which consists of at least CDC73, CTR9, LEO1, PAF1 and RTF1.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
CDC73Q0669710EBI-16303,EBI-29913
CTR9P8910510EBI-16303,EBI-5283
LEO1P384396EBI-16303,EBI-10108
PAF1P383519EBI-16303,EBI-12855
RPO21P040507EBI-16303,EBI-15760
SLT2Q007722EBI-16303,EBI-17372
SPT5P276925EBI-16303,EBI-17937

Protein-protein interaction databases

BioGridi32996. 326 interactions.
DIPiDIP-4065N.
IntActiP53064. 15 interactions.
MINTiMINT-502955.
STRINGi4932.YGL244W.

Structurei

3D structure databases

ProteinModelPortaliP53064.
SMRiP53064. Positions 243-361.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini238 – 370133Plus3
Add
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi72 – 765Poly-Glu

Sequence similaritiesi

Contains 1 Plus3 domain.

Phylogenomic databases

eggNOGiCOG5296.
GeneTreeiENSGT00390000012493.
HOGENOMiHOG000065976.
KOiK15178.
OMAiSEMKPVN.
OrthoDBiEOG7PVWZJ.

Family and domain databases

InterProiIPR004343. Plus-3.
IPR018144. Plus3-dom_subgr.
[Graphical view]
PfamiPF03126. Plus-3. 1 hit.
[Graphical view]
SMARTiSM00719. Plus3. 1 hit.
[Graphical view]
PROSITEiPS51360. PLUS3. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P53064-1 [UniParc]FASTAAdd to Basket

« Hide

MSDLDEDLLA LAGADESEEE DQVLTTTSAK RAKNNDQSLS KKRRIEVGSV    50
EDDDEEDDYN PYSVGNADYG SEEEEEANPF PLEGKYKDES DREHLESLPE 100
MERETLLFER SQIMQKYQER KLFRARGRDM KEQQQRAKND EDSRKTRAST 150
RSTHATGHSD IKASKLSQLK KQRARKNRHY SDNEDEDDEE DYREEDYKDD 200
EGSEYGDDEE YNPFDRRDTY DKREEVEWAE EEDEQDREPE ISDFNKLRIG 250
RSFVAKFCFY PGFEDAVKGC YGRVNVGTDK RTGKTSYRMV RIERVFLQKP 300
YNMGKFYTNQ YFGVTQGKDR KVFQMNYFSD GLFAEDEYQR YLRALDNSQM 350
IKPSLHSLSN KTKEVMDFVN TPLTDKTTDE VVRHRMQFNK KLSGTNAVLE 400
KTVLREKLQY AKETNNEKDI AKYSAQLRNF EKRMSVYEKH HENDQSDIKK 450
LGELTSKNRK LNMSNIRNAE HVKKEDSNNF DSKSDPFSRL KTRTKVYYQE 500
IQKEENAKAK EIAQQEKLQE DKDAKDKREK ELLVAQFRRL GGLERMVGEL 550
DIKFDLKF 558
Length:558
Mass (Da):65,869
Last modified:November 1, 1997 - v2
Checksum:i13AECCEC6D63CED4
GO

Sequence cautioni

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

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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.
PIRiS53936.
RefSeqiNP_011270.1. NM_001181110.1.

Genome annotation databases

EnsemblFungiiYGL244W; YGL244W; YGL244W.
GeneIDi852607.
KEGGisce:YGL244W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
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 .
PIRi S53936.
RefSeqi NP_011270.1. NM_001181110.1.

3D structure databases

ProteinModelPortali P53064.
SMRi P53064. Positions 243-361.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 32996. 326 interactions.
DIPi DIP-4065N.
IntActi P53064. 15 interactions.
MINTi MINT-502955.
STRINGi 4932.YGL244W.

Proteomic databases

MaxQBi P53064.
PaxDbi P53064.
PeptideAtlasi P53064.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YGL244W ; YGL244W ; YGL244W .
GeneIDi 852607.
KEGGi sce:YGL244W.

Organism-specific databases

CYGDi YGL244w.
SGDi S000003213. RTF1.

Phylogenomic databases

eggNOGi COG5296.
GeneTreei ENSGT00390000012493.
HOGENOMi HOG000065976.
KOi K15178.
OMAi SEMKPVN.
OrthoDBi EOG7PVWZJ.

Enzyme and pathway databases

BioCyci YEAST:G3O-30715-MONOMER.

Miscellaneous databases

NextBioi 971796.
PROi P53064.

Gene expression databases

Genevestigatori P53064.

Family and domain databases

InterProi IPR004343. Plus-3.
IPR018144. Plus3-dom_subgr.
[Graphical view ]
Pfami PF03126. Plus-3. 1 hit.
[Graphical view ]
SMARTi SM00719. Plus3. 1 hit.
[Graphical view ]
PROSITEi PS51360. PLUS3. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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.
    , 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. 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. Cited for: SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
  7. 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].

Entry informationi

Entry nameiRTF1_YEAST
AccessioniPrimary (citable) accession number: P53064
Secondary accession number(s): D6VV91, P89115
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: November 1, 1997
Last modified: September 3, 2014
This is version 124 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

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

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  3. Yeast chromosome VII
    Yeast (Saccharomyces cerevisiae) chromosome VII: entries and gene names

External Data

Dasty 3

Similar proteinsi