CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-005147
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Splicing factor, proline- and glutamine-rich 
Protein Synonyms/Alias
 100 kDa DNA-pairing protein; hPOMp100; DNA-binding p52/p100 complex, 100 kDa subunit; Polypyrimidine tract-binding protein-associated-splicing factor; PSF; PTB-associated-splicing factor 
Gene Name
 SFPQ 
Gene Synonyms/Alias
 PSF 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
271PGGRSEEKISDSEGFacetylation[1]
271PGGRSEEKISDSEGFubiquitination[1, 2, 3]
279ISDSEGFKANLSLLRubiquitination[1, 3, 4, 5, 6, 7]
314DITEDEFKRLFAKYGacetylation[8]
314DITEDEFKRLFAKYGmethylation[9]
319EFKRLFAKYGEPGEVacetylation[1, 10, 11]
319EFKRLFAKYGEPGEVubiquitination[1, 3, 4, 5, 7]
330PGEVFINKGKGFGFIacetylation[1, 10]
330PGEVFINKGKGFGFIubiquitination[1, 2, 3, 4, 5, 6, 7, 12]
332EVFINKGKGFGFIKLubiquitination[1, 3]
338GKGFGFIKLESRALAacetylation[1, 8, 10, 11]
338GKGFGFIKLESRALAubiquitination[1, 3, 4, 5, 6, 7]
349RALAEIAKAELDDTPubiquitination[2]
413DRGRSTGKGIVEFASubiquitination[1, 3, 5, 6]
421GIVEFASKPAARKAFacetylation[1, 8, 10, 11]
421GIVEFASKPAARKAFubiquitination[1, 2, 3, 4, 7]
466LPEKLAQKNPMYQKEubiquitination[2, 5]
472QKNPMYQKERETPPRacetylation[10]
472QKNPMYQKERETPPRubiquitination[5]
518NMKDAKDKLESEMEDubiquitination[3]
704EYEGPNKKPRF****acetylation[1]
Reference
 [1] 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]
 [2] 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]
 [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] A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles.
 Wagner SA, Beli P, Weinert BT, Nielsen ML, Cox J, Mann M, Choudhary C.
 Mol Cell Proteomics. 2011 Oct;10(10):M111.013284. [PMID: 21890473]
 [5] Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass.
 Povlsen LK, Beli P, Wagner SA, Poulsen SL, Sylvestersen KB, Poulsen JW, Nielsen ML, Bekker-Jensen S, Mailand N, Choudhary C.
 Nat Cell Biol. 2012 Oct;14(10):1089-98. [PMID: 23000965]
 [6] Landscape of the PARKIN-dependent ubiquitylome in response to mitochondrial depolarization.
 Sarraf SA, Raman M, Guarani-Pereira V, Sowa ME, Huttlin EL, Gygi SP, Harper JW.
 Nature. 2013 Apr 18;496(7445):372-6. [PMID: 23503661]
 [7] hCKSAAP_UbSite: improved prediction of human ubiquitination sites by exploiting amino acid pattern and properties.
 Chen Z, Zhou Y, Song J, Zhang Z.
 Biochim Biophys Acta. 2013 Aug;1834(8):1461-7. [PMID: 23603789]
 [8] Proteomic investigations of lysine acetylation identify diverse substrates of mitochondrial deacetylase sirt3.
 Sol EM, Wagner SA, Weinert BT, Kumar A, Kim HS, Deng CX, Choudhary C.
 PLoS One. 2012;7(12):e50545. [PMID: 23236377]
 [9] Update on activities at the Universal Protein Resource (UniProt) in 2013.
 e="String">UniProt Consortium.
 Nucleic Acids Res. 2013 Jan;41(Database issue):D43-7. [PMID: 23161681]
 [10] 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]
 [11] Proteomic investigations reveal a role for RNA processing factor THRAP3 in the DNA damage response.
 Beli P, Lukashchuk N, Wagner SA, Weinert BT, Olsen JV, Baskcomb L, Mann M, Jackson SP, Choudhary C.
 Mol Cell. 2012 Apr 27;46(2):212-25. [PMID: 22424773]
 [12] Global analysis of lysine ubiquitination by ubiquitin remnant immunoaffinity profiling.
 Xu G, Paige JS, Jaffrey SR.
 Nat Biotechnol. 2010 Aug;28(8):868-73. [PMID: 20639865] 
Functional Description
 DNA- and RNA binding protein, involved in several nuclear processes. Essential pre-mRNA splicing factor required early in spliceosome formation and for splicing catalytic step II, probably as a heteromer with NONO. Binds to pre-mRNA in spliceosome C complex, and specifically binds to intronic polypyrimidine tracts. Involved in regulation of signal-induced alternative splicing. During splicing of PTPRC/CD45, a phosphorylated form is sequestered by THRAP3 from the pre-mRNA in resting T-cells; T-cell activation and subsequent reduced phosphorylation is proposed to lead to release from THRAP3 allowing binding to pre-mRNA splicing regulatotry elements which represses exon inclusion. Interacts with U5 snRNA, probably by binding to a purine-rich sequence located on the 3' side of U5 snRNA stem 1b. May be involved in a pre-mRNA coupled splicing and polyadenylation process as component of a snRNP-free complex with SNRPA/U1A. The SFPQ-NONO heteromer associated with MATR3 may play a role in nuclear retention of defective RNAs. SFPQ may be involved in homologous DNA pairing; in vitro, promotes the invasion of ssDNA between a duplex DNA and produces a D-loop formation. The SFPQ-NONO heteromer may be involved in DNA unwinding by modulating the function of topoisomerase I/TOP1; in vitro, stimulates dissociation of TOP1 from DNA after cleavage and enhances its jumping between separate DNA helices. The SFPQ-NONO heteromer may be involved in DNA nonhomologous end joining (NHEJ) required for double-strand break repair and V(D)J recombination and may stabilize paired DNA ends; in vitro, the complex strongly stimulates DNA end joining, binds directly to the DNA substrates and cooperates with the Ku70/G22P1-Ku80/XRCC5 (Ku) dimer to establish a functional preligation complex. SFPQ is involved in transcriptional regulation. Transcriptional repression is probably mediated by an interaction of SFPQ with SIN3A and subsequent recruitment of histone deacetylases (HDACs). The SFPQ-NONO/SF-1 complex binds to the CYP17 promoter and regulates basal and cAMP- dependent transcriptional avtivity. SFPQ isoform Long binds to the DNA binding domains (DBD) of nuclear hormone receptors, like RXRA and probably THRA, and acts as transcriptional corepressor in absence of hormone ligands. Binds the DNA sequence 5'-CTGAGTC-3' in the insulin-like growth factor response element (IGFRE) and inhibits IGF-I-stimulated transcriptional activity. 
Sequence Annotation
 REPEAT 9 11 1.
 REPEAT 19 21 2.
 REPEAT 25 27 3.
 DOMAIN 297 369 RRM 1.
 DOMAIN 371 452 RRM 2.
 REGION 9 27 3 X 3 AA repeats of R-G-G.
 MOD_RES 8 8 Phosphoserine; by MKNK2.
 MOD_RES 33 33 Phosphoserine.
 MOD_RES 273 273 Phosphoserine.
 MOD_RES 283 283 Phosphoserine; by MKNK2.
 MOD_RES 293 293 Phosphotyrosine; by ALK.
 MOD_RES 314 314 N6,N6-dimethyllysine.
 MOD_RES 319 319 N6-acetyllysine.
 MOD_RES 338 338 N6-acetyllysine.
 MOD_RES 379 379 Phosphoserine.
 MOD_RES 421 421 N6-acetyllysine.
 MOD_RES 472 472 N6-acetyllysine.
 MOD_RES 571 571 Dimethylated arginine.
 MOD_RES 626 626 Phosphoserine.
 MOD_RES 681 681 Omega-N-methylarginine.
 MOD_RES 687 687 Phosphothreonine.
 MOD_RES 693 693 Dimethylated arginine.  
Keyword
 Acetylation; Activator; Alternative splicing; Chromosomal rearrangement; Complete proteome; Cytoplasm; Direct protein sequencing; DNA damage; DNA recombination; DNA repair; DNA-binding; Methylation; mRNA processing; mRNA splicing; Nucleus; Phosphoprotein; Reference proteome; Repeat; Repressor; RNA-binding; Transcription; Transcription regulation. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 707 AA 
Protein Sequence
MSRDRFRSRG GGGGGFHRRG GGGGRGGLHD FRSPPPGMGL NQNRGPMGPG PGQSGPKPPI 60
PPPPPHQQQQ QPPPQQPPPQ QPPPHQPPPH PQPHQQQQPP PPPQDSSKPV VAQGPGPAPG 120
VGSAPPASSS APPATPPTSG APPGSGPGPT PTPPPAVTSA PPGAPPPTPP SSGVPTTPPQ 180
AGGPPPPPAA VPGPGPGPKQ GPGPGGPKGG KMPGGPKPGG GPGLSTPGGH PKPPHRGGGE 240
PRGGRQHHPP YHQQHHQGPP PGGPGGRSEE KISDSEGFKA NLSLLRRPGE KTYTQRCRLF 300
VGNLPADITE DEFKRLFAKY GEPGEVFINK GKGFGFIKLE SRALAEIAKA ELDDTPMRGR 360
QLRVRFATHA AALSVRNLSP YVSNELLEEA FSQFGPIERA VVIVDDRGRS TGKGIVEFAS 420
KPAARKAFER CSEGVFLLTT TPRPVIVEPL EQLDDEDGLP EKLAQKNPMY QKERETPPRF 480
AQHGTFEYEY SQRWKSLDEM EKQQREQVEK NMKDAKDKLE SEMEDAYHEH QANLLRQDLM 540
RRQEELRRME ELHNQEMQKR KEMQLRQEEE RRRREEEMMI RQREMEEQMR RQREESYSRM 600
GYMDPRERDM RMGGGGAMNM GDPYGSGGQK FPPLGGGGGI GYEANPGVPP ATMSGSMMGS 660
DMRTERFGQG GAGPVGGQGP RGMGPGTPAG YGRGREEYEG PNKKPRF 707 
Gene Ontology
 GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
 GO:0016363; C:nuclear matrix; IDA:BHF-UCL.
 GO:0042382; C:paraspeckles; IDA:BHF-UCL.
 GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
 GO:0000166; F:nucleotide binding; IEA:InterPro.
 GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
 GO:0000380; P:alternative mRNA splicing, via spliceosome; IMP:BHF-UCL.
 GO:0006310; P:DNA recombination; IEA:UniProtKB-KW.
 GO:0006281; P:DNA repair; IEA:UniProtKB-KW.
 GO:0000122; P:negative regulation of transcription from RNA polymerase II promoter; IMP:BHF-UCL.
 GO:0006351; P:transcription, DNA-dependent; IEA:UniProtKB-KW. 
Interpro
 IPR012975; NOPS.
 IPR012677; Nucleotide-bd_a/b_plait.
 IPR000504; RRM_dom. 
Pfam
 PF08075; NOPS
 PF00076; RRM_1 
SMART
 SM00360; RRM 
PROSITE
 PS50102; RRM 
PRINTS