P53064 (RTF1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
RNA polymerase-associated protein RTF1

Gene names

Name:	RTF1
Synonyms:	CSL3
Ordered Locus Names:	YGL244W
ORF Names:	HRA458

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	558 AA.
Sequence status	Complete.
Protein existence	Evidence 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	Nucleus › nucleoplasm 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 process	Transcription Transcription regulation
Cellular component	Nucleus
Molecular function	Activator
PTM	Phosphoprotein
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	DNA-dependent transcription, initiation Inferred from electronic annotation. Source: InterPro global genome nucleotide-excision repair Inferred from mutant phenotype PubMed 21737840. Source: SGD histone modification Inferred from electronic annotation. Source: InterPro 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 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 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_component	Cdc73/Paf1 complex Inferred from physical interaction Ref.5PubMed 11927560. Source: SGD transcriptionally active chromatin Inferred from direct assay PubMed 12682017. Source: SGD
Molecular_function	DNA binding Inferred from electronic annotation. Source: InterPro RNA binding Inferred from direct assay PubMed 20732871. Source: SGD RNA polymerase II transcription factor binding transcription factor activity Inferred from physical interaction PubMed 11927560. Source: SGD
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
CTR9	P89105	10	EBI-16303,EBI-5283
LEO1	P38439	6	EBI-16303,EBI-10108
PAF1	P38351	9	EBI-16303,EBI-12855
SLT2	Q00772	2	EBI-16303,EBI-17372

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 558	558	RNA polymerase-associated protein RTF1		PRO_0000097512
Regions
	Domain	238 – 370	133	Plus3
	Compositional bias	72 – 76	5	Poly-Glu
Amino acid modifications
	Modified residue	17	1	Phosphoserine Ref.10
	Modified residue	69	1	Phosphotyrosine Ref.10
	Modified residue	71	1	Phosphoserine Ref.10
	Modified residue	477	1	Phosphoserine Ref.10

Sequences

	Sequence		Length	Mass (Da)
	P53064 [UniParc]. Last modified November 1, 1997. Version 2. Checksum: 13AECCEC6D63CED4	FASTA	558	65,869
	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

References

	« Hide 'large scale' referencesShow '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. , 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]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases 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]	"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; TYR-69; SER-71 AND SER-477, MASS SPECTROMETRY.
+	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.
PIR	S53936.
RefSeq	NP_011270.1. NM_001181110.1.
3D structure databases
ProteinModelPortal	P53064.
SMR	P53064. Positions 243-361.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-4065N.
IntAct	P53064. 17 interactions.
MINT	MINT-502955.
STRING	4932.YGL244W.
Proteomic databases
PaxDb	P53064.
PeptideAtlas	P53064.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YGL244W; YGL244W; YGL244W.
GeneID	852607.
KEGG	sce:YGL244W.
Organism-specific databases
CYGD	YGL244w.
SGD	S000003213. RTF1.
Phylogenomic databases
eggNOG	COG5296.
GeneTree	ENSGT00390000012493.
HOGENOM	HOG000065976.
KO	K15178.
OMA	YPLEGKY.
OrthoDB	EOG4WWVTN.
Gene expression databases
Genevestigator	P53064.
GermOnline	YGL244W. Saccharomyces cerevisiae.
Family and domain databases
InterPro	IPR004343. Plus-3. IPR018144. Plus3-dom_subgr. [Graphical view]
Pfam	PF03126. Plus-3. 1 hit. [Graphical view]
SMART	SM00719. Plus3. 1 hit. [Graphical view]
PROSITE	PS51360. PLUS3. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	971796.

Entry information

Entry name

RTF1_YEAST

Accession

Primary (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:	May 1, 2013
This is version 113 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program