RTF1_YEAST
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 03-AUG-2022, entry version 186.
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; 730.
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; P53064; -.
DR PRIDE; P53064; -.
DR EnsemblFungi; YGL244W_mRNA; YGL244W; YGL244W.
DR GeneID; 852607; -.
DR KEGG; sce:YGL244W; -.
DR SGD; S000003213; RTF1.
DR VEuPathDB; FungiDB:YGL244W; -.
DR eggNOG; KOG2402; Eukaryota.
DR HOGENOM; CLU_036626_1_0_1; -.
DR InParanoid; P53064; -.
DR OMA; SGCKSAV; -.
DR BioCyc; YEAST:G3O-30715-MON; -.
DR Reactome; R-SCE-674695; RNA Polymerase II Pre-transcription Events.
DR Reactome; R-SCE-75955; RNA Polymerase II Transcription Elongation.
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:0016571; P:histone methylation; IC:ComplexPortal.
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:2001165; P:positive regulation of phosphorylation of RNA polymerase II C-terminal domain serine 2 residues; IMP:SGD.
DR GO; GO:2001209; P:positive regulation of transcription elongation from RNA polymerase I promoter; IDA:SGD.
DR GO; GO:0032968; P:positive regulation of transcription elongation from RNA polymerase II promoter; IMP:SGD.
DR GO; GO:0034402; P:recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex; IMP:SGD.
DR GO; GO:2001173; P:regulation of histone H2B conserved C-terminal lysine ubiquitination; IDA:SGD.
DR GO; GO:2001166; P:regulation of histone H2B ubiquitination; IMP:SGD.
DR GO; GO:0051569; P:regulation of histone H3-K4 methylation; IMP:SGD.
DR GO; GO:2001160; P:regulation of histone H3-K79 methylation; IMP:SGD.
DR GO; GO:2001163; P:regulation of phosphorylation of RNA polymerase II C-terminal domain serine 2 residues; 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 from RNA polymerase II promoter; IMP:SGD.
DR Gene3D; 3.90.70.200; -; 1.
DR InterPro; IPR004343; Plus-3_dom.
DR InterPro; IPR036128; Plus3-like_sf.
DR Pfam; PF03126; Plus-3; 1.
DR SMART; SM00719; Plus3; 1.
DR SUPFAM; SSF159042; SSF159042; 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
