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P38351

- PAF1_YEAST

UniProt

P38351 - PAF1_YEAST

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Protein

RNA polymerase II-associated protein 1

Gene

PAF1

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 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.3 Publications

GO - Molecular functioni

  1. chromatin binding Source: SGD
  2. RNA polymerase II core binding Source: SGD
  3. RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity Source: SGD
  4. RNA polymerase II C-terminal domain phosphoserine binding Source: SGD
  5. RNA polymerase II transcription factor binding transcription factor activity Source: SGD
  6. TFIIF-class binding transcription factor activity Source: SGD

GO - Biological processi

  1. chromatin silencing at rDNA Source: SGD
  2. DNA-templated transcription, termination Source: SGD
  3. global genome nucleotide-excision repair Source: SGD
  4. mRNA 3'-end processing Source: SGD
  5. negative regulation of DNA recombination Source: SGD
  6. negative regulation of transcription from RNA polymerase II promoter Source: SGD
  7. positive regulation of histone H3-K36 trimethylation Source: SGD
  8. positive regulation of phosphorylation of RNA polymerase II C-terminal domain serine 2 residues Source: SGD
  9. positive regulation of transcription elongation from RNA polymerase II promoter Source: SGD
  10. positive regulation of transcription elongation from RNA polymerase I promoter 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 phosphorylation of RNA polymerase II C-terminal domain serine 2 residues Source: SGD
  16. regulation of transcription by chromatin organization Source: SGD
  17. regulation of transcription-coupled nucleotide-excision repair Source: SGD
  18. regulation of transcription from RNA polymerase II promoter Source: SGD
  19. regulation of transcription involved in G1/S transition of mitotic cell cycle Source: SGD
  20. rRNA processing Source: SGD
  21. snoRNA 3'-end processing Source: SGD
  22. snoRNA transcription from an RNA polymerase II promoter Source: SGD
  23. transcription elongation from RNA polymerase II promoter Source: SGD
  24. transcription elongation from RNA polymerase I promoter Source: SGD
  25. transcription from RNA polymerase I promoter Source: SGD
Complete GO annotation...

Keywords - Molecular functioni

Activator, Repressor

Keywords - Biological processi

Transcription, Transcription regulation

Enzyme and pathway databases

BioCyciYEAST:G3O-29199-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
RNA polymerase II-associated protein 1
Alternative name(s):
Protein PAF1
Gene namesi
Name:PAF1
Ordered Locus Names:YBR279W
ORF Names:YBR2016
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
ProteomesiUP000002311: Chromosome II

Organism-specific databases

CYGDiYBR279w.
SGDiS000000483. PAF1.

Subcellular locationi

Nucleusnucleoplasm 1 Publication

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 – 445445RNA polymerase II-associated protein 1PRO_0000058174Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei147 – 1471Phosphoserine3 Publications
Modified residuei422 – 4221Phosphothreonine1 Publication

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP38351.
PaxDbiP38351.
PeptideAtlasiP38351.
PRIDEiP38351.

Expressioni

Gene expression databases

GenevestigatoriP38351.

Interactioni

Subunit structurei

Component of the PAF1 complex which consists of at least CDC73, CTR9, LEO1, PAF1 and RTF1. Interacts with FACT subunits POB3 and SPT16.3 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
CDC73Q066978EBI-12855,EBI-29913
CTR9P891056EBI-12855,EBI-5283
LEO1P384395EBI-12855,EBI-10108
RTF1P530649EBI-12855,EBI-16303
SLT2Q007722EBI-12855,EBI-17372

Protein-protein interaction databases

BioGridi32973. 144 interactions.
DIPiDIP-1149N.
IntActiP38351. 10 interactions.
MINTiMINT-600620.
STRINGi4932.YBR279W.

Structurei

3D structure databases

ProteinModelPortaliP38351.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi363 – 44583Asp/Glu-rich (acidic)Add
BLAST

Sequence similaritiesi

Belongs to the PAF1 family.Curated

Phylogenomic databases

eggNOGiNOG276051.
HOGENOMiHOG000000738.
InParanoidiP38351.
KOiK15174.
OMAiDEWISMY.
OrthoDBiEOG7F2534.

Family and domain databases

InterProiIPR007133. RNA_pol_II-assoc_Paf1.
[Graphical view]
PANTHERiPTHR23188. PTHR23188. 1 hit.
PfamiPF03985. Paf1. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P38351 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSKKQEYIAP IKYQNSLPVP QLPPKLLVYP ESPETNADSS QLINSLYIKT
60 70 80 90 100
NVTNLIQQDE DLGMPVDLMK FPGLLNKLDS KLLYGFDNVK LDKDDRILLR
110 120 130 140 150
DPRIDRLTKT DISKVTFLRR TEYVSNTIAA HDNTSLKRKR RLDDGDSDDE
160 170 180 190 200
NLDVNHIISR VEGTFNKTDK WQHPVKKGVK MVKKWDLLPD TASMDQVYFI
210 220 230 240 250
LKFMGSASLD TKEKKSLNTG IFRPVELEED EWISMYATDH KDSAILENEL
260 270 280 290 300
EKGMDEMDDD SHEGKIYKFK RIRDYDMKQV AEKPMTELAI RLNDKDGIAY
310 320 330 340 350
YKPLRSKIEL RRRRVNDIIK PLVKEHDIDQ LNVTLRNPST KEANIRDKLR
360 370 380 390 400
MKFDPINFAT VDEEDDEDEE QPEDVKKESE GDSKTEGSEQ EGENEKDEEI
410 420 430 440
KQEKENEQDE ENKQDENRAA DTPETSDAVH TEQKPEEEKE TLQEE
Length:445
Mass (Da):51,801
Last modified:October 1, 1994 - v1
Checksum:i46FB5AB37C3C1AAE
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X76053 Genomic DNA. Translation: CAA53642.1.
Z36148 Genomic DNA. Translation: CAA85243.1.
BK006936 Genomic DNA. Translation: DAA07394.1.
PIRiS44541.
RefSeqiNP_009838.1. NM_001178627.1.

Genome annotation databases

EnsemblFungiiYBR279W; YBR279W; YBR279W.
GeneIDi852582.
KEGGisce:YBR279W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X76053 Genomic DNA. Translation: CAA53642.1 .
Z36148 Genomic DNA. Translation: CAA85243.1 .
BK006936 Genomic DNA. Translation: DAA07394.1 .
PIRi S44541.
RefSeqi NP_009838.1. NM_001178627.1.

3D structure databases

ProteinModelPortali P38351.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

BioGridi 32973. 144 interactions.
DIPi DIP-1149N.
IntActi P38351. 10 interactions.
MINTi MINT-600620.
STRINGi 4932.YBR279W.

Proteomic databases

MaxQBi P38351.
PaxDbi P38351.
PeptideAtlasi P38351.
PRIDEi P38351.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblFungii YBR279W ; YBR279W ; YBR279W .
GeneIDi 852582.
KEGGi sce:YBR279W.

Organism-specific databases

CYGDi YBR279w.
SGDi S000000483. PAF1.

Phylogenomic databases

eggNOGi NOG276051.
HOGENOMi HOG000000738.
InParanoidi P38351.
KOi K15174.
OMAi DEWISMY.
OrthoDBi EOG7F2534.

Enzyme and pathway databases

BioCyci YEAST:G3O-29199-MONOMER.

Miscellaneous databases

NextBioi 971727.
PROi P38351.

Gene expression databases

Genevestigatori P38351.

Family and domain databases

InterProi IPR007133. RNA_pol_II-assoc_Paf1.
[Graphical view ]
PANTHERi PTHR23188. PTHR23188. 1 hit.
Pfami PF03985. Paf1. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

« Hide 'large scale' publications
  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. 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. 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. "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, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Strain: ADR376.
  13. "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-147, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  14. "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 SER-147 AND THR-422, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].

Entry informationi

Entry nameiPAF1_YEAST
AccessioniPrimary (citable) accession number: P38351
Secondary accession number(s): D6VQS4, Q9URC9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1994
Last sequence update: October 1, 1994
Last modified: October 29, 2014
This is version 134 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Miscellaneous

Present with 1040 molecules/cell in log phase SD medium.1 Publication

Keywords - Technical termi

Complete proteome, Direct protein sequencing, 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 II
    Yeast (Saccharomyces cerevisiae) chromosome II: entries and gene names

External Data

Dasty 3