P38351 (PAF1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
RNA polymerase II-associated protein 1

Alternative name(s):
Protein PAF1

Gene names

Name:	PAF1
Ordered Locus Names:	YBR279W
ORF Names:	YBR2016

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	445 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 the RAD6/UBC2-BRE1 ubiquitin ligase complex, which ubiquitinates histone H2B to form H2BK123ub1. Also required for the methylation of histone H3 by the COMPASS complex to form H3K4me, by SET2 to form H3K36me, and by DOT1 to form H3K79me. RNA polymerase II associated protein important for transcription of a subset of genes. Required for both positive and negative regulation. Negatively regulates MAK16 expression. Also required for efficient CLN2 transcription in late G1 and may be involved in transcription of galactose-inducible genes. Ref.6 Ref.10 Ref.11
Subunit structure	Component of the PAF1 complex which consists of at least CDC73, CTR9, LEO1, PAF1 and RTF1. Interacts with FACT subunits POB3 and SPT16. Ref.6 Ref.7 Ref.8
Subcellular location	Nucleus › nucleoplasm Ref.10.
Miscellaneous	Present with 1040 molecules/cell in log phase SD medium.
Sequence similarities	Belongs to the PAF1 family.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Cellular component	Nucleus
Molecular function	Activator Repressor
PTM	Phosphoprotein
Technical term	Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	chromatin silencing at rDNA Inferred from mutant phenotype PubMed 16582434. Source: SGD global genome nucleotide-excision repair Inferred from mutant phenotype PubMed 21737840. Source: SGD mRNA 3'-end processing Inferred from mutant phenotype PubMed 15149594. Source: SGD negative regulation of DNA recombination Inferred from mutant phenotype PubMed 9891041. Source: SGD negative regulation of transcription from RNA polymerase II promoter Inferred from mutant phenotype PubMed 15180994. Source: SGD positive regulation of histone H3-K36 trimethylation Inferred from mutant phenotype PubMed 17948059. 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 rRNA processing Inferred from mutant phenotype PubMed 20299458. Source: SGD regulation of chromatin silencing at telomere Inferred from mutant phenotype PubMed 12667454PubMed 18194564. 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 12876294PubMed 15180994. Source: SGD regulation of transcription by chromatin organization Inferred from mutant phenotype PubMed 18194564. Source: SGD regulation of transcription involved in G1 phase of mitotic cell cycle Inferred from mutant phenotype Ref.6. 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.11. Source: SGD snoRNA transcription from an RNA polymerase II promoter Inferred from mutant phenotype Ref.11. Source: SGD transcription elongation from RNA polymerase I promoter Inferred from mutant phenotype PubMed 19164765. 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.7PubMed 11927560PubMed 9032243. Source: SGD transcriptionally active chromatin Inferred from direct assay PubMed 11983171. Source: SGD
Molecular_function	RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity Inferred from direct assay PubMed 16581788. Source: SGD TFIIF-class binding transcription factor activity Inferred from mutant phenotype PubMed 9032243. Source: SGD chromatin binding Inferred from direct assay PubMed 11983171. Source: SGD
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
CDC73	Q06697	6	EBI-12855,EBI-29913
CTR9	P89105	6	EBI-12855,EBI-5283
LEO1	P38439	5	EBI-12855,EBI-10108
RTF1	P53064	9	EBI-12855,EBI-16303
SLT2	Q00772	2	EBI-12855,EBI-17372

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 445	445	RNA polymerase II-associated protein 1		PRO_0000058174
Regions
	Compositional bias	363 – 445	83	Asp/Glu-rich (acidic)
Amino acid modifications
	Modified residue	32	1	Phosphoserine Ref.16
	Modified residue	35	1	Phosphothreonine Ref.16
	Modified residue	147	1	Phosphoserine Ref.12 Ref.13 Ref.14 Ref.15 Ref.16
	Modified residue	388	1	Phosphoserine Ref.16
	Modified residue	422	1	Phosphothreonine Ref.15

Sequences

	Sequence		Length	Mass (Da)
	P38351 [UniParc]. Last modified October 1, 1994. Version 1. Checksum: 46FB5AB37C3C1AAE	FASTA	445	51,801
	10 20 30 40 50 60 MSKKQEYIAP IKYQNSLPVP QLPPKLLVYP ESPETNADSS QLINSLYIKT NVTNLIQQDE 70 80 90 100 110 120 DLGMPVDLMK FPGLLNKLDS KLLYGFDNVK LDKDDRILLR DPRIDRLTKT DISKVTFLRR 130 140 150 160 170 180 TEYVSNTIAA HDNTSLKRKR RLDDGDSDDE NLDVNHIISR VEGTFNKTDK WQHPVKKGVK 190 200 210 220 230 240 MVKKWDLLPD TASMDQVYFI LKFMGSASLD TKEKKSLNTG IFRPVELEED EWISMYATDH 250 260 270 280 290 300 KDSAILENEL EKGMDEMDDD SHEGKIYKFK RIRDYDMKQV AEKPMTELAI RLNDKDGIAY 310 320 330 340 350 360 YKPLRSKIEL RRRRVNDIIK PLVKEHDIDQ LNVTLRNPST KEANIRDKLR MKFDPINFAT 370 380 390 400 410 420 VDEEDDEDEE QPEDVKKESE GDSKTEGSEQ EGENEKDEEI KQEKENEQDE ENKQDENRAA 430 440 DTPETSDAVH TEQKPEEEKE TLQEE

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The sequence of a 32,420 bp segment located on the right arm of chromosome II from Saccharomyces cerevisiae." Holmstroem K., Brandt T., Kallesoe T. Yeast 10:S47-S62(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[2]	"Complete DNA sequence of yeast chromosome II." Feldmann H., Aigle M., Aljinovic G., Andre B., Baclet M.C., Barthe C., Baur A., Becam A.-M., Biteau N., Boles E., Brandt T., Brendel M., Brueckner M., Bussereau F., Christiansen C., Contreras R., Crouzet M., Cziepluch C. , Demolis N., Delaveau T., Doignon F., Domdey H., Duesterhus S., Dubois E., Dujon B., El Bakkoury M., Entian K.-D., Feuermann M., Fiers W., Fobo G.M., Fritz C., Gassenhuber J., Glansdorff N., Goffeau A., Grivell L.A., de Haan M., Hein C., Herbert C.J., Hollenberg C.P., Holmstroem K., Jacq C., Jacquet M., Jauniaux J.-C., Jonniaux J.-L., Kallesoee T., Kiesau P., Kirchrath L., Koetter P., Korol S., Liebl S., Logghe M., Lohan A.J.E., Louis E.J., Li Z.Y., Maat M.J., Mallet L., Mannhaupt G., Messenguy F., Miosga T., Molemans F., Mueller S., Nasr F., Obermaier B., Perea J., Pierard A., Piravandi E., Pohl F.M., Pohl T.M., Potier S., Proft M., Purnelle B., Ramezani Rad M., Rieger M., Rose M., Schaaff-Gerstenschlaeger I., Scherens B., Schwarzlose C., Skala J., Slonimski P.P., Smits P.H.M., Souciet J.-L., Steensma H.Y., Stucka R., Urrestarazu L.A., van der Aart Q.J.M., Van Dyck L., Vassarotti A., Vetter I., Vierendeels F., Vissers S., Wagner G., de Wergifosse P., Wolfe K.H., Zagulski M., Zimmermann F.K., Mewes H.-W., Kleine K. EMBO J. 13:5795-5809(1994) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[3]	Saccharomyces Genome Database Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: ATCC 204508 / S288c.
[4]	"A novel collection of accessory factors associated with yeast RNA polymerase II." Wade P.A., Werel W., Fentzke R.C., Thompson N.E., Leykam J.F., Burgess R.R., Jaehning J.A., Burton Z.F. Protein Expr. Purif. 8:85-90(1996) [PubMed] [Europe PMC] [Abstract] Cited for: PROTEIN SEQUENCE OF 5-11 AND 419-426.
[5]	"Paf1p, an RNA polymerase II-associated factor in Saccharomyces cerevisiae, may have both positive and negative roles in transcription." Shi X., Finkelstein A., Wolf A.J., Wade P.A., Burton Z.F., Jaehning J.A. Mol. Cell. Biol. 16:669-676(1996) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION, CHARACTERIZATION.
[6]	"A role for Ctr9p and Paf1p in the regulation of G1 cyclin expression in yeast." Koch C., Wollmann P., Dahl M., Lottspeich F. Nucleic Acids Res. 27:2126-2134(1999) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, SUBUNIT.
[7]	"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.
[8]	"RNA polymerase II elongation factors of Saccharomyces cerevisiae: a targeted proteomics approach." Krogan N.J., Kim M., Ahn S.H., Zhong G., Kobor M.S., Cagney G., Emili A., Shilatifard A., Buratowski S., Greenblatt J.F. Mol. Cell. Biol. 22:6979-6992(2002) [PubMed] [Europe PMC] [Abstract] Cited for: INTERACTION WITH POB3 AND SPT16.
[9]	"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].
[10]	"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.
[11]	"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.
[12]	"Quantitative phosphoproteomics applied to the yeast pheromone signaling pathway." Gruhler A., Olsen J.V., Mohammed S., Mortensen P., Faergeman N.J., Mann M., Jensen O.N. Mol. Cell. Proteomics 4:310-327(2005) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-147, MASS SPECTROMETRY. Strain: YAL6B.
[13]	"Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae." Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P. J. Proteome Res. 6:1190-1197(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-147, MASS SPECTROMETRY. Strain: ADR376.
[14]	"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: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-147, MASS SPECTROMETRY.
[15]	"Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases." Smolka M.B., Albuquerque C.P., Chen S.H., Zhou H. Proc. Natl. Acad. Sci. U.S.A. 104:10364-10369(2007) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-147 AND THR-422, MASS SPECTROMETRY.
[16]	"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-32; THR-35; SER-147 AND SER-388, MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	X76053 Genomic DNA. Translation: CAA53642.1. Z36148 Genomic DNA. Translation: CAA85243.1. BK006936 Genomic DNA. Translation: DAA07394.1.
PIR	S44541.
RefSeq	NP_009838.1. NM_001178627.1.
3D structure databases
ProteinModelPortal	P38351.
ModBase	Search...
Protein-protein interaction databases
DIP	DIP-1149N.
IntAct	P38351. 10 interactions.
MINT	MINT-600620.
STRING	4932.YBR279W.
Proteomic databases
PaxDb	P38351.
PeptideAtlas	P38351.
PRIDE	P38351.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblFungi	YBR279W; YBR279W; YBR279W.
GeneID	852582.
KEGG	sce:YBR279W.
Organism-specific databases
CYGD	YBR279w.
SGD	S000000483. PAF1.
Phylogenomic databases
eggNOG	NOG276051.
GeneTree	ENSGT00390000001474.
HOGENOM	HOG000000738.
KO	K15174.
OMA	LEEDEWI.
OrthoDB	EOG40S3R0.
Gene expression databases
Genevestigator	P38351.
GermOnline	YBR279W. Saccharomyces cerevisiae.
Family and domain databases
InterPro	IPR007133. RNA_pol_II-assoc_Paf1. [Graphical view]
PANTHER	PTHR23188. PTHR23188. 1 hit.
Pfam	PF03985. Paf1. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	971727.

Entry information

Entry name

PAF1_YEAST

Accession

Primary (citable) accession number: P38351
Secondary accession number(s): D6VQS4, Q9URC9

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 1, 1994
Last sequence update:	October 1, 1994
Last modified:	April 3, 2013
This is version 120 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program