CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-022944
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Probable ATP-dependent RNA helicase DDX20 
Protein Synonyms/Alias
 Component of gems 3; DEAD box protein 20; DEAD box protein DP 103; Gemin-3 
Gene Name
 DDX20 
Gene Synonyms/Alias
 DP103; GEMIN3 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
91RPSPVQLKAIPLGRCubiquitination[1, 2, 3]
175GTPLSQDKTRLKKCHubiquitination[2]
192VGSPGRIKQLIELDYubiquitination[2, 4]
277DPSLIGLKQYYKVVNubiquitination[2, 4, 5]
281IGLKQYYKVVNSYPLubiquitination[2]
291NSYPLAHKVFEEKTQubiquitination[2, 4]
296AHKVFEEKTQHLQELubiquitination[2, 4, 6]
332LADILSSKGFPAECIubiquitination[2, 4, 7]
354QRLDAMAKLKHFHCRubiquitination[2, 4]
473SVPNQPLKKQIQKIEubiquitination[2]
474VPNQPLKKQIQKIERubiquitination[2]
487ERTLQIQKAHGDHMAubiquitination[2]
519TKQKLPVKSHSECGIubiquitination[2]
534IEKATSPKELGCDRQubiquitination[2]
565TNSQHQVKEALPVSLubiquitination[2]
608YIKEGLEKPVEIIRHubiquitination[2]
683GSSDNQLKDSESTPVubiquitination[8]
710SDTPNPEKYQESPGIubiquitination[2]
720ESPGIQMKTRLKEGAubiquitination[2, 6, 8]
Reference
 [1] 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]
 [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] 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] 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]
 [5] 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]
 [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] 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]
 [8] 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
Functional Description
 The SMN complex plays an essential role in spliceosomal snRNP assembly in the cytoplasm and is required for pre-mRNA splicing in the nucleus. It may also play a role in the metabolism of snoRNPs. 
Sequence Annotation
 DOMAIN 93 264 Helicase ATP-binding.
 DOMAIN 299 448 Helicase C-terminal.
 NP_BIND 109 114 ATP.
 REGION 456 548 SMN interacting.
 MOTIF 62 90 Q motif.
 MOTIF 211 214 DEAD box.
 BINDING 84 84 ATP; via carbonyl oxygen.
 BINDING 89 89 ATP.
 MOD_RES 48 48 Phosphoserine.
 MOD_RES 187 187 Phosphoserine.
 MOD_RES 500 500 Phosphoserine.
 MOD_RES 505 505 Phosphoserine.
 MOD_RES 532 532 Phosphoserine.
 MOD_RES 552 552 Phosphothreonine.
 MOD_RES 652 652 Phosphoserine.
 MOD_RES 654 654 Phosphoserine.
 MOD_RES 656 656 Phosphoserine.
 MOD_RES 672 672 Phosphoserine.
 MOD_RES 677 677 Phosphoserine.
 MOD_RES 678 678 Phosphoserine.
 MOD_RES 688 688 Phosphothreonine.
 MOD_RES 703 703 Phosphoserine.
 MOD_RES 705 705 Phosphothreonine.
 MOD_RES 714 714 Phosphoserine.  
Keyword
 3D-structure; ATP-binding; Complete proteome; Cytoplasm; DNA-binding; Helicase; Hydrolase; mRNA processing; mRNA splicing; Nucleotide-binding; Nucleus; Phosphoprotein; Polymorphism; Reference proteome; Spliceosome. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 824 AA 
Protein Sequence
MAAAFEASGA LAAVATAMPA EHVAVQVPAP EPTPGPVRIL RTAQDLSSPR TRTGDVLLAE 60
PADFESLLLS RPVLEGLRAA GFERPSPVQL KAIPLGRCGL DLIVQAKSGT GKTCVFSTIA 120
LDSLVLENLS TQILILAPTR EIAVQIHSVI TAIGIKMEGL ECHVFIGGTP LSQDKTRLKK 180
CHIAVGSPGR IKQLIELDYL NPGSIRLFIL DEADKLLEEG SFQEQINWIY SSLPASKQML 240
AVSATYPEFL ANALTKYMRD PTFVRLNSSD PSLIGLKQYY KVVNSYPLAH KVFEEKTQHL 300
QELFSRIPFN QALVFSNLHS RAQHLADILS SKGFPAECIS GNMNQNQRLD AMAKLKHFHC 360
RVLISTDLTS RGIDAEKVNL VVNLDVPLDW ETYMHRIGRA GRFGTLGLTV TYCCRGEEEN 420
MMMRIAQKCN INLLPLPDPI PSGLMEECVD WDVEVKAAVH TYGIASVPNQ PLKKQIQKIE 480
RTLQIQKAHG DHMASSRNNS VSGLSVKSKN NTKQKLPVKS HSECGIIEKA TSPKELGCDR 540
QSEEQMKNSV QTPVENSTNS QHQVKEALPV SLPQIPCLSS FKIHQPYTLT FAELVEDYEH 600
YIKEGLEKPV EIIRHYTGPG DQTVNPQNGF VRNKVIEQRV PVLASSSQSG DSESDSDSYS 660
SRTSSQSKGN KSYLEGSSDN QLKDSESTPV DDRISLEQPP NGSDTPNPEK YQESPGIQMK 720
TRLKEGASQR AKQSRRNLPR RSSFRLQTEA QEDDWYDCHR EIRLSFSDTY QDYEEYWRAY 780
YRAWQEYYAA ASHSYYWNAQ RHPSWMAAYH MNTIYLQEMM HSNQ 824 
Gene Ontology
 GO:0015030; C:Cajal body; IEA:UniProtKB-SubCell.
 GO:0005856; C:cytoskeleton; TAS:ProtInc.
 GO:0005829; C:cytosol; TAS:Reactome.
 GO:0005654; C:nucleoplasm; TAS:Reactome.
 GO:0005681; C:spliceosomal complex; IEA:UniProtKB-KW.
 GO:0017053; C:transcriptional repressor complex; IEA:Compara.
 GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
 GO:0004004; F:ATP-dependent RNA helicase activity; TAS:ProtInc.
 GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
 GO:0000244; P:assembly of spliceosomal tri-snRNP; TAS:ProtInc.
 GO:0006917; P:induction of apoptosis; IEA:Compara.
 GO:0034660; P:ncRNA metabolic process; TAS:Reactome.
 GO:0000122; P:negative regulation of transcription from RNA polymerase II promoter; IEA:Compara.
 GO:0043065; P:positive regulation of apoptotic process; ISS:UniProtKB. 
Interpro
 IPR011545; DNA/RNA_helicase_DEAD/DEAH_N.
 IPR014001; Helicase_ATP-bd.
 IPR001650; Helicase_C.
 IPR027417; P-loop_NTPase.
 IPR000629; RNA-helicase_DEAD-box_CS.
 IPR014014; RNA_helicase_DEAD_Q_motif. 
Pfam
 PF00270; DEAD
 PF00271; Helicase_C 
SMART
 SM00487; DEXDc
 SM00490; HELICc 
PROSITE
 PS00039; DEAD_ATP_HELICASE
 PS51192; HELICASE_ATP_BIND_1
 PS51194; HELICASE_CTER
 PS51195; Q_MOTIF 
PRINTS