ID   RTF1_YEAST              Reviewed;         558 AA.
AC   P53064; D6VV91; P89115;
DT   01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
DT   01-NOV-1997, sequence version 2.
DT   27-MAR-2024, entry version 194.
DE   RecName: Full=RNA polymerase-associated protein RTF1;
GN   Name=RTF1; Synonyms=CSL3; OrderedLocusNames=YGL244W; ORFNames=HRA458;
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].
RX   PubMed=9234706; DOI=10.1128/mcb.17.8.4490;
RA   Stolinski L.A., Eisenmann D.M., Arndt K.M.;
RT   "Identification of RTF1, a novel gene important for TATA site selection by
RT   TATA box-binding protein in Saccharomyces cerevisiae.";
RL   Mol. Cell. Biol. 17:4490-4500(1997).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=8750240; DOI=10.1002/yea.320111507;
RA   Vandenbol M., Durand P., Portetelle D., Hilger F.;
RT   "The sequence of an 11.1 kb DNA fragment between ADH4 and ADE5 on the left
RT   arm of chromosome VII, reveals the presence of eight open reading frames.";
RL   Yeast 11:1519-1523(1995).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 204508 / S288c;
RX   PubMed=9169869;
RA   Tettelin H., Agostoni-Carbone M.L., Albermann K., Albers M., Arroyo J.,
RA   Backes U., Barreiros T., Bertani I., Bjourson A.J., Brueckner M.,
RA   Bruschi C.V., Carignani G., Castagnoli L., Cerdan E., Clemente M.L.,
RA   Coblenz A., Coglievina M., Coissac E., Defoor E., Del Bino S., Delius H.,
RA   Delneri D., de Wergifosse P., Dujon B., Durand P., Entian K.-D., Eraso P.,
RA   Escribano V., Fabiani L., Fartmann B., Feroli F., Feuermann M.,
RA   Frontali L., Garcia-Gonzalez M., Garcia-Saez M.I., Goffeau A.,
RA   Guerreiro P., Hani J., Hansen M., Hebling U., Hernandez K., Heumann K.,
RA   Hilger F., Hofmann B., Indge K.J., James C.M., Klima R., Koetter P.,
RA   Kramer B., Kramer W., Lauquin G., Leuther H., Louis E.J., Maillier E.,
RA   Marconi A., Martegani E., Mazon M.J., Mazzoni C., McReynolds A.D.K.,
RA   Melchioretto P., Mewes H.-W., Minenkova O., Mueller-Auer S., Nawrocki A.,
RA   Netter P., Neu R., Nombela C., Oliver S.G., Panzeri L., Paoluzi S.,
RA   Plevani P., Portetelle D., Portillo F., Potier S., Purnelle B., Rieger M.,
RA   Riles L., Rinaldi T., Robben J., Rodrigues-Pousada C.,
RA   Rodriguez-Belmonte E., Rodriguez-Torres A.M., Rose M., Ruzzi M.,
RA   Saliola M., Sanchez-Perez M., Schaefer B., Schaefer M., Scharfe M.,
RA   Schmidheini T., Schreer A., Skala J., Souciet J.-L., Steensma H.Y.,
RA   Talla E., Thierry A., Vandenbol M., van der Aart Q.J.M., Van Dyck L.,
RA   Vanoni M., Verhasselt P., Voet M., Volckaert G., Wambutt R., Watson M.D.,
RA   Weber N., Wedler E., Wedler H., Wipfli P., Wolf K., Wright L.F.,
RA   Zaccaria P., Zimmermann M., Zollner A., Kleine K.;
RT   "The nucleotide sequence of Saccharomyces cerevisiae chromosome VII.";
RL   Nature 387:81-84(1997).
RN   [4]
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   [5]
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   [6]
RP   SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
RX   PubMed=14562095; DOI=10.1038/nature02026;
RA   Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
RA   Weissman J.S., O'Shea E.K.;
RT   "Global analysis of protein localization in budding yeast.";
RL   Nature 425:686-691(2003).
RN   [7]
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   [8]
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   [9]
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   [10]
RP   IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX   PubMed=17287358; DOI=10.1073/pnas.0607084104;
RA   Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L.,
RA   Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F.;
RT   "Analysis of phosphorylation sites on proteins from Saccharomyces
RT   cerevisiae by electron transfer dissociation (ETD) mass spectrometry.";
RL   Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007).
RN   [11]
RP   PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-17; SER-71 AND SER-477, AND
RP   IDENTIFICATION BY 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   [12]
RP   PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT TYR-69 AND SER-71, 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 RAD6 ubiquitin
CC       conjugate and the BRE1 ubiquitin ligase which ubiquitinate 'Lys-126'
CC       histone H2B. Activates the SET1 histone methyltransferase complex for
CC       methylation of 'Lys-4' of histone H3 and for methylation of 'Lys-73' of
CC       histone H3 by DOT1 and 'Lys-36' of histone H3 by SET2. Important for
CC       TATA site selection by TBP. Directly or indirectly regulates the DNA-
CC       binding properties of SPT15, the TATA box-binding protein, and the
CC       relative activities of different TATA elements.
CC       {ECO:0000269|PubMed:15643076, ECO:0000269|PubMed:16246725}.
CC   -!- SUBUNIT: Component of the PAF1 complex which consists of at least
CC       CDC73, CTR9, LEO1, PAF1 and RTF1. {ECO:0000269|PubMed:11884586}.
CC   -!- INTERACTION:
CC       P53064; Q06697: CDC73; NbExp=9; IntAct=EBI-16303, EBI-29913;
CC       P53064; P89105: CTR9; NbExp=8; IntAct=EBI-16303, EBI-5283;
CC       P53064; P38439: LEO1; NbExp=5; IntAct=EBI-16303, EBI-10108;
CC       P53064; P38351: PAF1; NbExp=8; IntAct=EBI-16303, EBI-12855;
CC       P53064; P04050: RPO21; NbExp=7; IntAct=EBI-16303, EBI-15760;
CC       P53064; Q00772: SLT2; NbExp=2; IntAct=EBI-16303, EBI-17372;
CC       P53064; P27692: SPT5; NbExp=5; IntAct=EBI-16303, EBI-17937;
CC   -!- SUBCELLULAR LOCATION: Nucleus, nucleoplasm
CC       {ECO:0000269|PubMed:14562095, ECO:0000269|PubMed:15643076}.
CC   -!- MISCELLANEOUS: Present with 6510 molecules/cell in log phase SD medium.
CC       {ECO:0000269|PubMed:14562106}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=CAA89011.1; Type=Erroneous initiation; Evidence={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; U86702; AAB47535.1; -; Genomic_DNA.
DR   EMBL; Z49149; CAA89011.1; ALT_INIT; Genomic_DNA.
DR   EMBL; Z72766; CAA96963.1; -; Genomic_DNA.
DR   EMBL; Z72767; CAA96965.1; -; Genomic_DNA.
DR   EMBL; BK006941; DAA07875.1; -; Genomic_DNA.
DR   PIR; S53936; S53936.
DR   RefSeq; NP_011270.1; NM_001181110.1.
DR   PDB; 5E8B; X-ray; 1.62 A; A/B=74-139.
DR   PDB; 5EMX; X-ray; 1.40 A; A/B=74-139.
DR   PDB; 7DKH; X-ray; 2.90 A; D/H/L=491-558.
DR   PDBsum; 5E8B; -.
DR   PDBsum; 5EMX; -.
DR   PDBsum; 7DKH; -.
DR   AlphaFoldDB; P53064; -.
DR   SMR; P53064; -.
DR   BioGRID; 32996; 746.
DR   ComplexPortal; CPX-1726; PAF1 complex.
DR   DIP; DIP-4065N; -.
DR   IntAct; P53064; 18.
DR   MINT; P53064; -.
DR   STRING; 4932.YGL244W; -.
DR   iPTMnet; P53064; -.
DR   MaxQB; P53064; -.
DR   PaxDb; 4932-YGL244W; -.
DR   PeptideAtlas; P53064; -.
DR   EnsemblFungi; YGL244W_mRNA; YGL244W; YGL244W.
DR   GeneID; 852607; -.
DR   KEGG; sce:YGL244W; -.
DR   AGR; SGD:S000003213; -.
DR   SGD; S000003213; RTF1.
DR   VEuPathDB; FungiDB:YGL244W; -.
DR   eggNOG; KOG2402; Eukaryota.
DR   HOGENOM; CLU_036626_1_0_1; -.
DR   InParanoid; P53064; -.
DR   OMA; HKMERFV; -.
DR   OrthoDB; 473523at2759; -.
DR   BioCyc; YEAST:G3O-30715-MONOMER; -.
DR   BioGRID-ORCS; 852607; 1 hit in 10 CRISPR screens.
DR   PRO; PR:P53064; -.
DR   Proteomes; UP000002311; Chromosome VII.
DR   RNAct; P53064; 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:0003677; F:DNA binding; IEA:InterPro.
DR   GO; GO:0003723; F:RNA binding; IDA:SGD.
DR   GO; GO:1990269; F:RNA polymerase II C-terminal domain phosphoserine binding; IDA:SGD.
DR   GO; GO:0006353; P:DNA-templated transcription termination; IMP:SGD.
DR   GO; GO:0070911; P:global genome nucleotide-excision repair; IMP:SGD.
DR   GO; GO:0042138; P:meiotic DNA double-strand break formation; IMP:SGD.
DR   GO; GO:0031124; P:mRNA 3'-end processing; 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:0034402; P:recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex; IMP:SGD.
DR   GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IGI:SGD.
DR   GO; GO:0090262; P:regulation of transcription-coupled nucleotide-excision repair; IGI:SGD.
DR   GO; GO:0031126; P:sno(s)RNA 3'-end processing; IMP:SGD.
DR   GO; GO:0001015; P:snoRNA transcription by RNA polymerase II; IMP:SGD.
DR   GO; GO:0006368; P:transcription elongation by RNA polymerase II; IMP:SGD.
DR   Gene3D; 3.90.70.200; Plus-3 domain; 1.
DR   InterPro; IPR004343; Plus-3_dom.
DR   InterPro; IPR036128; Plus3-like_sf.
DR   PANTHER; PTHR13115:SF8; RNA POLYMERASE-ASSOCIATED PROTEIN RTF1 HOMOLOG; 1.
DR   PANTHER; PTHR13115; UNCHARACTERIZED; 1.
DR   Pfam; PF03126; Plus-3; 1.
DR   SMART; SM00719; Plus3; 1.
DR   SUPFAM; SSF159042; Plus3-like; 1.
DR   PROSITE; PS51360; PLUS3; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Activator; Nucleus; Phosphoprotein; Reference proteome;
KW   Transcription; Transcription regulation.
FT   CHAIN           1..558
FT                   /note="RNA polymerase-associated protein RTF1"
FT                   /id="PRO_0000097512"
FT   DOMAIN          238..370
FT                   /note="Plus3"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00693"
FT   REGION          1..107
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          119..217
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        1..22
FT                   /note="Acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        35..49
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        78..107
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        119..149
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        184..208
FT                   /note="Acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   MOD_RES         17
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:18407956"
FT   MOD_RES         69
FT                   /note="Phosphotyrosine"
FT                   /evidence="ECO:0007744|PubMed:19779198"
FT   MOD_RES         71
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:18407956,
FT                   ECO:0007744|PubMed:19779198"
FT   MOD_RES         477
FT                   /note="Phosphoserine"
FT                   /evidence="ECO:0007744|PubMed:18407956"
FT   TURN            83..85
FT                   /evidence="ECO:0007829|PDB:5EMX"
FT   STRAND          86..88
FT                   /evidence="ECO:0007829|PDB:5EMX"
FT   HELIX           89..97
FT                   /evidence="ECO:0007829|PDB:5EMX"
FT   HELIX           100..125
FT                   /evidence="ECO:0007829|PDB:5EMX"
FT   HELIX           510..513
FT                   /evidence="ECO:0007829|PDB:7DKH"
FT   HELIX           515..533
FT                   /evidence="ECO:0007829|PDB:7DKH"
FT   HELIX           536..538
FT                   /evidence="ECO:0007829|PDB:7DKH"
FT   HELIX           542..548
FT                   /evidence="ECO:0007829|PDB:7DKH"
SQ   SEQUENCE   558 AA;  65869 MW;  13AECCEC6D63CED4 CRC64;
     MSDLDEDLLA LAGADESEEE DQVLTTTSAK RAKNNDQSLS KKRRIEVGSV EDDDEEDDYN
     PYSVGNADYG SEEEEEANPF PLEGKYKDES DREHLESLPE MERETLLFER SQIMQKYQER
     KLFRARGRDM KEQQQRAKND EDSRKTRAST RSTHATGHSD IKASKLSQLK KQRARKNRHY
     SDNEDEDDEE DYREEDYKDD EGSEYGDDEE YNPFDRRDTY DKREEVEWAE EEDEQDREPE
     ISDFNKLRIG RSFVAKFCFY PGFEDAVKGC YGRVNVGTDK RTGKTSYRMV RIERVFLQKP
     YNMGKFYTNQ YFGVTQGKDR KVFQMNYFSD GLFAEDEYQR YLRALDNSQM IKPSLHSLSN
     KTKEVMDFVN TPLTDKTTDE VVRHRMQFNK KLSGTNAVLE KTVLREKLQY AKETNNEKDI
     AKYSAQLRNF EKRMSVYEKH HENDQSDIKK LGELTSKNRK LNMSNIRNAE HVKKEDSNNF
     DSKSDPFSRL KTRTKVYYQE IQKEENAKAK EIAQQEKLQE DKDAKDKREK ELLVAQFRRL
     GGLERMVGEL DIKFDLKF
//