ID PAF1_YEAST Reviewed; 445 AA. AC P38351; D6VQS4; Q9URC9; DT 01-OCT-1994, integrated into UniProtKB/Swiss-Prot. DT 01-OCT-1994, sequence version 1. DT 04-NOV-2026, entry version 211. DE RecName: Full=RNA polymerase II-associated protein 1; DE AltName: Full=Protein PAF1; GN Name=PAF1; OrderedLocusNames=YBR279W; ORFNames=YBR2016; OS Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast). OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; OC Saccharomycetales; Saccharomycetaceae; Saccharomyces. OX NCBI_TaxID=559292; RN [1] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA]. RC STRAIN=ATCC 204508 / S288c; RX PubMed=8091861; DOI=10.1002/yea.320100007; RA Holmstroem K., Brandt T., Kallesoe T.; RT "The sequence of a 32,420 bp segment located on the right arm of chromosome RT II from Saccharomyces cerevisiae."; RL Yeast 10:S47-S62(1994). RN [2] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=ATCC 204508 / S288c; RX PubMed=7813418; DOI=10.1002/j.1460-2075.1994.tb06923.x; RA Feldmann H., Aigle M., Aljinovic G., Andre B., Baclet M.C., Barthe C., RA Baur A., Becam A.-M., Biteau N., Boles E., Brandt T., Brendel M., RA Brueckner M., Bussereau F., Christiansen C., Contreras R., Crouzet M., RA Cziepluch C., Demolis N., Delaveau T., Doignon F., Domdey H., RA Duesterhus S., Dubois E., Dujon B., El Bakkoury M., Entian K.-D., RA Feuermann M., Fiers W., Fobo G.M., Fritz C., Gassenhuber J., Glansdorff N., RA Goffeau A., Grivell L.A., de Haan M., Hein C., Herbert C.J., RA Hollenberg C.P., Holmstroem K., Jacq C., Jacquet M., Jauniaux J.-C., RA Jonniaux J.-L., Kallesoee T., Kiesau P., Kirchrath L., Koetter P., RA Korol S., Liebl S., Logghe M., Lohan A.J.E., Louis E.J., Li Z.Y., RA Maat M.J., Mallet L., Mannhaupt G., Messenguy F., Miosga T., Molemans F., RA Mueller S., Nasr F., Obermaier B., Perea J., Pierard A., Piravandi E., RA Pohl F.M., Pohl T.M., Potier S., Proft M., Purnelle B., Ramezani Rad M., RA Rieger M., Rose M., Schaaff-Gerstenschlaeger I., Scherens B., RA Schwarzlose C., Skala J., Slonimski P.P., Smits P.H.M., Souciet J.-L., RA Steensma H.Y., Stucka R., Urrestarazu L.A., van der Aart Q.J.M., RA Van Dyck L., Vassarotti A., Vetter I., Vierendeels F., Vissers S., RA Wagner G., de Wergifosse P., Wolfe K.H., Zagulski M., Zimmermann F.K., RA Mewes H.-W., Kleine K.; RT "Complete DNA sequence of yeast chromosome II."; RL EMBO J. 13:5795-5809(1994). RN [3] RP GENOME REANNOTATION. RC STRAIN=ATCC 204508 / S288c; RX PubMed=24374639; DOI=10.1534/g3.113.008995; RA Engel S.R., Dietrich F.S., Fisk D.G., Binkley G., Balakrishnan R., RA Costanzo M.C., Dwight S.S., Hitz B.C., Karra K., Nash R.S., Weng S., RA Wong E.D., Lloyd P., Skrzypek M.S., Miyasato S.R., Simison M., Cherry J.M.; RT "The reference genome sequence of Saccharomyces cerevisiae: Then and now."; RL G3 (Bethesda) 4:389-398(2014). RN [4] RP PROTEIN SEQUENCE OF 5-11 AND 419-426. RX PubMed=8812838; DOI=10.1006/prep.1996.0077; RA Wade P.A., Werel W., Fentzke R.C., Thompson N.E., Leykam J.F., RA Burgess R.R., Jaehning J.A., Burton Z.F.; RT "A novel collection of accessory factors associated with yeast RNA RT polymerase II."; RL Protein Expr. Purif. 8:85-90(1996). RN [5] RP IDENTIFICATION, AND CHARACTERIZATION. RX PubMed=8552095; DOI=10.1128/mcb.16.2.669; RA Shi X., Finkelstein A., Wolf A.J., Wade P.A., Burton Z.F., Jaehning J.A.; RT "Paf1p, an RNA polymerase II-associated factor in Saccharomyces cerevisiae, RT may have both positive and negative roles in transcription."; RL Mol. Cell. Biol. 16:669-676(1996). RN [6] RP FUNCTION, AND SUBUNIT. RX PubMed=10219085; DOI=10.1093/nar/27.10.2126; RA Koch C., Wollmann P., Dahl M., Lottspeich F.; RT "A role for Ctr9p and Paf1p in the regulation of G1 cyclin expression in RT yeast."; RL Nucleic Acids Res. 27:2126-2134(1999). RN [7] RP IDENTIFICATION IN THE PAF1 COMPLEX. RX PubMed=11884586; DOI=10.1128/mcb.22.7.1971-1980.2002; RA Mueller C.L., Jaehning J.A.; RT "Ctr9, Rtf1, and Leo1 are components of the Paf1/RNA polymerase II RT complex."; RL Mol. Cell. Biol. 22:1971-1980(2002). RN [8] RP INTERACTION WITH POB3 AND SPT16. RX PubMed=12242279; DOI=10.1128/mcb.22.20.6979-6992.2002; RA Krogan N.J., Kim M., Ahn S.H., Zhong G., Kobor M.S., Cagney G., Emili A., RA Shilatifard A., Buratowski S., Greenblatt J.F.; RT "RNA polymerase II elongation factors of Saccharomyces cerevisiae: a RT targeted proteomics approach."; RL Mol. Cell. Biol. 22:6979-6992(2002). RN [9] RP LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS]. RX PubMed=14562106; DOI=10.1038/nature02046; RA Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., RA O'Shea E.K., Weissman J.S.; RT "Global analysis of protein expression in yeast."; RL Nature 425:737-741(2003). RN [10] RP FUNCTION, AND SUBCELLULAR LOCATION. RX PubMed=15643076; DOI=10.1128/ec.4.1.209-220.2005; RA Porter S.E., Penheiter K.L., Jaehning J.A.; RT "Separation of the Saccharomyces cerevisiae Paf1 complex from RNA RT polymerase II results in changes in its subnuclear localization."; RL Eukaryot. Cell 4:209-220(2005). RN [11] RP FUNCTION. RX PubMed=16246725; DOI=10.1016/j.molcel.2005.08.026; RA Sheldon K.E., Mauger D.M., Arndt K.M.; RT "A requirement for the Saccharomyces cerevisiae Paf1 complex in snoRNA 3' RT end formation."; RL Mol. Cell 20:225-236(2005). RN [12] RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-147, AND IDENTIFICATION BY RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. RC STRAIN=ADR376; RX PubMed=17330950; DOI=10.1021/pr060559j; RA Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., RA Elias J.E., Gygi S.P.; RT "Large-scale phosphorylation analysis of alpha-factor-arrested RT Saccharomyces cerevisiae."; RL J. Proteome Res. 6:1190-1197(2007). RN [13] RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-147, AND IDENTIFICATION BY RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. RX PubMed=18407956; DOI=10.1074/mcp.m700468-mcp200; RA Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.; RT "A multidimensional chromatography technology for in-depth phosphoproteome RT analysis."; RL Mol. Cell. Proteomics 7:1389-1396(2008). RN [14] RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-147 AND THR-422, AND RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS]. RX PubMed=19779198; DOI=10.1126/science.1172867; RA Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.; RT "Global analysis of Cdk1 substrate phosphorylation sites provides insights RT into evolution."; RL Science 325:1682-1686(2009). CC -!- FUNCTION: The PAF1 complex is a multifunctional complex. Involved in CC transcription initiation via genetic interactions with TATA-binding CC proteins. Involved in elongation. It regulates 3'-end formation of CC snR47 by modulating the recruitment or stable association of NRD1 and CC NAB3 with RNA polymerase II. Also has a role in transcription-coupled CC histone modification. Required for activation of the RAD6/UBC2-BRE1 CC ubiquitin ligase complex, which ubiquitinates histone H2B to form CC H2BK123ub1. Also required for the methylation of histone H3 by the CC COMPASS complex to form H3K4me, by SET2 to form H3K36me, and by DOT1 to CC form H3K79me. RNA polymerase II associated protein important for CC transcription of a subset of genes. Required for both positive and CC negative regulation. Negatively regulates MAK16 expression. Also CC required for efficient CLN2 transcription in late G1 and may be CC involved in transcription of galactose-inducible genes. CC {ECO:0000269|PubMed:10219085, ECO:0000269|PubMed:15643076, CC ECO:0000269|PubMed:16246725}. CC -!- SUBUNIT: Component of the PAF1 complex which consists of at least CC CDC73, CTR9, LEO1, PAF1 and RTF1. Interacts with FACT subunits POB3 and CC SPT16. {ECO:0000269|PubMed:10219085, ECO:0000269|PubMed:11884586, CC ECO:0000269|PubMed:12242279}. CC -!- INTERACTION: CC P38351; Q06697: CDC73; NbExp=9; IntAct=EBI-12855, EBI-29913; CC P38351; P89105: CTR9; NbExp=6; IntAct=EBI-12855, EBI-5283; CC P38351; P38439: LEO1; NbExp=6; IntAct=EBI-12855, EBI-10108; CC P38351; P16370: RPB3; NbExp=2; IntAct=EBI-12855, EBI-15773; CC P38351; P53064: RTF1; NbExp=9; IntAct=EBI-12855, EBI-16303; CC P38351; Q00772: SLT2; NbExp=2; IntAct=EBI-12855, EBI-17372; CC -!- SUBCELLULAR LOCATION: Nucleus, nucleoplasm CC {ECO:0000269|PubMed:15643076}. CC -!- MISCELLANEOUS: Present with 1040 molecules/cell in log phase SD medium. CC {ECO:0000269|PubMed:14562106}. CC -!- SIMILARITY: Belongs to the PAF1 family. {ECO:0000305}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- DR EMBL; X76053; CAA53642.1; -; Genomic_DNA. DR EMBL; Z36148; CAA85243.1; -; Genomic_DNA. DR EMBL; BK006936; DAA07394.1; -; Genomic_DNA. DR PIR; S44541; S44541. DR RefSeq; NP_009838.1; NM_001178627.1. DR PDB; 5ZYP; X-ray; 2.53 A; A=34-103. DR PDB; 7DKH; X-ray; 2.90 A; B/F/J=1-103. DR AlphaFoldDB; P38351; -. DR SMR; P38351; -. DR BioGRID; 32973; 206. DR ComplexPortal; CPX-1726; PAF1 complex. DR DIP; DIP-1149N; -. DR FunCoup; P38351; 431. DR IntAct; P38351; 25. DR STRING; 4932.YBR279W; -. DR iPTMnet; P38351; -. DR PaxDb; 4932-YBR279W; -. DR PeptideAtlas; P38351; -. DR EnsemblFungi; YBR279W_mRNA; YBR279W; YBR279W. DR GeneID; 852582; -. DR KEGG; sce:YBR279W; -. DR AGR; SGD:S000000483; -. DR SGD; S000000483; PAF1. DR VEuPathDB; FungiDB:YBR279W; -. DR eggNOG; KOG2478; Eukaryota. DR HOGENOM; CLU_021991_3_1_1; -. DR InParanoid; P38351; -. DR OMA; AAWKAPK; -. DR OrthoDB; 10260285at2759; -. DR BioCyc; YEAST:G3O-29199-MONOMER; -. DR BioGRID-ORCS; 852582; 3 hits in 10 CRISPR screens. DR PRO; PR:P38351; -. DR Proteomes; UP000002311; Chromosome II. DR RNAct; P38351; protein. DR GO; GO:0016593; C:Cdc73/Paf1 complex; IPI:SGD. DR GO; GO:0000791; C:euchromatin; IDA:SGD. DR GO; GO:0005634; C:nucleus; IDA:SGD. DR GO; GO:0003682; F:chromatin binding; IDA:SGD. DR GO; GO:1990269; F:RNA polymerase II C-terminal domain phosphoserine binding; IDA:SGD. DR GO; GO:0000993; F:RNA polymerase II complex binding; IPI:SGD. DR GO; GO:0006353; P:DNA-templated transcription termination; IMP:SGD. DR GO; GO:0000082; P:G1/S transition of mitotic cell cycle; IMP:SGD. DR GO; GO:0070911; P:global genome nucleotide-excision repair; IMP:SGD. DR GO; GO:0031124; P:mRNA 3'-end processing; IMP:SGD. DR GO; GO:0045910; P:negative regulation of DNA recombination; IMP:SGD. DR GO; GO:1901525; P:negative regulation of mitophagy; IMP:SGD. DR GO; GO:0000122; P:negative regulation of transcription by RNA polymerase II; IMP:SGD. DR GO; GO:2001209; P:positive regulation of transcription elongation by RNA polymerase I; IDA:SGD. DR GO; GO:0032968; P:positive regulation of transcription elongation by RNA polymerase II; IMP:SGD. DR GO; GO:0000183; P:rDNA heterochromatin formation; IMP:SGD. DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IMP:SGD. DR GO; GO:0090262; P:regulation of transcription-coupled nucleotide-excision repair; IGI:SGD. DR GO; GO:0006364; P:rRNA processing; IMP:SGD. DR GO; GO:0031126; P:sno(s)RNA 3'-end processing; IMP:SGD. DR GO; GO:0009302; P:sno(s)RNA transcription; IMP:SGD. DR GO; GO:0001015; P:snoRNA transcription by RNA polymerase II; IDA:SGD. DR GO; GO:0006360; P:transcription by RNA polymerase I; IMP:SGD. DR GO; GO:0006383; P:transcription by RNA polymerase III; IMP:SGD. DR GO; GO:0006362; P:transcription elongation by RNA polymerase I; IMP:SGD. DR GO; GO:0006368; P:transcription elongation by RNA polymerase II; IMP:SGD. DR InterPro; IPR007133; RNA_pol_II-assoc_Paf1. DR PANTHER; PTHR23188; RNA POLYMERASE II-ASSOCIATED FACTOR 1 HOMOLOG; 1. DR PANTHER; PTHR23188:SF12; RNA POLYMERASE II-ASSOCIATED FACTOR 1 HOMOLOG; 1. DR Pfam; PF03985; Paf1; 1. PE 1: Evidence at protein level; KW 3D-structure; Activator; Direct protein sequencing; Nucleus; KW Phosphoprotein; Reference proteome; Repressor; Transcription; KW Transcription regulation. FT CHAIN 1..445 FT /note="RNA polymerase II-associated protein 1" FT /id="PRO_0000058174" FT REGION 358..445 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 361..372 FT /note="Acidic residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 373..387 FT /note="Basic and acidic residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 388..397 FT /note="Acidic residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 414..445 FT /note="Basic and acidic residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT MOD_RES 147 FT /note="Phosphoserine" FT /evidence="ECO:0007744|PubMed:17330950, FT ECO:0007744|PubMed:18407956, ECO:0007744|PubMed:19779198" FT MOD_RES 422 FT /note="Phosphothreonine" FT /evidence="ECO:0007744|PubMed:19779198" FT HELIX 28..31 FT /evidence="ECO:0007829|PDB:7DKH" FT HELIX 33..35 FT /evidence="ECO:0007829|PDB:7DKH" FT HELIX 43..56 FT /evidence="ECO:0007829|PDB:5ZYP" FT TURN 60..63 FT /evidence="ECO:0007829|PDB:5ZYP" FT HELIX 68..70 FT /evidence="ECO:0007829|PDB:5ZYP" FT HELIX 74..77 FT /evidence="ECO:0007829|PDB:5ZYP" FT HELIX 81..84 FT /evidence="ECO:0007829|PDB:5ZYP" FT HELIX 93..96 FT /evidence="ECO:0007829|PDB:5ZYP" FT HELIX 97..99 FT /evidence="ECO:0007829|PDB:5ZYP" SQ SEQUENCE 445 AA; 51801 MW; 46FB5AB37C3C1AAE CRC64; MSKKQEYIAP IKYQNSLPVP QLPPKLLVYP ESPETNADSS QLINSLYIKT NVTNLIQQDE DLGMPVDLMK FPGLLNKLDS KLLYGFDNVK LDKDDRILLR DPRIDRLTKT DISKVTFLRR TEYVSNTIAA HDNTSLKRKR RLDDGDSDDE NLDVNHIISR VEGTFNKTDK WQHPVKKGVK MVKKWDLLPD TASMDQVYFI LKFMGSASLD TKEKKSLNTG IFRPVELEED EWISMYATDH KDSAILENEL EKGMDEMDDD SHEGKIYKFK RIRDYDMKQV AEKPMTELAI RLNDKDGIAY YKPLRSKIEL RRRRVNDIIK PLVKEHDIDQ LNVTLRNPST KEANIRDKLR MKFDPINFAT VDEEDDEDEE QPEDVKKESE GDSKTEGSEQ EGENEKDEEI KQEKENEQDE ENKQDENRAA DTPETSDAVH TEQKPEEEKE TLQEE //