CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-015433
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 WD repeat-containing protein 82 
Protein Synonyms/Alias
 Protein TMEM113; Swd2 
Gene Name
 WDR82 
Gene Synonyms/Alias
 TMEM113; WDR82A; UNQ9342/PRO34047 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
2******MKLTDSVLRubiquitination[1, 2]
62PKRTLYSKKYGVDLIubiquitination[3]
63KRTLYSKKYGVDLIRubiquitination[1, 2, 3, 4, 5]
84TVVYSSNKIDDTIRYubiquitination[1, 2, 6, 7]
98YLSLHDNKYIRYFPGacetylation[8, 9]
98YLSLHDNKYIRYFPGubiquitination[1, 4, 5]
129FISGSLDKTIRLWDLubiquitination[1, 6, 7]
181YDLRSFDKGPFATFKacetylation[8]
181YDLRSFDKGPFATFKubiquitination[1, 3]
188KGPFATFKMQYDRTCubiquitination[3, 4, 5]
201TCEWTGLKFSNDGKLubiquitination[1]
225IRLIDAFKGVVMHTFubiquitination[1]
280KVAVLDGKHTGPITCubiquitination[1, 2, 3, 10]
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] 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] 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]
 [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] 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]
 [7] 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]
 [8] 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]
 [9] 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]
 [10] 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
Functional Description
 Regulatory component of the SET1 complex implicated in the tethering of this complex to transcriptional start sites of active genes. Facilitates histone H3 'Lys-4' methylation via recruitment of the SETD1A or SETD1B to the 'Ser-5' phosphorylated C-terminal domain (CTD) of RNA polymerase II large subunit (POLR2A). Component of PTW/PP1 phosphatase complex, which plays a role in the control of chromatin structure and cell cycle progression during the transition from mitosis into interphase. 
Sequence Annotation
 REPEAT 19 58 WD 1.
 REPEAT 105 144 WD 2.
 REPEAT 146 184 WD 3.
 REPEAT 192 231 WD 4.
 REPEAT 236 276 WD 5.
 REPEAT 280 313 WD 6.
 MOD_RES 154 154 Phosphoserine (By similarity).  
Keyword
 Complete proteome; Nucleus; Phosphoprotein; Reference proteome; Repeat; WD repeat. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 313 AA 
Protein Sequence
MKLTDSVLRS FRVAKVFREN SDKINCFDFS PNGETVISSS DDDSIVLYDC QEGKPKRTLY 60
SKKYGVDLIR YTHAANTVVY SSNKIDDTIR YLSLHDNKYI RYFPGHSKRV VALSMSPVDD 120
TFISGSLDKT IRLWDLRSPN CQGLMHLQGK PVCSFDPEGL IFAAGVNSEM VKLYDLRSFD 180
KGPFATFKMQ YDRTCEWTGL KFSNDGKLIL ISTNGSFIRL IDAFKGVVMH TFGGYANSKA 240
VTLEASFTPD SQFIMIGSED GKIHVWNGES GIKVAVLDGK HTGPITCLQF NPKFMTFASA 300
CSNMAFWLPT IDD 313 
Gene Ontology
 GO:0000785; C:chromatin; IDA:UniProtKB.
 GO:0072357; C:PTW/PP1 phosphatase complex; IDA:UniProtKB.
 GO:0048188; C:Set1C/COMPASS complex; IDA:UniProtKB.
 GO:0003682; F:chromatin binding; IEA:Compara.
 GO:0051568; P:histone H3-K4 methylation; IDA:UniProtKB. 
Interpro
 IPR020472; G-protein_beta_WD-40_rep.
 IPR015943; WD40/YVTN_repeat-like_dom.
 IPR001680; WD40_repeat.
 IPR019775; WD40_repeat_CS.
 IPR017986; WD40_repeat_dom. 
Pfam
 PF00400; WD40 
SMART
 SM00320; WD40 
PROSITE
 PS00678; WD_REPEATS_1
 PS50082; WD_REPEATS_2
 PS50294; WD_REPEATS_REGION 
PRINTS
 PR00320; GPROTEINBRPT.