CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-011573
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 ATP-dependent RNA helicase A 
Protein Synonyms/Alias
 RHA; DEAH box protein 9; Leukophysin; LKP; Nuclear DNA helicase II; NDH II 
Gene Name
 DHX9 
Gene Synonyms/Alias
 DDX9; LKP; NDH2 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
5***MGDVKNFLYAWCubiquitination[1, 2]
16YAWCGKRKMTPSYEIubiquitination[2, 3]
76LVRINEIKSEEVPAFsumoylation[4]
120LPPHLALKAENNSEVmethylation[5]
120LPPHLALKAENNSEVsumoylation[4]
146WDRGANLKDYYSRKEacetylation[6]
146WDRGANLKDYYSRKEubiquitination[1, 2, 3, 6, 7, 8, 9]
191RLNQYFQKEKIQGEYacetylation[10, 11]
191RLNQYFQKEKIQGEYubiquitination[2, 3]
193NQYFQKEKIQGEYKYubiquitination[2]
199EKIQGEYKYTQVGPDacetylation[6, 10, 12, 13]
199EKIQGEYKYTQVGPDubiquitination[2, 6, 7]
391ERELLPVKKFESEILubiquitination[2]
392RELLPVKKFESEILEubiquitination[2]
417RGATGCGKTTQVPQFubiquitination[1, 2, 6, 8, 14]
467ERGEEPGKSCGYSVRubiquitination[1, 2, 6, 8, 15]
697IPREEQRKVFDPVPVubiquitination[2, 3, 16, 17]
755YATVWASKTNLEQRKubiquitination[2, 7, 8, 9]
806HEIALSIKLLRLGGIubiquitination[2, 6, 8]
819GIGQFLAKAIEPPPLubiquitination[2, 7, 9]
857PLGRILAKLPIEPRFubiquitination[2, 3, 6, 7, 8, 9, 14, 16, 17]
957LRMTWEAKVQLKEILubiquitination[7, 8]
1011CYHKEKRKILTTEGRubiquitination[2, 6]
1024GRNALIHKSSVNCPFacetylation[10, 12]
1024GRNALIHKSSVNCPFubiquitination[1, 2, 6, 8]
1037PFSSQDMKYPSPFFVacetylation[12]
1037PFSSQDMKYPSPFFVubiquitination[1, 2, 3, 6, 8]
1048PFFVFGEKIRTRAISubiquitination[1, 2, 3, 6, 7, 8, 9, 14, 16, 17]
1116ALVVEVTKQPAIISQubiquitination[7, 8, 9]
1163GDGPRPPKMARYDNGubiquitination[2, 3, 6]
Reference
 [1] 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]
 [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] 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]
 [4] A functional interaction between RHA and Ubc9, an E2-like enzyme specific for Sumo-1.
 Argasinska J, Zhou K, Donnelly RJ, Hay RT, Lee CG.
 J Mol Biol. 2004 Jul 30;341(1):15-25. [PMID: 15312759]
 [5] Mass spectrometry-based identification and characterisation of lysine and arginine methylation in the human proteome.
 Bremang M, Cuomo A, Agresta AM, Stugiewicz M, Spadotto V, Bonaldi T.
 Mol Biosyst. 2013 Jul 30;9(9):2231-47. [PMID: 23748837]
 [6] 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]
 [7] 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]
 [8] 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]
 [9] 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]
 [10] 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]
 [11] 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]
 [12] Monoclonal antibody cocktail as an enrichment tool for acetylome analysis.
 Shaw PG, Chaerkady R, Zhang Z, Davidson NE, Pandey A.
 Anal Chem. 2011 May 15;83(10):3623-6. [PMID: 21466224]
 [13] 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]
 [14] 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]
 [15] 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]
 [16] 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]
 [17] 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
 Unwinds double-stranded DNA and RNA in a 3' to 5' direction. Alteration of secondary structure may subsequently influence interactions with proteins or other nucleic acids. Functions as a transcriptional activator. Component of the CRD- mediated complex that promotes MYC mRNA stability. Involved with LARP6 in the stabilization of type I collagen mRNAs for CO1A1 and CO1A2. Positively regulates HIV-1 LTR-directed gene expression. 
Sequence Annotation
 DOMAIN 3 71 DRBM 1.
 DOMAIN 180 252 DRBM 2.
 DOMAIN 398 564 Helicase ATP-binding.
 DOMAIN 636 809 Helicase C-terminal.
 NP_BIND 411 419 ATP.
 REGION 1 250 Interaction with CREBBP.
 REGION 230 325 Interaction with BRCA1.
 REGION 331 380 MTAD.
 REGION 1151 1260 NTD.
 MOTIF 511 514 DEIH box.
 MOTIF 586 595 Nuclear localization signal (Potential).
 MOD_RES 87 87 Phosphoserine.
 MOD_RES 191 191 N6-acetyllysine.
 MOD_RES 199 199 N6-acetyllysine.
 MOD_RES 321 321 Phosphoserine.
 MOD_RES 1024 1024 N6-acetyllysine.  
Keyword
 3D-structure; Acetylation; Activator; Alternative splicing; ATP-binding; Complete proteome; Cytoplasm; Direct protein sequencing; DNA-binding; Helicase; Hydrolase; Methylation; Nucleotide-binding; Nucleus; Phosphoprotein; Polymorphism; Reference proteome; Repeat; RNA-binding. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 1270 AA 
Protein Sequence
MGDVKNFLYA WCGKRKMTPS YEIRAVGNKN RQKFMCEVQV EGYNYTGMGN STNKKDAQSN 60
AARDFVNYLV RINEIKSEEV PAFGVASPPP LTDTPDTTAN AEGDLPTTMG GPLPPHLALK 120
AENNSEVGAS GYGVPGPTWD RGANLKDYYS RKEEQEVQAT LESEEVDLNA GLHGNWTLEN 180
AKARLNQYFQ KEKIQGEYKY TQVGPDHNRS FIAEMTIYIK QLGRRIFARE HGSNKKLAAQ 240
SCALSLVRQL YHLGVVEAYS GLTKKKEGET VEPYKVNLSQ DLEHQLQNII QELNLEILPP 300
PEDPSVPVAL NIGKLAQFEP SQRQNQVGVV PWSPPQSNWN PWTSSNIDEG PLAFATPEQI 360
SMDLKNELMY QLEQDHDLQA ILQERELLPV KKFESEILEA ISQNSVVIIR GATGCGKTTQ 420
VPQFILDDFI QNDRAAECNI VVTQPRRISA VSVAERVAFE RGEEPGKSCG YSVRFESILP 480
RPHASIMFCT VGVLLRKLEA GIRGISHVIV DEIHERDINT DFLLVVLRDV VQAYPEVRIV 540
LMSATIDTSM FCEYFFNCPI IEVYGRTYPV QEYFLEDCIQ MTHFVPPPKD KKKKDKDDDG 600
GEDDDANCNL ICGDEYGPET RLSMSQLNEK ETPFELIEAL LKYIETLNVP GAVLVFLPGW 660
NLIYTMQKHL EMNPHFGSHR YQILPLHSQI PREEQRKVFD PVPVGVTKVI LSTNIAETSI 720
TINDVVYVID SCKQKVKLFT AHNNMTNYAT VWASKTNLEQ RKGRAGRVRP GFCFHLCSRA 780
RFERLETHMT PEMFRTPLHE IALSIKLLRL GGIGQFLAKA IEPPPLDAVI EAEHTLRELD 840
ALDANDELTP LGRILAKLPI EPRFGKMMIM GCIFYVGDAI CTIAAATCFP EPFINEGKRL 900
GYIHRNFAGN RFSDHVALLS VFQAWDDARM GGEEAEIRFC EHKRLNMATL RMTWEAKVQL 960
KEILINSGFP EDCLLTQVFT NTGPDNNLDV VISLLAFGVY PNVCYHKEKR KILTTEGRNA 1020
LIHKSSVNCP FSSQDMKYPS PFFVFGEKIR TRAISAKGMT LVTPLQLLLF ASKKVQSDGQ 1080
IVLVDDWIKL QISHEAAACI TGLRAAMEAL VVEVTKQPAI ISQLDPVNER MLNMIRQISR 1140
PSAAGINLMI GSTRYGDGPR PPKMARYDNG SGYRRGGSSY SGGGYGGGYS SGGYGSGGYG 1200
GSANSFRAGY GAGVGGGYRG VSRGGFRGNS GGDYRGPSGG YRGSGGFQRG GGRGAYGTGY 1260
FGQGRGGGGY 1270 
Gene Ontology
 GO:0005813; C:centrosome; IDA:UniProtKB.
 GO:0070937; C:CRD-mediated mRNA stability complex; IDA:UniProtKB.
 GO:0005730; C:nucleolus; IEA:UniProtKB-SubCell.
 GO:0005654; C:nucleoplasm; TAS:Reactome.
 GO:0030529; C:ribonucleoprotein complex; IDA:UniProtKB.
 GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
 GO:0004003; F:ATP-dependent DNA helicase activity; TAS:ProtInc.
 GO:0004004; F:ATP-dependent RNA helicase activity; TAS:ProtInc.
 GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
 GO:0003725; F:double-stranded RNA binding; IEA:InterPro.
 GO:0034605; P:cellular response to heat; IEA:Compara.
 GO:0007623; P:circadian rhythm; IEA:Compara.
 GO:0070934; P:CRD-mediated mRNA stabilization; IMP:UniProtKB.
 GO:0000398; P:mRNA splicing, via spliceosome; TAS:Reactome. 
Interpro
 IPR011545; DNA/RNA_helicase_DEAD/DEAH_N.
 IPR002464; DNA/RNA_helicase_DEAH_CS.
 IPR001159; Ds-RNA-bd.
 IPR014720; dsRNA-bd-like_dom.
 IPR011709; DUF1605.
 IPR007502; Helicase-assoc_dom.
 IPR014001; Helicase_ATP-bd.
 IPR001650; Helicase_C.
 IPR027417; P-loop_NTPase. 
Pfam
 PF00270; DEAD
 PF00035; dsrm
 PF04408; HA2
 PF00271; Helicase_C
 PF07717; OB_NTP_bind 
SMART
 SM00487; DEXDc
 SM00358; DSRM
 SM00847; HA2
 SM00490; HELICc 
PROSITE
 PS00690; DEAH_ATP_HELICASE
 PS50137; DS_RBD
 PS51192; HELICASE_ATP_BIND_1
 PS51194; HELICASE_CTER 
PRINTS