CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-022182
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 DDB1- and CUL4-associated factor 13 
Protein Synonyms/Alias
 WD repeat and SOF domain-containing protein 1 
Gene Name
 DCAF13 
Gene Synonyms/Alias
 WDSOF1; HSPC064 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
18DNYVRETKLDLQRVPubiquitination[1]
49IRALNATKLERVFAKacetylation[2]
49IRALNATKLERVFAKubiquitination[1, 3]
56KLERVFAKPFLASLDubiquitination[1, 3, 4, 5]
74DGVNCLAKHPEKLATubiquitination[1]
78CLAKHPEKLATVLSGubiquitination[1]
131FFTVGDDKTVKQWKMubiquitination[1]
134VGDDKTVKQWKMDGPubiquitination[1]
137DKTVKQWKMDGPGYGubiquitination[1, 3]
234RQATPLKKVILDMRTubiquitination[1]
304FVSASFDKSIRIFPVubiquitination[1, 3, 4, 5, 6]
313IRIFPVDKSRSREVYubiquitination[1, 6]
353EMNIRLWKANASEKLubiquitination[1]
359WKANASEKLGVLTSRubiquitination[1, 3, 4, 5, 6]
376AAKDYNQKLKEKFQHubiquitination[1]
398ARHRHLPKSIYSQIQubiquitination[3, 4, 5, 7, 8]
Reference
 [1] 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]
 [2] 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]
 [3] 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]
 [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] 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]
 [6] 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]
 [7] Methods for quantification of in vivo changes in protein ubiquitination following proteasome and deubiquitinase inhibition.
 Udeshi ND, Mani DR, Eisenhaure T, Mertins P, Jaffe JD, Clauser KR, Hacohen N, Carr SA.
 Mol Cell Proteomics. 2012 May;11(5):148-59. [PMID: 22505724]
 [8] 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] 
Functional Description
 Possible role in ribosomal RNA processing (By similarity). May function as a substrate receptor for CUL4-DDB1 E3 ubiquitin-protein ligase complex. 
Sequence Annotation
 REPEAT 64 104 WD 1.
 REPEAT 107 146 WD 2.
 REPEAT 149 191 WD 3.
 REPEAT 194 234 WD 4.
 REPEAT 236 276 WD 5.
 REPEAT 280 319 WD 6.
 REPEAT 323 362 WD 7.
 MOD_RES 49 49 N6-acetyllysine.  
Keyword
 Acetylation; Alternative splicing; Complete proteome; Nucleus; Polymorphism; Reference proteome; Repeat; Ribonucleoprotein; Ribosome biogenesis; rRNA processing; Ubl conjugation pathway; WD repeat. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 445 AA 
Protein Sequence
MKVKMLSRNP DNYVRETKLD LQRVPRNYDP ALHPFEVPRE YIRALNATKL ERVFAKPFLA 60
SLDGHRDGVN CLAKHPEKLA TVLSGACDGE VRIWNLTQRN CIRTIQAHEG FVRGICTRFC 120
GTSFFTVGDD KTVKQWKMDG PGYGDEEEPL HTILGKTVYT GIDHHWKEAV FATCGQQVDI 180
WDEQRTNPIC SMTWGFDSIS SVKFNPIETF LLGSCASDRN IVLYDMRQAT PLKKVILDMR 240
TNTICWNPME AFIFTAANED YNLYTFDMRA LDTPVMVHMD HVSAVLDVDY SPTGKEFVSA 300
SFDKSIRIFP VDKSRSREVY HTKRMQHVIC VKWTSDSKYI MCGSDEMNIR LWKANASEKL 360
GVLTSREKAA KDYNQKLKEK FQHYPHIKRI ARHRHLPKSI YSQIQEQRIM KEARRRKEVN 420
RIKHSKPGSV PLVSEKKKHV VAVVK 445 
Gene Ontology
 GO:0080008; C:Cul4-RING ubiquitin ligase complex; IDA:UniProtKB.
 GO:0005730; C:nucleolus; IEA:UniProtKB-SubCell.
 GO:0030529; C:ribonucleoprotein complex; IEA:UniProtKB-KW.
 GO:0016567; P:protein ubiquitination; IC:UniProtKB.
 GO:0006364; P:rRNA processing; IEA:UniProtKB-KW. 
Interpro
 IPR007287; Sof1.
 IPR015943; WD40/YVTN_repeat-like_dom.
 IPR001680; WD40_repeat.
 IPR019775; WD40_repeat_CS.
 IPR017986; WD40_repeat_dom. 
Pfam
 PF04158; Sof1
 PF00400; WD40 
SMART
 SM00320; WD40 
PROSITE
 PS00678; WD_REPEATS_1
 PS50082; WD_REPEATS_2
 PS50294; WD_REPEATS_REGION 
PRINTS