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Protein

RNA polymerase-associated protein RTF1

Gene

RTF1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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 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.2 Publications

Miscellaneous

Present with 6510 molecules/cell in log phase SD medium.1 Publication

GO - Molecular functioni

  • DNA binding Source: InterPro
  • RNA binding Source: SGD
  • RNA polymerase II C-terminal domain phosphoserine binding Source: SGD
  • transcription factor activity, RNA polymerase II transcription factor binding Source: SGD

GO - Biological processi

  • 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 transcription from RNA polymerase II promoter 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
  • recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex 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 histone H3-K79 methylation Source: SGD
  • regulation of phosphorylation of RNA polymerase II C-terminal domain serine 2 residues Source: SGD
  • regulation of transcription-coupled nucleotide-excision repair Source: SGD
  • regulation of transcription from RNA polymerase II promoter Source: SGD
  • snoRNA 3'-end processing Source: SGD
  • snoRNA transcription from an RNA polymerase II promoter Source: SGD
  • transcription elongation from RNA polymerase II promoter Source: SGD

Keywordsi

Molecular functionActivator
Biological processTranscription, Transcription regulation

Enzyme and pathway databases

BioCyciYEAST:G3O-30715-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
RNA polymerase-associated protein RTF1
Gene namesi
Name:RTF1
Synonyms:CSL3
Ordered Locus Names:YGL244W
ORF Names:HRA458
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome VII

Organism-specific databases

EuPathDBiFungiDB:YGL244W.
SGDiS000003213. RTF1.

Subcellular locationi

GO - Cellular componenti

  • Cdc73/Paf1 complex Source: SGD
  • nucleus Source: SGD
  • transcriptionally active chromatin Source: SGD

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000975121 – 558RNA polymerase-associated protein RTF1Add BLAST558

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei17PhosphoserineCombined sources1
Modified residuei69PhosphotyrosineCombined sources1
Modified residuei71PhosphoserineCombined sources1
Modified residuei477PhosphoserineCombined sources1

Keywords - PTMi

Phosphoprotein

Proteomic databases

MaxQBiP53064.
PRIDEiP53064.

PTM databases

iPTMnetiP53064.

Interactioni

Subunit structurei

Component of the PAF1 complex which consists of at least CDC73, CTR9, LEO1, PAF1 and RTF1.1 Publication

Binary interactionsi

Show more details

GO - Molecular functioni

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

Protein-protein interaction databases

BioGridi32996. 670 interactors.
DIPiDIP-4065N.
IntActiP53064. 15 interactors.
MINTiMINT-502955.

Structurei

Secondary structure

1558
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Turni83 – 85Combined sources3
Beta strandi86 – 88Combined sources3
Helixi89 – 97Combined sources9
Helixi100 – 125Combined sources26

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5E8BX-ray1.62A/B74-139[»]
5EMXX-ray1.40A/B74-139[»]
ProteinModelPortaliP53064.
SMRiP53064.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini238 – 370Plus3PROSITE-ProRule annotationAdd BLAST133

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi72 – 76Poly-Glu5

Phylogenomic databases

GeneTreeiENSGT00390000012493.
HOGENOMiHOG000065976.
InParanoidiP53064.
KOiK15178.
OMAiSGCKSAV.
OrthoDBiEOG092C52EI.

Family and domain databases

InterProiView protein in InterPro
IPR004343. Plus-3_dom.
IPR031102. Rtf1.
PANTHERiPTHR13115. PTHR13115. 1 hit.
PfamiView protein in Pfam
PF03126. Plus-3. 1 hit.
SMARTiView protein in SMART
SM00719. Plus3. 1 hit.
SUPFAMiSSF159042. SSF159042. 1 hit.
PROSITEiView protein in PROSITE
PS51360. PLUS3. 1 hit.

Sequencei

Sequence statusi: Complete.

P53064-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSDLDEDLLA LAGADESEEE DQVLTTTSAK RAKNNDQSLS KKRRIEVGSV
60 70 80 90 100
EDDDEEDDYN PYSVGNADYG SEEEEEANPF PLEGKYKDES DREHLESLPE
110 120 130 140 150
MERETLLFER SQIMQKYQER KLFRARGRDM KEQQQRAKND EDSRKTRAST
160 170 180 190 200
RSTHATGHSD IKASKLSQLK KQRARKNRHY SDNEDEDDEE DYREEDYKDD
210 220 230 240 250
EGSEYGDDEE YNPFDRRDTY DKREEVEWAE EEDEQDREPE ISDFNKLRIG
260 270 280 290 300
RSFVAKFCFY PGFEDAVKGC YGRVNVGTDK RTGKTSYRMV RIERVFLQKP
310 320 330 340 350
YNMGKFYTNQ YFGVTQGKDR KVFQMNYFSD GLFAEDEYQR YLRALDNSQM
360 370 380 390 400
IKPSLHSLSN KTKEVMDFVN TPLTDKTTDE VVRHRMQFNK KLSGTNAVLE
410 420 430 440 450
KTVLREKLQY AKETNNEKDI AKYSAQLRNF EKRMSVYEKH HENDQSDIKK
460 470 480 490 500
LGELTSKNRK LNMSNIRNAE HVKKEDSNNF DSKSDPFSRL KTRTKVYYQE
510 520 530 540 550
IQKEENAKAK EIAQQEKLQE DKDAKDKREK ELLVAQFRRL GGLERMVGEL

DIKFDLKF
Length:558
Mass (Da):65,869
Last modified:November 1, 1997 - v2
Checksum:i13AECCEC6D63CED4
GO

Sequence cautioni

The sequence CAA89011 differs from that shown. Reason: Erroneous initiation.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U86702 Genomic DNA. Translation: AAB47535.1.
Z49149 Genomic DNA. Translation: CAA89011.1. Different initiation.
Z72766 Genomic DNA. Translation: CAA96963.1.
Z72767 Genomic DNA. Translation: CAA96965.1.
BK006941 Genomic DNA. Translation: DAA07875.1.
PIRiS53936.
RefSeqiNP_011270.1. NM_001181110.1.

Genome annotation databases

EnsemblFungiiYGL244W; YGL244W; YGL244W.
GeneIDi852607.
KEGGisce:YGL244W.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U86702 Genomic DNA. Translation: AAB47535.1.
Z49149 Genomic DNA. Translation: CAA89011.1. Different initiation.
Z72766 Genomic DNA. Translation: CAA96963.1.
Z72767 Genomic DNA. Translation: CAA96965.1.
BK006941 Genomic DNA. Translation: DAA07875.1.
PIRiS53936.
RefSeqiNP_011270.1. NM_001181110.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
5E8BX-ray1.62A/B74-139[»]
5EMXX-ray1.40A/B74-139[»]
ProteinModelPortaliP53064.
SMRiP53064.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi32996. 670 interactors.
DIPiDIP-4065N.
IntActiP53064. 15 interactors.
MINTiMINT-502955.

PTM databases

iPTMnetiP53064.

Proteomic databases

MaxQBiP53064.
PRIDEiP53064.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYGL244W; YGL244W; YGL244W.
GeneIDi852607.
KEGGisce:YGL244W.

Organism-specific databases

EuPathDBiFungiDB:YGL244W.
SGDiS000003213. RTF1.

Phylogenomic databases

GeneTreeiENSGT00390000012493.
HOGENOMiHOG000065976.
InParanoidiP53064.
KOiK15178.
OMAiSGCKSAV.
OrthoDBiEOG092C52EI.

Enzyme and pathway databases

BioCyciYEAST:G3O-30715-MONOMER.

Miscellaneous databases

PROiPR:P53064.

Family and domain databases

InterProiView protein in InterPro
IPR004343. Plus-3_dom.
IPR031102. Rtf1.
PANTHERiPTHR13115. PTHR13115. 1 hit.
PfamiView protein in Pfam
PF03126. Plus-3. 1 hit.
SMARTiView protein in SMART
SM00719. Plus3. 1 hit.
SUPFAMiSSF159042. SSF159042. 1 hit.
PROSITEiView protein in PROSITE
PS51360. PLUS3. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiRTF1_YEAST
AccessioniPrimary (citable) accession number: P53064
Secondary accession number(s): D6VV91, P89115
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 1, 1996
Last sequence update: November 1, 1997
Last modified: June 7, 2017
This is version 148 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  3. Yeast chromosome VII
    Yeast (Saccharomyces cerevisiae) chromosome VII: entries and gene names

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.