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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: -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

Miscellaneous

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

GO - Molecular functioni

  • chromatin binding Source: SGD
  • RNA polymerase II core binding Source: SGD
  • RNA polymerase II C-terminal domain phosphoserine binding Source: SGD
  • transcription factor activity, RNA polymerase II core promoter sequence-specific DNA binding Source: SGD
  • transcription factor activity, RNA polymerase II transcription factor binding Source: SGD
  • transcription factor activity, TFIIF-class transcription factor binding Source: SGD

GO - Biological processi

  • chromatin silencing at rDNA Source: SGD
  • DNA-templated transcription, termination Source: SGD
  • global genome nucleotide-excision repair Source: SGD
  • histone modification Source: InterPro
  • mRNA 3'-end processing Source: SGD
  • negative regulation of DNA recombination Source: SGD
  • negative regulation of transcription by RNA polymerase II Source: SGD
  • positive regulation of histone H3-K36 trimethylation Source: SGD
  • positive regulation of phosphorylation of RNA polymerase II C-terminal domain serine 2 residues Source: SGD
  • positive regulation of transcription elongation from RNA polymerase II promoter Source: SGD
  • positive regulation of transcription elongation from RNA polymerase I promoter Source: SGD
  • regulation of chromatin silencing at telomere Source: SGD
  • regulation of histone H2B conserved C-terminal lysine ubiquitination Source: SGD
  • regulation of histone H2B ubiquitination Source: SGD
  • regulation of histone H3-K4 methylation Source: SGD
  • regulation of phosphorylation of RNA polymerase II C-terminal domain serine 2 residues Source: SGD
  • regulation of transcription by RNA polymerase II Source: SGD
  • regulation of transcription-coupled nucleotide-excision repair Source: SGD
  • regulation of transcription involved in G1/S transition of mitotic cell cycle Source: SGD
  • rRNA processing Source: SGD
  • snoRNA 3'-end processing Source: SGD
  • snoRNA transcription by RNA polymerase II Source: SGD
  • transcription by RNA polymerase I Source: SGD
  • transcription elongation from RNA polymerase II promoter Source: SGD
  • transcription elongation from RNA polymerase I promoter Source: SGD

Keywordsi

Molecular functionActivator, Repressor
Biological processTranscription, 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
Proteomesi
  • UP000002311 Componenti: Chromosome II

Organism-specific databases

EuPathDBiFungiDB:YBR279W
SGDiS000000483 PAF1

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000581741 – 445RNA polymerase II-associated protein 1Add BLAST445

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei147PhosphoserineCombined sources1
Modified residuei422PhosphothreonineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP38351
PaxDbiP38351
PRIDEiP38351

PTM databases

iPTMnetiP38351

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

Show more details

GO - Molecular functioni

  • RNA polymerase II core binding Source: SGD
  • RNA polymerase II C-terminal domain phosphoserine binding Source: SGD

Protein-protein interaction databases

BioGridi32973152 interactors.
DIPiDIP-1149N
IntActiP38351 24 interactors.
MINTiP38351
STRINGi4932.YBR279W

Structurei

3D structure databases

ProteinModelPortaliP38351
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi363 – 445Asp/Glu-rich (acidic)Add BLAST83

Sequence similaritiesi

Belongs to the PAF1 family.Curated

Phylogenomic databases

HOGENOMiHOG000000738
InParanoidiP38351
KOiK15174
OMAiDPRLDCA
OrthoDBiEOG092C46AS

Family and domain databases

InterProiView protein in InterPro
IPR007133 RNA_pol_II-assoc_Paf1
PANTHERiPTHR23188 PTHR23188, 1 hit
PfamiView protein in Pfam
PF03985 Paf1, 1 hit

Sequencei

Sequence statusi: Complete.

P38351-1 [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:
EMBLi
GenBanki
DDBJi
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

Similar proteinsi

Entry informationi

Entry nameiPAF1_YEAST
AccessioniPrimary (citable) accession number: P38351
Secondary accession number(s): D6VQS4, Q9URC9
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 1, 1994
Last sequence update: October 1, 1994
Last modified: March 28, 2018
This is version 165 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome