CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-022044
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Nucleolar RNA helicase 2 
Protein Synonyms/Alias
 DEAD box protein 21; Gu-alpha; Nucleolar RNA helicase Gu; Nucleolar RNA helicase II; RH II/Gu 
Gene Name
 DDX21 
Gene Synonyms/Alias
  
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
60PKAKQVKKKAEPSEVubiquitination[1]
112KVVSSKTKKVTKNEEacetylation[2]
116SKTKKVTKNEEPSEEacetylation[2]
137PKKMKKEKEMNGETRacetylation[1]
236QARTGTGKTFSFAIPubiquitination[3]
402EQVDLIGKKTQKTAIacetylation[4]
474LHGDIPQKQREITLKubiquitination[5]
481KQREITLKGFRNGSFubiquitination[6, 7]
779GQKRSFSKAFGQ***acetylation[8, 9]
779GQKRSFSKAFGQ***ubiquitination[3]
Reference
 [1] 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]
 [2] Regulation of cellular metabolism by protein lysine acetylation.
 Zhao S, Xu W, Jiang W, Yu W, Lin Y, Zhang T, Yao J, Zhou L, Zeng Y, Li H, Li Y, Shi J, An W, Hancock SM, He F, Qin L, Chin J, Yang P, Chen X, Lei Q, Xiong Y, Guan KL.
 Science. 2010 Feb 19;327(5968):1000-4. [PMID: 20167786]
 [3] 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]
 [4] Proteomic investigations of lysine acetylation identify diverse substrates of mitochondrial deacetylase sirt3.
 Sol EM, Wagner SA, Weinert BT, Kumar A, Kim HS, Deng CX, Choudhary C.
 PLoS One. 2012;7(12):e50545. [PMID: 23236377]
 [5] 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]
 [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]
 [8] 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]
 [9] Proteomic investigations reveal a role for RNA processing factor THRAP3 in the DNA damage response.
 Beli P, Lukashchuk N, Wagner SA, Weinert BT, Olsen JV, Baskcomb L, Mann M, Jackson SP, Choudhary C.
 Mol Cell. 2012 Apr 27;46(2):212-25. [PMID: 22424773] 
Functional Description
 Can unwind double-stranded RNA (helicase) and can fold or introduce a secondary structure to a single-stranded RNA (foldase). Functions as cofactor for JUN-activated transcription. Involved in rRNA processing. 
Sequence Annotation
 DOMAIN 217 396 Helicase ATP-binding.
 DOMAIN 429 573 Helicase C-terminal.
 REPEAT 724 728 1.
 REPEAT 734 738 2.
 REPEAT 744 748 3.
 NP_BIND 230 237 ATP (By similarity).
 REGION 724 748 3 X 5 AA repeats.
 MOTIF 186 214 Q motif.
 MOTIF 339 342 DEVD box.
 MOD_RES 13 13 Phosphoserine.
 MOD_RES 71 71 Phosphoserine.
 MOD_RES 89 89 Phosphoserine.
 MOD_RES 121 121 Phosphoserine.
 MOD_RES 147 147 Phosphoserine (By similarity).
 MOD_RES 164 164 Phosphoserine (By similarity).
 MOD_RES 173 173 Phosphoserine (By similarity).
 MOD_RES 189 189 Phosphoserine (By similarity).
 MOD_RES 296 296 Phosphothreonine.
 MOD_RES 567 567 Phosphoserine.
 MOD_RES 779 779 N6-acetyllysine.  
Keyword
 3D-structure; Acetylation; Alternative splicing; ATP-binding; Complete proteome; Direct protein sequencing; Helicase; Hydrolase; Nucleotide-binding; Nucleus; Phosphoprotein; Polymorphism; Reference proteome; Repeat; RNA-binding. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 783 AA 
Protein Sequence
MPGKLRSDAG LESDTAMKKG ETLRKQTEEK EKKEKPKSDK TEEIAEEEET VFPKAKQVKK 60
KAEPSEVDMN SPKSKKAKKK EEPSQNDISP KTKSLRKKKE PIEKKVVSSK TKKVTKNEEP 120
SEEEIDAPKP KKMKKEKEMN GETREKSPKL KNGFPHPEPD CNPSEAASEE SNSEIEQEIP 180
VEQKEGAFSN FPISEETIKL LKGRGVTFLF PIQAKTFHHV YSGKDLIAQA RTGTGKTFSF 240
AIPLIEKLHG ELQDRKRGRA PQVLVLAPTR ELANQVSKDF SDITKKLSVA CFYGGTPYGG 300
QFERMRNGID ILVGTPGRIK DHIQNGKLDL TKLKHVVLDE VDQMLDMGFA DQVEEILSVA 360
YKKDSEDNPQ TLLFSATCPH WVFNVAKKYM KSTYEQVDLI GKKTQKTAIT VEHLAIKCHW 420
TQRAAVIGDV IRVYSGHQGR TIIFCETKKE AQELSQNSAI KQDAQSLHGD IPQKQREITL 480
KGFRNGSFGV LVATNVAARG LDIPEVDLVI QSSPPKDVES YIHRSGRTGR AGRTGVCICF 540
YQHKEEYQLV QVEQKAGIKF KRIGVPSATE IIKASSKDAI RLLDSVPPTA ISHFKQSAEK 600
LIEEKGAVEA LAAALAHISG ATSVDQRSLI NSNVGFVTMI LQCSIEMPNI SYAWKELKEQ 660
LGEEIDSKVK GMVFLKGKLG VCFDVPTASV TEIQEKWHDS RRWQLSVATE QPELEGPREG 720
YGGFRGQREG SRGFRGQRDG NRRFRGQREG SRGPRGQRSG GGNKSNRSQN KGQKRSFSKA 780
FGQ 783 
Gene Ontology
 GO:0005730; C:nucleolus; IDA:HPA.
 GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
 GO:0004004; F:ATP-dependent RNA helicase activity; TAS:ProtInc.
 GO:0003725; F:double-stranded RNA binding; IEA:Compara.
 GO:0043330; P:response to exogenous dsRNA; IEA:Compara.
 GO:0009615; P:response to virus; IEA:Compara. 
Interpro
 IPR011545; DNA/RNA_helicase_DEAD/DEAH_N.
 IPR012562; GUCT.
 IPR014001; Helicase_ATP-bd.
 IPR001650; Helicase_C.
 IPR027417; P-loop_NTPase.
 IPR014014; RNA_helicase_DEAD_Q_motif. 
Pfam
 PF00270; DEAD
 PF08152; GUCT
 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