CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-019734
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Phosphoinositide 3-kinase regulatory subunit 4 
Protein Synonyms/Alias
 PI3-kinase regulatory subunit 4; PI3-kinase p150 subunit; Phosphoinositide 3-kinase adaptor protein 
Gene Name
 PIK3R4 
Gene Synonyms/Alias
  
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
68TLPLTSYKQELEELKubiquitination[1, 2, 3]
75KQELEELKIRLNSAQubiquitination[2, 4]
89QNCLPFQKASEKASEubiquitination[2, 4, 5, 6]
97ASEKASEKAAMLFRQubiquitination[1, 2, 4]
280FPEQVLNKIEDHSIRubiquitination[1, 2, 5]
309LEAEDYLKQQRGNAFubiquitination[1, 2, 3]
443EALRTLTKVLALVKEubiquitination[2, 5]
449TKVLALVKEVPRNDIubiquitination[1, 2]
553SDPENIVKQTLMENGubiquitination[1]
713PIIQIERKLVLLSVLubiquitination[2]
736FDYALRSKDITSLFRubiquitination[2]
772PAIAQLLKKLLSQGMubiquitination[2, 6]
773AIAQLLKKLLSQGMTubiquitination[1, 2]
786MTEEEEDKLLALKDFubiquitination[2]
791EDKLLALKDFMMKSNubiquitination[1, 2]
801MMKSNKAKANIVDQSubiquitination[2]
816HLHDSSQKGVIDLAAubiquitination[2]
850KRARKHVKQDSNVNEubiquitination[1, 2]
888QEVIQTGKPPRSESSubiquitination[1, 2, 4]
918VTTVQNKKPVIPVLSubiquitination[2, 4]
941QIRITTCKTELQQLIubiquitination[2]
951LQQLIQQKREQCNAEubiquitination[1, 2]
1081SKLPKSPKIHPLQSRubiquitination[2]
1293PSVSYYRKIIEGTEVubiquitination[2, 7, 8]
1307VVQEIQNKQKVGPSDubiquitination[1, 2]
1309QEIQNKQKVGPSDDTubiquitination[2]
Reference
 [1] 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]
 [2] 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]
 [3] 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]
 [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] Global identification of modular cullin-RING ligase substrates.
 Emanuele MJ, Elia AE, Xu Q, Thoma CR, Izhar L, Leng Y, Guo A, Chen YN, Rush J, Hsu PW, Yen HC, Elledge SJ.
 Cell. 2011 Oct 14;147(2):459-74. [PMID: 21963094]
 [6] 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]
 [7] 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]
 [8] 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
 Regulatory subunit of the PI3K complex. May regulate membrane trafficking late in the endocytic pathway. 
Sequence Annotation
 DOMAIN 26 324 Protein kinase.
 REPEAT 413 450 HEAT 1.
 REPEAT 458 495 HEAT 2.
 REPEAT 572 610 HEAT 3.
 REPEAT 991 1030 WD 1.
 REPEAT 1040 1079 WD 2.
 REPEAT 1093 1134 WD 3.
 REPEAT 1139 1178 WD 4.
 REPEAT 1182 1223 WD 5.
 REPEAT 1237 1278 WD 6.
 REPEAT 1327 1358 WD 7.
 NP_BIND 32 40 ATP (By similarity).
 ACT_SITE 148 148 Proton acceptor (By similarity).
 BINDING 53 53 ATP (By similarity).
 MOD_RES 808 808 Phosphoserine.
 MOD_RES 853 853 Phosphoserine.
 MOD_RES 865 865 Phosphoserine.
 MOD_RES 894 894 Phosphoserine (By similarity).
 MOD_RES 905 905 Phosphoserine (By similarity).
 MOD_RES 1316 1316 Phosphothreonine.
 LIPID 2 2 N-myristoyl glycine.  
Keyword
 ATP-binding; Complete proteome; Direct protein sequencing; Endosome; Kinase; Lipoprotein; Myristate; Nucleotide-binding; Phosphoprotein; Polymorphism; Reference proteome; Repeat; Serine/threonine-protein kinase; Transferase; WD repeat. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 1358 AA 
Protein Sequence
MGNQLAGIAP SQILSVESYF SDIHDFEYDK SLGSTRFFKV ARAKHREGLV VVKVFAIQDP 60
TLPLTSYKQE LEELKIRLNS AQNCLPFQKA SEKASEKAAM LFRQYVRDNL YDRISTRPFL 120
NNIEKRWIAF QILTAVDQAH KSGVRHGDIK TENVMVTSWN WVLLTDFASF KPTYLPEDNP 180
ADFNYFFDTS RRRTCYIAPE RFVDGGMFAT ELEYMRDPST PLVDLNSNQR TRGELKRAMD 240
IFSAGCVIAE LFTEGVPLFD LSQLLAYRNG HFFPEQVLNK IEDHSIRELV TQMIHREPDK 300
RLEAEDYLKQ QRGNAFPEIF YTFLQPYMAQ FAKETFLSAD ERILVIRKDL GNIIHNLCGH 360
DLPEKAEGEP KENGLVILVS VITSCLQTLK YCDSKLAALE LILHLAPRLS VEILLDRITP 420
YLLHFSNDSV PRVRAEALRT LTKVLALVKE VPRNDINIYP EYILPGIAHL AQDDATIVRL 480
AYAENIALLA ETALRFLELV QLKNLNMEND PNNEEIDEVT HPNGNYDTEL QALHEMVQQK 540
VVTLLSDPEN IVKQTLMENG ITRLCVFFGR QKANDVLLSH MITFLNDKND WHLRGAFFDS 600
IVGVAAYVGW QSSSILKPLL QQGLSDAEEF VIVKALYALT CMCQLGLLQK PHVYEFASDI 660
APFLCHPNLW IRYGAVGFIT VVARQISTAD VYCKLMPYLD PYITQPIIQI ERKLVLLSVL 720
KEPVSRSIFD YALRSKDITS LFRHLHMRQK KRNGSLPDCP PPEDPAIAQL LKKLLSQGMT 780
EEEEDKLLAL KDFMMKSNKA KANIVDQSHL HDSSQKGVID LAALGITGRQ VDLVKTKQEP 840
DDKRARKHVK QDSNVNEEWK SMFGSLDPPN MPQALPKGSD QEVIQTGKPP RSESSAGICV 900
PLSTSSQVPE VTTVQNKKPV IPVLSSTILP STYQIRITTC KTELQQLIQQ KREQCNAERI 960
AKQMMENAEW ESKPPPPGWR PKGLLVAHLH EHKSAVNRIR VSDEHSLFAT CSNDGTVKIW 1020
NSQKMEGKTT TTRSILTYSR IGGRVKTLTF CQGSHYLAIA SDNGAVQLLG IEASKLPKSP 1080
KIHPLQSRIL DQKEDGCVVD MHHFNSGAQS VLAYATVNGS LVGWDLRSSS NAWTLKHDLK 1140
SGLITSFAVD IHQCWLCIGT SSGTMACWDM RFQLPISSHC HPSRARIRRL SMHPLYQSWV 1200
IAAVQGNNEV SMWDMETGDR RFTLWASSAP PLSELQPSPH SVHGIYCSPA DGNPILLTAG 1260
SDMKIRFWDL AYPERSYVVA GSTSSPSVSY YRKIIEGTEV VQEIQNKQKV GPSDDTPRRG 1320
PESLPVGHHD IITDVATFQT TQGFIVTASR DGIVKVWK 1358 
Gene Ontology
 GO:0005829; C:cytosol; TAS:Reactome.
 GO:0005770; C:late endosome; IDA:UniProtKB.
 GO:0005524; F:ATP binding; NAS:UniProtKB.
 GO:0004672; F:protein kinase activity; NAS:UniProtKB.
 GO:0004674; F:protein serine/threonine kinase activity; IEA:UniProtKB-KW.
 GO:0045087; P:innate immune response; TAS:Reactome.
 GO:0008286; P:insulin receptor signaling pathway; TAS:Reactome.
 GO:0006661; P:phosphatidylinositol biosynthetic process; TAS:Reactome.
 GO:0044281; P:small molecule metabolic process; TAS:Reactome.
 GO:0034162; P:toll-like receptor 9 signaling pathway; TAS:Reactome. 
Interpro
 IPR011989; ARM-like.
 IPR016024; ARM-type_fold.
 IPR021133; HEAT_type_2.
 IPR011009; Kinase-like_dom.
 IPR000719; Prot_kinase_cat_dom.
 IPR008271; Ser/Thr_kinase_AS.
 IPR015943; WD40/YVTN_repeat-like_dom.
 IPR001680; WD40_repeat.
 IPR019775; WD40_repeat_CS.
 IPR017986; WD40_repeat_dom. 
Pfam
 PF00069; Pkinase
 PF00400; WD40 
SMART
 SM00320; WD40 
PROSITE
 PS50077; HEAT_REPEAT
 PS00107; PROTEIN_KINASE_ATP
 PS50011; PROTEIN_KINASE_DOM
 PS00108; PROTEIN_KINASE_ST
 PS00678; WD_REPEATS_1
 PS50082; WD_REPEATS_2
 PS50294; WD_REPEATS_REGION 
PRINTS