CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-006509
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Coatomer subunit beta' 
Protein Synonyms/Alias
 Beta'-coat protein; Beta'-COP; p102 
Gene Name
 COPB2 
Gene Synonyms/Alias
  
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
69AAKFVARKNWVVTGAubiquitination[1]
168ASLDRTIKVWQLGSSubiquitination[1, 2, 3, 4]
199DYYSGGDKPYLISGAubiquitination[1]
318NGKIIWAKHSEVQQAacetylation[5]
318NGKIIWAKHSEVQQAubiquitination[1, 2, 4]
328EVQQANLKAMGDAEIubiquitination[2, 4]
346ERLPLAVKDMGSCEIubiquitination[2, 3, 4]
386TAMALRNKSFGSAQEubiquitination[2, 4]
608RDFSMADKVLPTIPKubiquitination[1, 2, 3, 4, 6]
627RVAHFLEKQGFKQQAacetylation[5]
627RVAHFLEKQGFKQQAubiquitination[1]
724EGAERDGKNNVAFMSubiquitination[1, 3, 6]
771SQVSRVVKLWRENLSubiquitination[1]
783NLSKVNQKAAESLADubiquitination[1, 6, 7]
822HADLWPAKQYPLVTPubiquitination[1, 6, 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] 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]
 [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] 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]
 [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]
 [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] 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
 The coatomer is a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi non- clathrin-coated vesicles, which further mediate biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network. Coatomer complex is required for budding from Golgi membranes, and is essential for the retrograde Golgi-to-ER transport of dilysine-tagged proteins. In mammals, the coatomer can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins; the complex also influences the Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors (By similarity). 
Sequence Annotation
 REPEAT 13 52 WD 1.
 REPEAT 55 94 WD 2.
 REPEAT 97 136 WD 3.
 REPEAT 140 180 WD 4.
 REPEAT 183 224 WD 5.
 REPEAT 227 266 WD 6.
 REPEAT 350 388 WD 7.
 REPEAT 390 425 WD 8.
 REPEAT 746 783 WD 9.
 MOD_RES 627 627 N6-acetyllysine.
 MOD_RES 859 859 Phosphoserine.  
Keyword
 Acetylation; Coiled coil; Complete proteome; Cytoplasm; Cytoplasmic vesicle; Direct protein sequencing; ER-Golgi transport; Golgi apparatus; Membrane; Phosphoprotein; Protein transport; Reference proteome; Repeat; Transport; WD repeat. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 906 AA 
Protein Sequence
MPLRLDIKRK LTARSDRVKS VDLHPTEPWM LASLYNGSVC VWNHETQTLV KTFEVCDLPV 60
RAAKFVARKN WVVTGADDMQ IRVFNYNTLE RVHMFEAHSD YIRCIAVHPT QPFILTSSDD 120
MLIKLWDWDK KWSCSQVFEG HTHYVMQIVI NPKDNNQFAS ASLDRTIKVW QLGSSSPNFT 180
LEGHEKGVNC IDYYSGGDKP YLISGADDRL VKIWDYQNKT CVQTLEGHAQ NVSCASFHPE 240
LPIIITGSED GTVRIWHSST YRLESTLNYG MERVWCVASL RGSNNVALGY DEGSIIVKLG 300
REEPAMSMDA NGKIIWAKHS EVQQANLKAM GDAEIKDGER LPLAVKDMGS CEIYPQTIQH 360
NPNGRFVVVC GDGEYIIYTA MALRNKSFGS AQEFAWAHDS SEYAIRESNS IVKIFKNFKE 420
KKSFKPDFGA ESIYGGFLLG VRSVNGLAFY DWDNTELIRR IEIQPKHIFW SDSGELVCIA 480
TEESFFILKY LSEKVLAAQE THEGVTEDGI EDAFEVLGEI QEIVKTGLWV GDCFIYTSSV 540
NRLNYYVGGE IVTIAHLDRT MYLLGYIPKD NRLYLGDKEL NIISYSLLVS VLEYQTAVMR 600
RDFSMADKVL PTIPKEQRTR VAHFLEKQGF KQQALTVSTD PEHRFELALQ LGELKIAYQL 660
AVEAESEQKW KQLAELAISK CQFGLAQECL HHAQDYGGLL LLATASGNAN MVNKLAEGAE 720
RDGKNNVAFM SYFLQGKVDA CLELLIRTGR LPEAAFLART YLPSQVSRVV KLWRENLSKV 780
NQKAAESLAD PTEYENLFPG LKEAFVVEEW VKETHADLWP AKQYPLVTPN EERNVMEEGK 840
DFQPSRSTAQ QELDGKPASP TPVIVASHTA NKEEKSLLEL EVDLDNLELE DIDTTDINLD 900
EDILDD 906 
Gene Ontology
 GO:0015629; C:actin cytoskeleton; IDA:HPA.
 GO:0030126; C:COPI vesicle coat; IDA:UniProtKB.
 GO:0005829; C:cytosol; TAS:Reactome.
 GO:0005198; F:structural molecule activity; IEA:InterPro.
 GO:0048205; P:COPI coating of Golgi vesicle; TAS:Reactome.
 GO:0006891; P:intra-Golgi vesicle-mediated transport; IDA:UniProtKB.
 GO:0006886; P:intracellular protein transport; IEA:InterPro.
 GO:0006890; P:retrograde vesicle-mediated transport, Golgi to ER; TAS:UniProtKB. 
Interpro
 IPR006692; Coatomer_WD-assoc_reg.
 IPR016453; COPB2.
 IPR020472; G-protein_beta_WD-40_rep.
 IPR015943; WD40/YVTN_repeat-like_dom.
 IPR001680; WD40_repeat.
 IPR017986; WD40_repeat_dom. 
Pfam
 PF04053; Coatomer_WDAD
 PF00400; WD40 
SMART
 SM00320; WD40 
PROSITE
 PS00678; WD_REPEATS_1
 PS50082; WD_REPEATS_2
 PS50294; WD_REPEATS_REGION 
PRINTS
 PR00320; GPROTEINBRPT.