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P38351 (PAF1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified June 11, 2014. Version 131. 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 II-associated protein 1
Alternative name(s):
Protein PAF1
Gene names
Name:PAF1
Ordered Locus Names:YBR279W
ORF Names:YBR2016
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length445 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 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

Nucleusnucleoplasm Ref.10.

Miscellaneous

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

Sequence similarities

Belongs to the PAF1 family.

Ontologies

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

Inferred from mutant phenotype PubMed 23109428. Source: SGD

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 H2B ubiquitination

Inferred from mutant phenotype PubMed 12876294. Source: SGD

regulation of histone H3-K4 methylation

Inferred from mutant phenotype PubMed 12667454PubMed 12876294PubMed 15180994. 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 by chromatin organization

Inferred from mutant phenotype PubMed 18194564. Source: SGD

regulation of transcription from RNA polymerase II promoter

Inferred from mutant phenotype Ref.7. Source: SGD

regulation of transcription involved in G1/S transition 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 direct assay 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

transcription from RNA polymerase I promoter

Inferred from mutant phenotype PubMed 20299458. Source: SGD

   Cellular_componentCdc73/Paf1 complex

Inferred from physical interaction Ref.7PubMed 11927560PubMed 9032243. Source: SGD

nucleus

Inferred from direct assay PubMed 15149594Ref.10. Source: SGD

transcriptionally active chromatin

Inferred from direct assay PubMed 11983171. Source: SGD

   Molecular_functionRNA polymerase II C-terminal domain phosphoserine binding

Inferred from direct assay PubMed 22796944. Source: SGD

RNA polymerase II core binding

Inferred from physical interaction PubMed 16581788. Source: SGD

RNA polymerase II core promoter sequence-specific DNA binding transcription factor activity

Inferred from direct assay PubMed 16581788. Source: SGD

RNA polymerase II transcription factor binding transcription factor activity

Inferred from physical interaction PubMed 11927560PubMed 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

protein binding

Inferred from physical interaction PubMed 11805826PubMed 11927560Ref.8PubMed 16429126PubMed 18719252PubMed 19531475PubMed 21376235PubMed 22796944. Source: IntAct

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 445445RNA polymerase II-associated protein 1
PRO_0000058174

Regions

Compositional bias363 – 44583Asp/Glu-rich (acidic)

Amino acid modifications

Modified residue1471Phosphoserine Ref.12 Ref.13 Ref.14
Modified residue4221Phosphothreonine Ref.14

Sequences

Sequence LengthMass (Da)Tools
P38351 [UniParc].

Last modified October 1, 1994. Version 1.
Checksum: 46FB5AB37C3C1AAE

FASTA44551,801
        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 

« Hide

References

« Hide '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. expand/collapse author list , 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]"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.
[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]"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].
+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.
PIRS44541.
RefSeqNP_009838.1. NM_001178627.1.

3D structure databases

ProteinModelPortalP38351.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid32973. 143 interactions.
DIPDIP-1149N.
IntActP38351. 10 interactions.
MINTMINT-600620.
STRING4932.YBR279W.

Proteomic databases

MaxQBP38351.
PaxDbP38351.
PeptideAtlasP38351.
PRIDEP38351.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYBR279W; YBR279W; YBR279W.
GeneID852582.
KEGGsce:YBR279W.

Organism-specific databases

CYGDYBR279w.
SGDS000000483. PAF1.

Phylogenomic databases

eggNOGNOG276051.
HOGENOMHOG000000738.
KOK15174.
OMADEWISMY.
OrthoDBEOG7F2534.

Enzyme and pathway databases

BioCycYEAST:G3O-29199-MONOMER.

Gene expression databases

GenevestigatorP38351.

Family and domain databases

InterProIPR007133. RNA_pol_II-assoc_Paf1.
[Graphical view]
PANTHERPTHR23188. PTHR23188. 1 hit.
PfamPF03985. Paf1. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

NextBio971727.
PROP38351.

Entry information

Entry namePAF1_YEAST
AccessionPrimary (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: June 11, 2014
This is version 131 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome II

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

Yeast

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

SIMILARITY comments

Index of protein domains and families