CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-000647
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Putative pre-mRNA-splicing factor ATP-dependent RNA helicase DHX15 
Protein Synonyms/Alias
 ATP-dependent RNA helicase #46; DEAH box protein 15 
Gene Name
 DHX15 
Gene Synonyms/Alias
 DBP1; DDX15 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
17GEDYPSGKKRAGTDGacetylation[1, 2, 3]
17GEDYPSGKKRAGTDGubiquitination[4]
18EDYPSGKKRAGTDGKmethylation[5]
132PRYYDILKKRLQLPVacetylation[1, 3, 6]
132PRYYDILKKRLQLPVubiquitination[4, 7]
133RYYDILKKRLQLPVWubiquitination[3, 8]
143QLPVWEYKDRFTDILubiquitination[3, 4, 7, 8, 9, 10]
166VGETGSGKTTQIPQWacetylation[11]
166VGETGSGKTTQIPQWubiquitination[7]
185MRSLPGPKRGVACTQacetylation[11]
230FEDCSSAKTILKYMTubiquitination[3, 7, 8, 12, 13]
234SSAKTILKYMTDGMLubiquitination[3, 4, 7, 8, 13, 14]
384GPEVGDIKIIPLYSTubiquitination[4, 7, 8, 14]
407IFEPPPPKKQNGAIGubiquitination[4, 8]
408FEPPPPKKQNGAIGRubiquitination[8]
445DPGFAKQKVYNPRIRacetylation[3]
463LLVTAISKASAQQRAubiquitination[3, 7, 8]
480AGRTRPGKCFRLYTEubiquitination[3, 8]
488CFRLYTEKAYKTEMQacetylation[1, 3]
488CFRLYTEKAYKTEMQubiquitination[3, 4, 8]
491LYTEKAYKTEMQDNTubiquitination[3, 4, 7, 8, 13, 14, 15]
515GSVVLQLKKLGIDDLubiquitination[4, 7, 8, 14]
516SVVLQLKKLGIDDLVubiquitination[8]
754IRTCTDIKPEWLVKIacetylation[1]
754IRTCTDIKPEWLVKIubiquitination[3, 7, 8]
760IKPEWLVKIAPQYYDubiquitination[7]
786QLDRIIAKLQSKEYSacetylation[3]
786QLDRIIAKLQSKEYSubiquitination[3, 8, 9, 10]
790IIAKLQSKEYSQY**ubiquitination[3, 4, 7, 8, 13, 14]
Reference
 [1] 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]
 [2] 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]
 [3] 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]
 [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] 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] 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]
 [7] 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]
 [8] 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]
 [9] 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]
 [10] 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]
 [11] 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]
 [12] 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]
 [13] 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]
 [14] 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]
 [15] 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
Functional Description
 Pre-mRNA processing factor involved in disassembly of spliceosomes after the release of mature mRNA (By similarity). 
Sequence Annotation
 DOMAIN 147 313 Helicase ATP-binding.
 DOMAIN 338 518 Helicase C-terminal.
 NP_BIND 160 167 ATP (By similarity).
 MOTIF 260 263 DEAH box.
 MOD_RES 132 132 N6-acetyllysine.
 MOD_RES 488 488 N6-acetyllysine.  
Keyword
 Acetylation; ATP-binding; Complete proteome; Helicase; Hydrolase; mRNA processing; mRNA splicing; Nucleotide-binding; Nucleus; Reference proteome. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 795 AA 
Protein Sequence
MSKRHRLDLG EDYPSGKKRA GTDGKDRDRD RDREDRSKDR DRERDRGDRE REREKEKEKE 60
LRASTNAMLI SAGLPPLKAS HSAHSTHSAH STHSTHSAHS THAGHAGHTS LPQCINPFTN 120
LPHTPRYYDI LKKRLQLPVW EYKDRFTDIL VRHQSFVLVG ETGSGKTTQI PQWCVEYMRS 180
LPGPKRGVAC TQPRRVAAMS VAQRVADEMD VMLGQEVGYS IRFEDCSSAK TILKYMTDGM 240
LLREAMNDPL LERYGVIILD EAHERTLATD ILMGVLKEVV RQRSDLKVIV MSATLDAGKF 300
QIYFDNCPLL TIPGRTHPVE IFYTPEPERD YLEAAIRTVI QIHMCEEEEG DLLLFLTGQE 360
EIDEACKRIK REVDDLGPEV GDIKIIPLYS TLPPQQQQRI FEPPPPKKQN GAIGRKVVVS 420
TNIAETSLTI DGVVFVIDPG FAKQKVYNPR IRVESLLVTA ISKASAQQRA GRAGRTRPGK 480
CFRLYTEKAY KTEMQDNTYP EILRSNLGSV VLQLKKLGID DLVHFDFMDP PAPETLMRAL 540
ELLNYLAALN DDGDLTELGS MMAEFPLDPQ LAKMVIASCD YNCSNEVLSI TAMLSVPQCF 600
VRPTEAKKAA DEAKMRFAHI DGDHLTLLNV YHAFKQNHES VQWCYDNFIN YRSLMSADNV 660
RQQLSRIMDR FNLPRRSTDF TSRDYYINIR KALVTGYFMQ VAHLERTGHY LTVKDNQVVQ 720
LHPSTVLDHK PEWVLYNEFV LTTKNYIRTC TDIKPEWLVK IAPQYYDMSN FPQCEAKRQL 780
DRIIAKLQSK EYSQY 795 
Gene Ontology
 GO:0005730; C:nucleolus; IEA:UniProtKB-SubCell.
 GO:0005689; C:U12-type spliceosomal complex; IDA:HGNC.
 GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
 GO:0008026; F:ATP-dependent helicase activity; IEA:InterPro.
 GO:0003676; F:nucleic acid binding; IEA:InterPro.
 GO:0003724; F:RNA helicase activity; TAS:ProtInc.
 GO:0006397; P:mRNA processing; TAS:ProtInc.
 GO:0008380; P:RNA splicing; IC:HGNC. 
Interpro
 IPR003593; AAA+_ATPase.
 IPR011545; DNA/RNA_helicase_DEAD/DEAH_N.
 IPR002464; DNA/RNA_helicase_DEAH_CS.
 IPR011709; DUF1605.
 IPR007502; Helicase-assoc_dom.
 IPR014001; Helicase_ATP-bd.
 IPR001650; Helicase_C.
 IPR027417; P-loop_NTPase. 
Pfam
 PF00270; DEAD
 PF04408; HA2
 PF00271; Helicase_C
 PF07717; OB_NTP_bind 
SMART
 SM00382; AAA
 SM00487; DEXDc
 SM00847; HA2
 SM00490; HELICc 
PROSITE
 PS00690; DEAH_ATP_HELICASE
 PS51192; HELICASE_ATP_BIND_1
 PS51194; HELICASE_CTER 
PRINTS