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RNA polymerase-associated protein RTF1

 RTF1_YEAST              Reviewed;         558 AA.
P53064; D6VV91; P89115;
01-OCT-1996, integrated into UniProtKB/Swiss-Prot.
01-NOV-1997, sequence version 2.
27-SEP-2017, entry version 151.
RecName: Full=RNA polymerase-associated protein RTF1;
Name=RTF1; Synonyms=CSL3; OrderedLocusNames=YGL244W; ORFNames=HRA458;
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast).
Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina;
Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces.
NCBI_TaxID=559292;
[1]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
PubMed=9234706; DOI=10.1128/MCB.17.8.4490;
Stolinski L.A., Eisenmann D.M., Arndt K.M.;
"Identification of RTF1, a novel gene important for TATA site
selection by TATA box-binding protein in Saccharomyces cerevisiae.";
Mol. Cell. Biol. 17:4490-4500(1997).
[2]
NUCLEOTIDE SEQUENCE [GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=8750240; DOI=10.1002/yea.320111507;
Vandenbol M., Durand P., Portetelle D., Hilger F.;
"The sequence of an 11.1 kb DNA fragment between ADH4 and ADE5 on the
left arm of chromosome VII, reveals the presence of eight open reading
frames.";
Yeast 11:1519-1523(1995).
[3]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 204508 / S288c;
PubMed=9169869;
Tettelin H., Agostoni-Carbone M.L., Albermann K., Albers M.,
Arroyo J., Backes U., Barreiros T., Bertani I., Bjourson A.J.,
Brueckner M., Bruschi C.V., Carignani G., Castagnoli L., Cerdan E.,
Clemente M.L., Coblenz A., Coglievina M., Coissac E., Defoor E.,
Del Bino S., Delius H., Delneri D., de Wergifosse P., Dujon B.,
Durand P., Entian K.-D., Eraso P., Escribano V., Fabiani L.,
Fartmann B., Feroli F., Feuermann M., Frontali L., Garcia-Gonzalez M.,
Garcia-Saez M.I., Goffeau A., Guerreiro P., Hani J., Hansen M.,
Hebling U., Hernandez K., Heumann K., Hilger F., Hofmann B.,
Indge K.J., James C.M., Klima R., Koetter P., Kramer B., Kramer W.,
Lauquin G., Leuther H., Louis E.J., Maillier E., Marconi A.,
Martegani E., Mazon M.J., Mazzoni C., McReynolds A.D.K.,
Melchioretto P., Mewes H.-W., Minenkova O., Mueller-Auer S.,
Nawrocki A., Netter P., Neu R., Nombela C., Oliver S.G., Panzeri L.,
Paoluzi S., Plevani P., Portetelle D., Portillo F., Potier S.,
Purnelle B., Rieger M., Riles L., Rinaldi T., Robben J.,
Rodrigues-Pousada C., Rodriguez-Belmonte E., Rodriguez-Torres A.M.,
Rose M., Ruzzi M., Saliola M., Sanchez-Perez M., Schaefer B.,
Schaefer M., Scharfe M., Schmidheini T., Schreer A., Skala J.,
Souciet J.-L., Steensma H.Y., Talla E., Thierry A., Vandenbol M.,
van der Aart Q.J.M., Van Dyck L., Vanoni M., Verhasselt P., Voet M.,
Volckaert G., Wambutt R., Watson M.D., Weber N., Wedler E., Wedler H.,
Wipfli P., Wolf K., Wright L.F., Zaccaria P., Zimmermann M.,
Zollner A., Kleine K.;
"The nucleotide sequence of Saccharomyces cerevisiae chromosome VII.";
Nature 387:81-84(1997).
[4]
GENOME REANNOTATION.
STRAIN=ATCC 204508 / S288c;
PubMed=24374639; DOI=10.1534/g3.113.008995;
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.;
"The reference genome sequence of Saccharomyces cerevisiae: Then and
now.";
G3 (Bethesda) 4:389-398(2014).
[5]
IDENTIFICATION IN THE PAF1 COMPLEX.
PubMed=11884586; DOI=10.1128/MCB.22.7.1971-1980.2002;
Mueller C.L., Jaehning J.A.;
"Ctr9, Rtf1, and Leo1 are components of the Paf1/RNA polymerase II
complex.";
Mol. Cell. Biol. 22:1971-1980(2002).
[6]
SUBCELLULAR LOCATION [LARGE SCALE ANALYSIS].
PubMed=14562095; DOI=10.1038/nature02026;
Huh W.-K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W.,
Weissman J.S., O'Shea E.K.;
"Global analysis of protein localization in budding yeast.";
Nature 425:686-691(2003).
[7]
LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
PubMed=14562106; DOI=10.1038/nature02046;
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A.,
Dephoure N., O'Shea E.K., Weissman J.S.;
"Global analysis of protein expression in yeast.";
Nature 425:737-741(2003).
[8]
FUNCTION, AND SUBCELLULAR LOCATION.
PubMed=15643076; DOI=10.1128/EC.4.1.209-220.2005;
Porter S.E., Penheiter K.L., Jaehning J.A.;
"Separation of the Saccharomyces cerevisiae Paf1 complex from RNA
polymerase II results in changes in its subnuclear localization.";
Eukaryot. Cell 4:209-220(2005).
[9]
FUNCTION.
PubMed=16246725; DOI=10.1016/j.molcel.2005.08.026;
Sheldon K.E., Mauger D.M., Arndt K.M.;
"A requirement for the Saccharomyces cerevisiae Paf1 complex in snoRNA
3' end formation.";
Mol. Cell 20:225-236(2005).
[10]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=17287358; DOI=10.1073/pnas.0607084104;
Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L.,
Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F.;
"Analysis of phosphorylation sites on proteins from Saccharomyces
cerevisiae by electron transfer dissociation (ETD) mass
spectrometry.";
Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007).
[11]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-17; SER-71 AND SER-477,
AND IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=18407956; DOI=10.1074/mcp.M700468-MCP200;
Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.;
"A multidimensional chromatography technology for in-depth
phosphoproteome analysis.";
Mol. Cell. Proteomics 7:1389-1396(2008).
[12]
PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT TYR-69 AND SER-71, AND
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
PubMed=19779198; DOI=10.1126/science.1172867;
Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.;
"Global analysis of Cdk1 substrate phosphorylation sites provides
insights into evolution.";
Science 325:1682-1686(2009).
-!- 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 RAD6 ubiquitin conjugate and the BRE1 ubiquitin
ligase which ubiquitinate 'Lys-126' histone H2B. Activates the
SET1 histone methyltransferase complex for methylation of 'Lys-4'
of histone H3 and for methylation of 'Lys-73' of histone H3 by
DOT1 and 'Lys-36' of histone H3 by SET2. Important for TATA site
selection by TBP. Directly or indirectly regulates the DNA-binding
properties of SPT15, the TATA box-binding protein, and the
relative activities of different TATA elements.
{ECO:0000269|PubMed:15643076, ECO:0000269|PubMed:16246725}.
-!- SUBUNIT: Component of the PAF1 complex which consists of at least
CDC73, CTR9, LEO1, PAF1 and RTF1. {ECO:0000269|PubMed:11884586}.
-!- INTERACTION:
Self; NbExp=2; IntAct=EBI-16303, EBI-16303;
Q06697:CDC73; NbExp=34; IntAct=EBI-16303, EBI-29913;
P89105:CTR9; NbExp=32; IntAct=EBI-16303, EBI-5283;
P38439:LEO1; NbExp=26; IntAct=EBI-16303, EBI-10108;
P38351:PAF1; NbExp=24; IntAct=EBI-16303, EBI-12855;
Q04636:POB3; NbExp=6; IntAct=EBI-16303, EBI-27863;
P04050:RPO21; NbExp=7; IntAct=EBI-16303, EBI-15760;
Q00772:SLT2; NbExp=2; IntAct=EBI-16303, EBI-17372;
P32558:SPT16; NbExp=24; IntAct=EBI-16303, EBI-4334;
P27692:SPT5; NbExp=5; IntAct=EBI-16303, EBI-17937;
Q12159:YRA1; NbExp=3; IntAct=EBI-16303, EBI-29516;
-!- SUBCELLULAR LOCATION: Nucleus, nucleoplasm
{ECO:0000269|PubMed:14562095, ECO:0000269|PubMed:15643076}.
-!- MISCELLANEOUS: Present with 6510 molecules/cell in log phase SD
medium. {ECO:0000269|PubMed:14562106}.
-!- SEQUENCE CAUTION:
Sequence=CAA89011.1; Type=Erroneous initiation; Evidence={ECO:0000305};
-----------------------------------------------------------------------
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EMBL; U86702; AAB47535.1; -; Genomic_DNA.
EMBL; Z49149; CAA89011.1; ALT_INIT; Genomic_DNA.
EMBL; Z72766; CAA96963.1; -; Genomic_DNA.
EMBL; Z72767; CAA96965.1; -; Genomic_DNA.
EMBL; BK006941; DAA07875.1; -; Genomic_DNA.
PIR; S53936; S53936.
RefSeq; NP_011270.1; NM_001181110.1.
PDB; 5E8B; X-ray; 1.62 A; A/B=74-139.
PDB; 5EMX; X-ray; 1.40 A; A/B=74-139.
PDBsum; 5E8B; -.
PDBsum; 5EMX; -.
ProteinModelPortal; P53064; -.
SMR; P53064; -.
BioGrid; 32996; 671.
DIP; DIP-4065N; -.
IntAct; P53064; 26.
MINT; MINT-502955; -.
STRING; 4932.YGL244W; -.
iPTMnet; P53064; -.
MaxQB; P53064; -.
PRIDE; P53064; -.
EnsemblFungi; YGL244W; YGL244W; YGL244W.
GeneID; 852607; -.
KEGG; sce:YGL244W; -.
EuPathDB; FungiDB:YGL244W; -.
SGD; S000003213; RTF1.
GeneTree; ENSGT00390000012493; -.
HOGENOM; HOG000065976; -.
InParanoid; P53064; -.
KO; K15178; -.
OMA; SGCKSAV; -.
OrthoDB; EOG092C52EI; -.
BioCyc; YEAST:G3O-30715-MONOMER; -.
PRO; PR:P53064; -.
Proteomes; UP000002311; Chromosome VII.
GO; GO:0016593; C:Cdc73/Paf1 complex; IPI:SGD.
GO; GO:0005634; C:nucleus; IDA:SGD.
GO; GO:0035327; C:transcriptionally active chromatin; IDA:SGD.
GO; GO:0003677; F:DNA binding; IEA:InterPro.
GO; GO:0003723; F:RNA binding; IDA:SGD.
GO; GO:1990269; F:RNA polymerase II C-terminal domain phosphoserine binding; IDA:SGD.
GO; GO:0001076; F:transcription factor activity, RNA polymerase II transcription factor binding; IPI:SGD.
GO; GO:0006353; P:DNA-templated transcription, termination; IMP:SGD.
GO; GO:0070911; P:global genome nucleotide-excision repair; IMP:SGD.
GO; GO:0016570; P:histone modification; IEA:InterPro.
GO; GO:0031124; P:mRNA 3'-end processing; IMP:SGD.
GO; GO:0000122; P:negative regulation of transcription from RNA polymerase II promoter; IMP:SGD.
GO; GO:2001165; P:positive regulation of phosphorylation of RNA polymerase II C-terminal domain serine 2 residues; IMP:SGD.
GO; GO:2001209; P:positive regulation of transcription elongation from RNA polymerase I promoter; IDA:SGD.
GO; GO:0032968; P:positive regulation of transcription elongation from RNA polymerase II promoter; IMP:SGD.
GO; GO:0034402; P:recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex; IMP:SGD.
GO; GO:0031938; P:regulation of chromatin silencing at telomere; IMP:SGD.
GO; GO:2001173; P:regulation of histone H2B conserved C-terminal lysine ubiquitination; IDA:SGD.
GO; GO:2001166; P:regulation of histone H2B ubiquitination; IMP:SGD.
GO; GO:0051569; P:regulation of histone H3-K4 methylation; IMP:SGD.
GO; GO:2001160; P:regulation of histone H3-K79 methylation; IMP:SGD.
GO; GO:2001163; P:regulation of phosphorylation of RNA polymerase II C-terminal domain serine 2 residues; IMP:SGD.
GO; GO:0006357; P:regulation of transcription from RNA polymerase II promoter; IGI:SGD.
GO; GO:0090262; P:regulation of transcription-coupled nucleotide-excision repair; IGI:SGD.
GO; GO:0031126; P:snoRNA 3'-end processing; IMP:SGD.
GO; GO:0001015; P:snoRNA transcription from an RNA polymerase II promoter; IMP:SGD.
GO; GO:0006368; P:transcription elongation from RNA polymerase II promoter; IMP:SGD.
InterPro; IPR004343; Plus-3_dom.
InterPro; IPR031102; Rtf1.
PANTHER; PTHR13115; PTHR13115; 1.
Pfam; PF03126; Plus-3; 1.
SMART; SM00719; Plus3; 1.
SUPFAM; SSF159042; SSF159042; 1.
PROSITE; PS51360; PLUS3; 1.
1: Evidence at protein level;
3D-structure; Activator; Complete proteome; Nucleus; Phosphoprotein;
Reference proteome; Transcription; Transcription regulation.
CHAIN 1 558 RNA polymerase-associated protein RTF1.
/FTId=PRO_0000097512.
DOMAIN 238 370 Plus3. {ECO:0000255|PROSITE-
ProRule:PRU00693}.
COMPBIAS 72 76 Poly-Glu.
MOD_RES 17 17 Phosphoserine.
{ECO:0000244|PubMed:18407956}.
MOD_RES 69 69 Phosphotyrosine.
{ECO:0000244|PubMed:19779198}.
MOD_RES 71 71 Phosphoserine.
{ECO:0000244|PubMed:18407956,
ECO:0000244|PubMed:19779198}.
MOD_RES 477 477 Phosphoserine.
{ECO:0000244|PubMed:18407956}.
TURN 83 85 {ECO:0000244|PDB:5EMX}.
STRAND 86 88 {ECO:0000244|PDB:5EMX}.
HELIX 89 97 {ECO:0000244|PDB:5EMX}.
HELIX 100 125 {ECO:0000244|PDB:5EMX}.
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


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