CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-018703
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 ATP-dependent RNA helicase DDX1 
Protein Synonyms/Alias
 DEAD box protein 1; DEAD box protein retinoblastoma; DBP-RB 
Gene Name
 DDX1 
Gene Synonyms/Alias
  
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
82KKGKTTIKTGASVLNubiquitination[1]
90TGASVLNKWQMNPYDubiquitination[1, 2]
117CCQSREVKEWHGCRAacetylation[3]
117CCQSREVKEWHGCRAubiquitination[1, 3]
132TKGLMKGKHYYEVSCubiquitination[1, 3]
172FGFGGTGKKSHNKQFubiquitination[4]
234LFPACVLKNAELKFNmethylation[5]
239VLKNAELKFNFGEEEacetylation[6, 7]
268APDGYIVKSQHSGNAacetylation[6]
268APDGYIVKSQHSGNAubiquitination[1, 8]
281NAQVTQTKFLPNAPKacetylation[3, 6, 7]
281NAQVTQTKFLPNAPKubiquitination[1, 2, 3, 8]
288KFLPNAPKALIVEPSubiquitination[1, 2, 3]
307EQTLNNIKQFKKYIDubiquitination[2]
317KKYIDNPKLRELLIIacetylation[3]
317KKYIDNPKLRELLIIubiquitination[1]
358DDLVSTGKLNLSQVRubiquitination[2, 3, 4]
416TLHSFDVKKLSEKIMacetylation[3]
490EMWSEAIKILKGEYAubiquitination[8]
493SEAIKILKGEYAVRAubiquitination[1, 3, 8]
516AIIFCRTKIDCDNLEacetylation[3]
596NVTLPDEKQNYVHRIacetylation[7]
596NVTLPDEKQNYVHRIubiquitination[1]
687PVDEFDGKVTYGQKRubiquitination[9]
702AAGGGSYKGHVDILAubiquitination[8]
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] 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] 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]
 [5] A general molecular affinity strategy for global detection and proteomic analysis of lysine methylation.
 Moore KE, Carlson SM, Camp ND, Cheung P, James RG, Chua KF, Wolf-Yadlin A, Gozani O.
 Mol Cell. 2013 May 9;50(3):444-56. [PMID: 23583077]
 [6] 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]
 [7] 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]
 [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] 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] 
Functional Description
 Acts as an ATP-dependent RNA helicase, able to unwind both RNA-RNA and RNA-DNA duplexes. Possesses 5' single-stranded RNA overhang nuclease activity. Possesses ATPase activity on various RNA, but not DNA polynucleotides. May play a role in RNA clearance at DNA double-strand breaks (DSBs), thereby facilitating the template-guided repair of transcriptionally active regions of the genome. Together with RELA, acts as a coactivator to enhance NF-kappa-B-mediated transcriptional activation. Acts as a positive transcriptional regulator of cyclin CCND2 expression. Binds to the cyclin CCND2 promoter region. Associates with chromatin at the NF- kappa-B promoter region via association with RELA. Binds to poly(A) RNA. May be involved in 3'-end cleavage and polyadenylation of pre-mRNAs. Required for HIV-1 Rev function as well as for HIV-1 replication. Binds to the RRE sequence of HIV-1 mRNAs. 
Sequence Annotation
 DOMAIN 2 428 Helicase ATP-binding.
 DOMAIN 70 247 B30.2/SPRY.
 DOMAIN 493 681 Helicase C-terminal.
 NP_BIND 46 53 ATP (By similarity).
 REGION 1 525 Necessary for interaction with RELA.
 REGION 1 295 Necessary for interaction with HNRNPK.
 REGION 525 740 Necessary for interaction with HNRNPK.
 REGION 536 631 Necessary for interaction with replicase
 MOTIF 370 373 DEAD box.
 MOD_RES 239 239 N6-acetyllysine.
 MOD_RES 268 268 N6-acetyllysine.
 MOD_RES 281 281 N6-acetyllysine.
 MOD_RES 481 481 Phosphoserine.  
Keyword
 Acetylation; Activator; ATP-binding; Complete proteome; Cytoplasm; DNA-binding; Exonuclease; Helicase; Hydrolase; mRNA processing; Nuclease; Nucleotide-binding; Nucleus; Phosphoprotein; Reference proteome; RNA-binding; Transcription; Transcription regulation. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 740 AA 
Protein Sequence
MAAFSEMGVM PEIAQAVEEM DWLLPTDIQA ESIPLILGGG DVLMAAETGS GKTGAFSIPV 60
IQIVYETLKD QQEGKKGKTT IKTGASVLNK WQMNPYDRGS AFAIGSDGLC CQSREVKEWH 120
GCRATKGLMK GKHYYEVSCH DQGLCRVGWS TMQASLDLGT DKFGFGFGGT GKKSHNKQFD 180
NYGEEFTMHD TIGCYLDIDK GHVKFSKNGK DLGLAFEIPP HMKNQALFPA CVLKNAELKF 240
NFGEEEFKFP PKDGFVALSK APDGYIVKSQ HSGNAQVTQT KFLPNAPKAL IVEPSRELAE 300
QTLNNIKQFK KYIDNPKLRE LLIIGGVAAR DQLSVLENGV DIVVGTPGRL DDLVSTGKLN 360
LSQVRFLVLD EADGLLSQGY SDFINRMHNQ IPQVTSDGKR LQVIVCSATL HSFDVKKLSE 420
KIMHFPTWVD LKGEDSVPDT VHHVVVPVNP KTDRLWERLG KSHIRTDDVH AKDNTRPGAN 480
SPEMWSEAIK ILKGEYAVRA IKEHKMDQAI IFCRTKIDCD NLEQYFIQQG GGPDKKGHQF 540
SCVCLHGDRK PHERKQNLER FKKGDVRFLI CTDVAARGID IHGVPYVINV TLPDEKQNYV 600
HRIGRVGRAE RMGLAISLVA TEKEKVWYHV CSSRGKGCYN TRLKEDGGCT IWYNEMQLLS 660
EIEEHLNCTI SQVEPDIKVP VDEFDGKVTY GQKRAAGGGS YKGHVDILAP TVQELAALEK 720
EAQTSFLHLG YLPNQLFRTF 740 
Gene Ontology
 GO:0071920; C:cleavage body; IDA:UniProtKB.
 GO:0010494; C:cytoplasmic stress granule; IDA:UniProtKB.
 GO:0072669; C:tRNA-splicing ligase complex; IDA:UniProtKB.
 GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
 GO:0008026; F:ATP-dependent helicase activity; IDA:UniProtKB.
 GO:0003682; F:chromatin binding; IDA:UniProtKB.
 GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
 GO:0033677; F:DNA/RNA helicase activity; IDA:UniProtKB.
 GO:0003725; F:double-stranded RNA binding; IEA:Compara.
 GO:0004527; F:exonuclease activity; IEA:UniProtKB-KW.
 GO:0004518; F:nuclease activity; IDA:UniProtKB.
 GO:0008143; F:poly(A) RNA binding; IDA:UniProtKB.
 GO:0003724; F:RNA helicase activity; TAS:ProtInc.
 GO:0003712; F:transcription cofactor activity; IDA:UniProtKB.
 GO:0032508; P:DNA duplex unwinding; IDA:UniProtKB.
 GO:0006302; P:double-strand break repair; IDA:UniProtKB.
 GO:0007275; P:multicellular organismal development; IEP:UniProtKB.
 GO:0006355; P:regulation of transcription, DNA-dependent; IEA:UniProtKB-KW.
 GO:0006446; P:regulation of translational initiation; NAS:UniProtKB.
 GO:0043330; P:response to exogenous dsRNA; IEA:Compara.
 GO:0009615; P:response to virus; IEA:Compara.
 GO:0000245; P:spliceosomal complex assembly; NAS:UniProtKB.
 GO:0006351; P:transcription, DNA-dependent; IEA:UniProtKB-KW. 
Interpro
 IPR001870; B30.2/SPRY.
 IPR008985; ConA-like_lec_gl_sf.
 IPR011545; DNA/RNA_helicase_DEAD/DEAH_N.
 IPR014001; Helicase_ATP-bd.
 IPR001650; Helicase_C.
 IPR027417; P-loop_NTPase.
 IPR014014; RNA_helicase_DEAD_Q_motif.
 IPR018355; SPla/RYanodine_receptor_subgr.
 IPR003877; SPRY_rcpt. 
Pfam
 PF00270; DEAD
 PF00271; Helicase_C
 PF00622; SPRY 
SMART
 SM00487; DEXDc
 SM00490; HELICc
 SM00449; SPRY 
PROSITE
 PS50188; B302_SPRY
 PS00039; DEAD_ATP_HELICASE
 PS51192; HELICASE_ATP_BIND_1
 PS51194; HELICASE_CTER
 PS51195; Q_MOTIF 
PRINTS