CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-019614
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Intraflagellar transport protein 140 homolog 
Protein Synonyms/Alias
 WD and tetratricopeptide repeats protein 2 
Gene Name
 IFT140 
Gene Synonyms/Alias
 KIAA0590; WDTC2 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
145VQGTPLLKHEYGKHLubiquitination[1, 2]
150LLKHEYGKHLTHCIFubiquitination[1]
171EDLVQLAKAAVSGDEubiquitination[1, 2, 3, 4, 5]
179AAVSGDEKALDMFNWubiquitination[1]
188LDMFNWKKSSSGSLLubiquitination[1]
270GKAEEVMKVKLSGKTubiquitination[1]
318YILSPDEKFGFEKGEubiquitination[1, 2, 3]
323DEKFGFEKGENMNCVubiquitination[1, 2]
336CVCYCKVKGLLAAGTubiquitination[1, 2]
353GRVAMWRKVPDFLGSubiquitination[1]
366GSPGAEGKDRWALQTubiquitination[1, 2, 3, 5]
590TISILPSKADNSPDSubiquitination[1]
634FNEQETNKSHLFVDEubiquitination[1]
644LFVDEGLKNYVPVNHubiquitination[1, 3, 5]
733PYYYFTRKPEEADREubiquitination[1]
770VGLEDCDKATRDAMLubiquitination[1, 2]
799FKSIKLIKSEAVWENubiquitination[1, 3]
821TQRLDVAKVCLGNMGubiquitination[1]
877KRHDLLNKFYQAAGRubiquitination[1, 5, 6, 7]
926RALSYYEKSDTHRFEubiquitination[1, 2, 3]
951SLELYVNKMKDKTLWubiquitination[1, 3]
1040YTRAQAFKNAIRLCKubiquitination[1, 4]
1077AARYYEEKGVQMDRAubiquitination[1, 3]
1090RAVMLYHKAGHFSKAubiquitination[1]
1178AEKMTVAKDSSDLPEubiquitination[1, 2, 3, 5]
1312GALTEAYKCLAKAKAubiquitination[1]
1320CLAKAKAKSPLDQETubiquitination[1]
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] 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] 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]
 [5] 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]
 [6] 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]
 [7] 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
 Component of the IFT complex A (IFT-A), a complex required for retrograde ciliary transport. Plays a pivotal role in proper development and function of ciliated cells. Involved in ciliogenesis and cilia maintenance. 
Sequence Annotation
 REPEAT 13 57 WD 1.
 REPEAT 59 98 WD 2.
 REPEAT 101 140 WD 3.
 REPEAT 263 313 WD 4.
 REPEAT 322 361 WD 5.
 REPEAT 772 807 TPR 1.
 REPEAT 869 904 TPR 2.
 REPEAT 906 934 TPR 3.
 REPEAT 955 988 TPR 4.
 REPEAT 1010 1043 TPR 5.
 REPEAT 1078 1111 TPR 6.
 REPEAT 1123 1156 TPR 7.
 REPEAT 1189 1222 TPR 8.
 REPEAT 1376 1409 TPR 9.
 MOD_RES 1443 1443 Phosphoserine.  
Keyword
 Cell projection; Ciliopathy; Cilium; Cilium biogenesis/degradation; Complete proteome; Cytoplasm; Cytoskeleton; Disease mutation; Phosphoprotein; Polymorphism; Reference proteome; Repeat; TPR repeat; WD repeat. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 1462 AA 
Protein Sequence
MALYYDHQIE APDAAGSPSF ISWHPVHPFL AVAYISTTST GSVDIYLEQG ECVPDTHVER 60
PFRVASLCWH PTRLVLAVGW ETGEVTVFNK QDKEQHTMPL THTADITVLR WSPSGNCLLS 120
GDRLGVLLLW RLDQRGRVQG TPLLKHEYGK HLTHCIFRLP PPGEDLVQLA KAAVSGDEKA 180
LDMFNWKKSS SGSLLKMGSH EGLLFFVSLM DGTVHYVDEK GKTTQVVSAD STIQMLFYME 240
KREALVVVTE NLRLSLYTVP PEGKAEEVMK VKLSGKTGRR ADIALIEGSL LVMAVGEAAL 300
RFWDIERGEN YILSPDEKFG FEKGENMNCV CYCKVKGLLA AGTDRGRVAM WRKVPDFLGS 360
PGAEGKDRWA LQTPTELQGN ITQIQWGSRK NLLAVNSVIS VAILSERAMS SHFHQQVAAM 420
QVSPSLLNVC FLSTGVAHSL RTDMHISGVF ATKDAVAVWN GRQVAIFELS GAAIRSAGTF 480
LCETPVLAMH EENVYTVESN RVQVRTWQGT VKQLLLFSET EGNPCFLDIC GNFLVVGTDL 540
AHFKSFDLSR REAKAHCSCR SLAELVPGVG GIASLRCSSS GSTISILPSK ADNSPDSKIC 600
FYDVEMDTVT VFDFKTGQID RRETLSFNEQ ETNKSHLFVD EGLKNYVPVN HFWDQSEPRL 660
FVCEAVQETP RSQPQSANGQ PQDGRAGPAA DVLILSFFIS EEHGFLLHES FPRPATSHSL 720
LGMEVPYYYF TRKPEEADRE DEVEPGCHHI PQMVSRRPLR DFVGLEDCDK ATRDAMLHFS 780
FFVTIGDMDE AFKSIKLIKS EAVWENMARM CVKTQRLDVA KVCLGNMGHA RGARALREAE 840
QEPELEARVA VLATQLGMLE DAEQLYRKCK RHDLLNKFYQ AAGRWQEALQ VAEHHDRVHL 900
RSTYHRYAGH LEASADCSRA LSYYEKSDTH RFEVPRMLSE DLPSLELYVN KMKDKTLWRW 960
WAQYLESQGE MDAALHYYEL ARDHFSLVRI HCFQGNVQKA AQIANETGNL AASYHLARQY 1020
ESQEEVGQAV HFYTRAQAFK NAIRLCKENG LDDQLMNLAL LSSPEDMIEA ARYYEEKGVQ 1080
MDRAVMLYHK AGHFSKALEL AFATQQFVAL QLIAEDLDET SDPALLARCS DFFIEHSQYE 1140
RAVELLLAAR KYQEALQLCL GQNMSITEEM AEKMTVAKDS SDLPEESRRE LLEQIADCCM 1200
RQGSYHLATK KYTQAGNKLK AMRALLKSGD TEKITFFASV SRQKEIYIMA ANYLQSLDWR 1260
KEPEIMKNII GFYTKGRALD LLAGFYDACA QVEIDEYQNY DKAHGALTEA YKCLAKAKAK 1320
SPLDQETRLA QLQSRMALVK RFIQARRTYT EDPKESIKQC ELLLEEPDLD STIRIGDVYG 1380
FLVEHYVRKE EYQTAYRFLE EMRRRLPLAN MSYYVSPQAV DAVHRGLGLP LPRTVPEQVR 1440
HNSMEDAREL DEEVVEEADD DP 1462 
Gene Ontology
 GO:0035085; C:cilium axoneme; IEA:Compara.
 GO:0036064; C:cilium basal body; IDA:UniProtKB.
 GO:0030991; C:intraflagellar transport particle A; IDA:UniProtKB.
 GO:0032391; C:photoreceptor connecting cilium; IEA:Compara.
 GO:0042384; P:cilium assembly; IEA:Compara. 
Interpro
 IPR015943; WD40/YVTN_repeat-like_dom.
 IPR001680; WD40_repeat.
 IPR017986; WD40_repeat_dom. 
Pfam
 PF00400; WD40 
SMART
 SM00320; WD40 
PROSITE
 PS50005; TPR
 PS50293; TPR_REGION
 PS00678; WD_REPEATS_1
 PS50082; WD_REPEATS_2
 PS50294; WD_REPEATS_REGION 
PRINTS