CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-018732
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 RNA polymerase-associated protein RTF1 homolog 
Protein Synonyms/Alias
  
Gene Name
 RTF1 
Gene Synonyms/Alias
 KIAA0252 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
44RGTTMVKKRKGRVVImethylation[1]
202RLEQMTEKEREQELFacetylation[2]
202RLEQMTEKEREQELFubiquitination[2, 3]
265SQVTSHNKERRSKRDacetylation[2]
302RTAELLAKKQPLKTSubiquitination[4]
413TGVVETAKVYQLGGTacetylation[5]
424LGGTRTNKGLQLRHGubiquitination[3]
555ALDRQRTKNISAISYubiquitination[3]
705LNLEDYKKRRGLI**ubiquitination[3]
Reference
 [1] Large-scale global identification of protein lysine methylation in vivo.
 Cao XJ, Arnaudo AM, Garcia BA.
 Epigenetics. 2013 May 1;8(5):477-85. [PMID: 23644510]
 [2] Integrated proteomic analysis of post-translational modifications by serial enrichment.
 Mertins P, Qiao JW, Patel J, Udeshi ND, Clauser KR, Mani DR, Burgess MW, Gillette MA, Jaffe JD, Carr SA.
 Nat Methods. 2013 Jul;10(7):634-7. [PMID: 23749302]
 [3] Refined preparation and use of anti-diglycine remnant (K-ε-GG) antibody enables routine quantification of 10,000s of ubiquitination sites in single proteomics experiments.
 Udeshi ND, Svinkina T, Mertins P, Kuhn E, Mani DR, Qiao JW, Carr SA.
 Mol Cell Proteomics. 2013 Mar;12(3):825-31. [PMID: 23266961]
 [4] Systematic and quantitative assessment of the ubiquitin-modified proteome.
 Kim W, Bennett EJ, Huttlin EL, Guo A, Li J, Possemato A, Sowa ME, Rad R, Rush J, Comb MJ, Harper JW, Gygi SP.
 Mol Cell. 2011 Oct 21;44(2):325-40. [PMID: 21906983]
 [5] Lysine acetylation targets protein complexes and co-regulates major cellular functions.
 Choudhary C, Kumar C, Gnad F, Nielsen ML, Rehman M, Walther TC, Olsen JV, Mann M.
 Science. 2009 Aug 14;325(5942):834-40. [PMID: 19608861] 
Functional Description
 Component of the PAF1 complex (PAF1C) which has multiple functions during transcription by RNA polymerase II and is implicated in regulation of development and maintenance of embryonic stem cell pluripotency. PAF1C associates with RNA polymerase II through interaction with POLR2A CTD non- phosphorylated and 'Ser-2'- and 'Ser-5'-phosphorylated forms and is involved in transcriptional elongation, acting both indepentently and synergistically with TCEA1 and in cooperation with the DSIF complex and HTATSF1. PAF1C is required for transcription of Hox and Wnt target genes. PAF1C is involved in hematopoiesis and stimulates transcriptional activity of KMT2A/MLL1; it promotes leukemogenesis through association with KMT2A/MLL1-rearranged oncoproteins, such as KMT2A/MLL1-MLLT3/AF9 and KMT2A/MLL1-MLLT1/ENL. PAF1C is involved in histone modifications such as ubiquitination of histone H2B and methylation on histone H3 'Lys-4' (H3K4me3). PAF1C recruits the RNF20/40 E3 ubiquitin-protein ligase complex and the E2 enzyme UBE2A or UBE2B to chromatin which mediate monoubiquitination of 'Lys-120' of histone H2B (H2BK120ub1); UB2A/B-mediated H2B ubiquitination is proposed to be coupled to transcription. PAF1C is involved in mRNA 3' end formation probably through association with cleavage and poly(A) factors. In case of infection by influenza A strain H3N2, PAF1C associates with viral NS1 protein, thereby regulating gene transcription. Binds single-stranded DNA. Required for maximal induction of heat-shock genes. Required for the trimethylation of histone H3 'Lys-4' (H3K4me3) on genes involved in stem cell pluripotency; this function is synergistic with CXXC1 indicative for an involvement of a SET1 complex (By similarity). 
Sequence Annotation
 DOMAIN 353 484 Plus3.
 MOD_RES 53 53 Phosphoserine.
 MOD_RES 55 55 Phosphothreonine.
 MOD_RES 650 650 Phosphoserine.
 MOD_RES 697 697 Phosphoserine.  
Keyword
 3D-structure; Activator; Coiled coil; Complete proteome; DNA-binding; Nucleus; Phosphoprotein; Reference proteome; Transcription; Transcription regulation; Wnt signaling pathway. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 710 AA 
Protein Sequence
MRGRLCVGRA AAAAAAVAVP LAGGQEGSPG GGRRGSRGTT MVKKRKGRVV IDSDTEDSGS 60
DENLDQELLS LAKRKRSDSE EKEPPVSQPA ASSDSETSDS DDEWTFGSNK NKKKGKARKI 120
EKKGTMKKQA NKTASSGSSD KDSSAESSAP EEGEVSDSDS NSSSSSSDSD SSSEDEEFHD 180
GYGEDLMGDE EDRARLEQMT EKEREQELFN RIEKREVLKR RFEIKKKLKT AKKKEKKEKK 240
KKQEEEQEKK KLTQIQESQV TSHNKERRSK RDEKLDKKSQ AMEELKAERE KRKNRTAELL 300
AKKQPLKTSE VYSDDEEEEE DDKSSEKSDR SSRTSSSDEE EEKEEIPPKS QPVSLPEELN 360
RVRLSRHKLE RWCHMPFFAK TVTGCFVRIG IGNHNSKPVY RVAEITGVVE TAKVYQLGGT 420
RTNKGLQLRH GNDQRVFRLE FVSNQEFTES EFMKWKEAMF SAGMQLPTLD EINKKELSIK 480
EALNYKFNDQ DIEEIVKEKE RFRKAPPNYA MKKTQLLKEK AMAEDLGDQD KAKQIQDQLN 540
ELEERAEALD RQRTKNISAI SYINQRNREW NIVESEKALV AESHNMKNQQ MDPFTRRQCK 600
PTIVSNSRDP AVQAAILAQL NAKYGSGVLP DAPKEMSKGQ GKDKDLNSKS ASDLSEDLFK 660
VHDFDVKIDL QVPSSESKAL AITSKAPPAK DGAPRRSLNL EDYKKRRGLI 710 
Gene Ontology
 GO:0016593; C:Cdc73/Paf1 complex; IDA:UniProtKB.
 GO:0005730; C:nucleolus; IEA:Compara.
 GO:0003697; F:single-stranded DNA binding; IDA:UniProtKB.
 GO:0006352; P:DNA-dependent transcription, initiation; IEA:InterPro.
 GO:0001711; P:endodermal cell fate commitment; ISS:UniProtKB.
 GO:0080182; P:histone H3-K4 trimethylation; IEA:Compara.
 GO:0000122; P:negative regulation of transcription from RNA polymerase II promoter; ISS:UniProtKB.
 GO:0051571; P:positive regulation of histone H3-K4 methylation; IEA:Compara.
 GO:0032968; P:positive regulation of transcription elongation from RNA polymerase II promoter; IDA:UniProtKB.
 GO:0045944; P:positive regulation of transcription from RNA polymerase II promoter; IDA:UniProtKB.
 GO:0019827; P:stem cell maintenance; IDA:UniProtKB.
 GO:0016055; P:Wnt receptor signaling pathway; IEA:UniProtKB-KW. 
Interpro
 IPR004343; Plus-3.
 IPR018144; Plus3-dom_subgr. 
Pfam
 PF03126; Plus-3 
SMART
 SM00719; Plus3 
PROSITE
 PS51360; PLUS3 
PRINTS