CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-000658
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 U4/U6 small nuclear ribonucleoprotein Prp4 
Protein Synonyms/Alias
 PRP4 homolog; hPrp4; U4/U6 snRNP 60 kDa protein; WD splicing factor Prp4 
Gene Name
 PRPF4 
Gene Synonyms/Alias
 PRP4 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
27LVAPVVKKPHIYYGSacetylation[1, 2]
45KERERLAKGESGILGubiquitination[3]
53GESGILGKDGLKAGIacetylation[4]
147VGTDALKKTKKDDEKubiquitination[3]
159DEKSKKSKEEYQQTWubiquitination[3, 5, 6]
200LEEARLHKEIPETTRubiquitination[3]
216SQMQELHKSLRSLNNubiquitination[3]
284GAIVFHPKSTVSLDPubiquitination[3]
Reference
 [1] 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]
 [2] 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]
 [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] 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]
 [5] 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]
 [6] 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
Functional Description
 Participates in pre-mRNA splicing. Part of the U4/U5/U6 tri-snRNP complex, one of the building blocks of the spliceosome. 
Sequence Annotation
 REPEAT 229 268 WD 1.
 REPEAT 271 318 WD 2.
 REPEAT 321 360 WD 3.
 REPEAT 363 402 WD 4.
 REPEAT 405 444 WD 5.
 REPEAT 447 487 WD 6.
 REPEAT 490 521 WD 7.
 MOD_RES 27 27 N6-acetyllysine.  
Keyword
 3D-structure; Acetylation; Alternative splicing; Complete proteome; Direct protein sequencing; mRNA processing; mRNA splicing; Nucleus; Reference proteome; Repeat; Spliceosome; WD repeat. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 522 AA 
Protein Sequence
MASSRASSTQ ATKTKAPDDL VAPVVKKPHI YYGSLEEKER ERLAKGESGI LGKDGLKAGI 60
EAGNINITSG EVFEIEEHIS ERQAEVLAEF ERRKRARQIN VSTDDSEVKA CLRALGEPIT 120
LFGEGPAERR ERLRNILSVV GTDALKKTKK DDEKSKKSKE EYQQTWYHEG PNSLKVARLW 180
IANYSLPRAM KRLEEARLHK EIPETTRTSQ MQELHKSLRS LNNFCSQIGD DRPISYCHFS 240
PNSKMLATAC WSGLCKLWSV PDCNLLHTLR GHNTNVGAIV FHPKSTVSLD PKDVNLASCA 300
ADGSVKLWSL DSDEPVADIE GHTVRVARVM WHPSGRFLGT TCYDRSWRLW DLEAQEEILH 360
QEGHSMGVYD IAFHQDGSLA GTGGLDAFGR VWDLRTGRCI MFLEGHLKEI YGINFSPNGY 420
HIATGSGDNT CKVWDLRQRR CVYTIPAHQN LVTGVKFEPI HGNFLLTGAY DNTAKIWTHP 480
GWSPLKTLAG HEGKVMGLDI SSDGQLIATC SYDRTFKLWM AE 522 
Gene Ontology
 GO:0015030; C:Cajal body; IDA:BHF-UCL.
 GO:0016607; C:nuclear speck; IEA:UniProtKB-SubCell.
 GO:0005681; C:spliceosomal complex; NAS:UniProtKB.
 GO:0071001; C:U4/U6 snRNP; IDA:BHF-UCL.
 GO:0000398; P:mRNA splicing, via spliceosome; IC:BHF-UCL. 
Interpro
 IPR020472; G-protein_beta_WD-40_rep.
 IPR014906; PRP4.
 IPR027106; Prp4/Asa1.
 IPR003648; SFM.
 IPR015943; WD40/YVTN_repeat-like_dom.
 IPR001680; WD40_repeat.
 IPR019775; WD40_repeat_CS.
 IPR017986; WD40_repeat_dom. 
Pfam
 PF08799; PRP4
 PF00400; WD40 
SMART
 SM00500; SFM
 SM00320; WD40 
PROSITE
 PS00678; WD_REPEATS_1
 PS50082; WD_REPEATS_2
 PS50294; WD_REPEATS_REGION 
PRINTS
 PR00320; GPROTEINBRPT.