CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-012571
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Helicase SKI2W 
Protein Synonyms/Alias
 Ski2; Helicase-like protein; HLP 
Gene Name
 SKIV2L 
Gene Synonyms/Alias
 DDX13; SKI2W; SKIV2; W 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
84SARKWQRKTDPWSLLubiquitination[1]
192TIPPGFKKGMDFAPKubiquitination[1]
316FEPDVFQKQAILHLEubiquitination[1]
351YAIALAQKHMTRTIYubiquitination[1]
363TIYTSPIKALSNQKFubiquitination[1, 2, 3]
369IKALSNQKFRDFRNTubiquitination[1]
516SRGAFHTKGYYAAVEubiquitination[1, 4]
525YYAAVEAKKERMSKHubiquitination[4]
526YAAVEAKKERMSKHAubiquitination[1]
531AKKERMSKHAQTFGAubiquitination[1]
539HAQTFGAKQPTHQGGubiquitination[1, 4]
597DLTTSSEKSEIHLFLubiquitination[1]
720GTVILLCKGRVPEMAubiquitination[1]
736LHRMMMGKPSQLQSQubiquitination[1]
767LRVEDMMKRSFSEFPubiquitination[1]
780FPSRKDSKAHEQALAubiquitination[1, 4]
791QALAELTKRLGALEEubiquitination[1, 4, 5]
837MESVNGLKSLSAGRVubiquitination[1, 4, 5]
879TTLVLCDKPLSQDPQubiquitination[1]
919PCDHTVVKLQPGDMAubiquitination[1]
931DMAAITTKVLRVNGEubiquitination[1]
939VLRVNGEKILEDFSKubiquitination[1]
946KILEDFSKRQQPKFKubiquitination[1]
953KRQQPKFKKDPPLAAubiquitination[1]
954RQQPKFKKDPPLAAVubiquitination[1]
991PVNDLQLKDMSVVEGubiquitination[1, 4]
1004EGGLRARKLEELIQGubiquitination[1]
1026RFPAQYLKLRERMQIubiquitination[1, 5]
1035RERMQIQKEMERLRFubiquitination[1]
1075VDEAGTVKLAGRVACubiquitination[1, 4, 6]
1225GEPVLGAKMETAATLubiquitination[1, 4]
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] 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]
 [4] 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]
 [5] Ubiquitin ligase substrate identification through quantitative proteomics at both the protein and peptide levels.
 Lee KA, Hammerle LP, Andrews PS, Stokes MP, Mustelin T, Silva JC, Black RA, Doedens JR.
 J Biol Chem. 2011 Dec 2;286(48):41530-8. [PMID: 21987572]
 [6] Proteome-wide identification of ubiquitylation sites by conjugation of engineered lysine-less ubiquitin.
 Oshikawa K, Matsumoto M, Oyamada K, Nakayama KI.
 J Proteome Res. 2012 Feb 3;11(2):796-807. [PMID: 22053931] 
Functional Description
 Helicase; has ATPase activity. Component of the SKI complex which is thought to be involved in exosome-mediated RNA decay and associates with transcriptionally active genes in a manner dependent on PAF1 complex (PAF1C). 
Sequence Annotation
 DOMAIN 319 475 Helicase ATP-binding.
 DOMAIN 585 755 Helicase C-terminal.
 NP_BIND 332 339 ATP (Potential).
 MOTIF 423 426 DEVH box.
 MOD_RES 245 245 Phosphoserine.
 MOD_RES 256 256 Phosphoserine.  
Keyword
 ATP-binding; Complete proteome; Cytoplasm; Disease mutation; Helicase; Hydrolase; Nucleotide-binding; Nucleus; Phosphoprotein; Polymorphism; Reference proteome; RNA-binding. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 1246 AA 
Protein Sequence
MMETERLVLP PPDPLDLPLR AVELGCTGHW ELLNLPGAPE SSLPHGLPPC APDLQQEAEQ 60
LFLSSPAWLP LHGVEHSARK WQRKTDPWSL LAVLGAPVPS DLQAQRHPTT GQILGYKEVL 120
LENTNLSATT SLSLRRPPGP ASQSLWGNPT QYPFWPGGMD EPTITDLNTR EEAEEEIDFE 180
KDLLTIPPGF KKGMDFAPKD CPTPAPGLLS LSCMLEPLDL GGGDEDENEA VGQPGGPRGD 240
TVSASPCSAP LARASSLEDL VLKEASTAVS TPEAPEPPSQ EQWAIPVDAT SPVGDFYRLI 300
PQPAFQWAFE PDVFQKQAIL HLERHDSVFV AAHTSAGKTV VAEYAIALAQ KHMTRTIYTS 360
PIKALSNQKF RDFRNTFGDV GLLTGDVQLH PEASCLIMTT EILRSMLYSG SDVIRDLEWV 420
IFDEVHYIND VERGVVWEEV LIMLPDHVSI ILLSATVPNA LEFADWIGRL KRRQIYVIST 480
VTRPVPLEHY LFTGNSSKTQ GELFLLLDSR GAFHTKGYYA AVEAKKERMS KHAQTFGAKQ 540
PTHQGGPAQD RGVYLSLLAS LRTRAQLPVV VFTFSRGRCD EQASGLTSLD LTTSSEKSEI 600
HLFLQRCLAR LRGSDRQLPQ VLHMSELLNR GLGVHHSGIL PILKEIVEML FSRGLVKVLF 660
ATETFAMGVN MPARTVVFDS MRKHDGSTFR DLLPGEYVQM AGRAGRRGLD PTGTVILLCK 720
GRVPEMADLH RMMMGKPSQL QSQFRLTYTM ILNLLRVDAL RVEDMMKRSF SEFPSRKDSK 780
AHEQALAELT KRLGALEEPD MTGQLVDLPE YYSWGEELTE TQHMIQRRIM ESVNGLKSLS 840
AGRVVVVKNQ EHHNALGVIL QVSSNSTSRV FTTLVLCDKP LSQDPQDRGP ATAEVPYPDD 900
LVGFKLFLPE GPCDHTVVKL QPGDMAAITT KVLRVNGEKI LEDFSKRQQP KFKKDPPLAA 960
VTTAVQELLR LAQAHPAGPP TLDPVNDLQL KDMSVVEGGL RARKLEELIQ GAQCVHSPRF 1020
PAQYLKLRER MQIQKEMERL RFLLSDQSLL LLPEYHQRVE VLRTLGYVDE AGTVKLAGRV 1080
ACAMSSHELL LTELMFDNAL STLRPEEIAA LLSGLVCQSP GDAGDQLPNT LKQGIERVRA 1140
VAKRIGEVQV ACGLNQTVEE FVGELNFGLV EVVYEWARGM PFSELAGLSG TPEGLVVRCI 1200
QRLAEMCRSL RGAARLVGEP VLGAKMETAA TLLRRDIVFA ASLYTQ 1246 
Gene Ontology
 GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
 GO:0055087; C:Ski complex; IDA:UniProtKB.
 GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
 GO:0004004; F:ATP-dependent RNA helicase activity; TAS:ProtInc.
 GO:0003723; F:RNA binding; IEA:UniProtKB-KW. 
Interpro
 IPR011545; DNA/RNA_helicase_DEAD/DEAH_N.
 IPR012961; DSH_C.
 IPR014001; Helicase_ATP-bd.
 IPR001650; Helicase_C.
 IPR027417; P-loop_NTPase.
 IPR016438; RNA_helicase_ATP-dep_SK12/DOB1.
 IPR025696; rRNA_proc-arch_dom. 
Pfam
 PF00270; DEAD
 PF08148; DSHCT
 PF00271; Helicase_C
 PF13234; rRNA_proc-arch 
SMART
 SM00487; DEXDc
 SM00490; HELICc 
PROSITE
 PS51192; HELICASE_ATP_BIND_1
 PS51194; HELICASE_CTER 
PRINTS