CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-022372
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Probable ATP-dependent RNA helicase DDX56 
Protein Synonyms/Alias
 ATP-dependent 61 kDa nucleolar RNA helicase; DEAD box protein 21; DEAD box protein 56 
Gene Name
 DDX56 
Gene Synonyms/Alias
 DDX21; NOH61 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
45IPLALEGKDLLARARubiquitination[1]
73LQLLLHRKATGPVVEubiquitination[1]
92GLVLVPTKELARQAQubiquitination[1]
134QRAVLMEKPDVVVGTubiquitination[2]
155HLQQDSLKLRDSLELubiquitination[2]
337GRGPKGDKASDPEAGubiquitination[1]
439DAMRSVTKQAIREARubiquitination[1]
461LLHSEKLKTYFEDNPubiquitination[1]
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] 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
 May play a role in later stages of the processing of the pre-ribosomal particles leading to mature 60S ribosomal subunits. Has intrinsic ATPase activity. 
Sequence Annotation
 DOMAIN 38 218 Helicase ATP-binding.
 DOMAIN 230 424 Helicase C-terminal.
 NP_BIND 51 58 ATP (By similarity).
 MOTIF 7 35 Q motif.
 MOTIF 166 169 DEAD box.
 MOD_RES 126 126 Phosphoserine.  
Keyword
 Alternative splicing; ATP-binding; Complete proteome; Helicase; Hydrolase; Nucleotide-binding; Nucleus; Phosphoprotein; Reference proteome; Ribosome biogenesis; RNA-binding; rRNA processing. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 547 AA 
Protein Sequence
MEDSEALGFE HMGLDPRLLQ AVTDLGWSRP TLIQEKAIPL ALEGKDLLAR ARTGSGKTAA 60
YAIPMLQLLL HRKATGPVVE QAVRGLVLVP TKELARQAQS MIQQLATYCA RDVRVANVSA 120
AEDSVSQRAV LMEKPDVVVG TPSRILSHLQ QDSLKLRDSL ELLVVDEADL LFSFGFEEEL 180
KSLLCHLPRI YQAFLMSATF NEDVQALKEL ILHNPVTLKL QESQLPGPDQ LQQFQVVCET 240
EEDKFLLLYA LLKLSLIRGK SLLFVNTLER SYRLRLFLEQ FSIPTCVLNG ELPLRSRCHI 300
ISQFNQGFYD CVIATDAEVL GAPVKGKRRG RGPKGDKASD PEAGVARGID FHHVSAVLNF 360
DLPPTPEAYI HRAGRTARAN NPGIVLTFVL PTEQFHLGKI EELLSGENRG PILLPYQFRM 420
EEIEGFRYRC RDAMRSVTKQ AIREARLKEI KEELLHSEKL KTYFEDNPRD LQLLRHDLPL 480
HPAVVKPHLG HVPDYLVPPA LRGLVRPHKK RKKLSSSCRK AKRAKSQNPL RSFKHKGKKF 540
RPTAKPS 547 
Gene Ontology
 GO:0005730; C:nucleolus; IDA:LIFEdb.
 GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
 GO:0004004; F:ATP-dependent RNA helicase activity; TAS:ProtInc.
 GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
 GO:0006364; P:rRNA processing; IEA:UniProtKB-KW. 
Interpro
 IPR011545; DNA/RNA_helicase_DEAD/DEAH_N.
 IPR014001; Helicase_ATP-bd.
 IPR001650; Helicase_C.
 IPR027417; P-loop_NTPase. 
Pfam
 PF00270; DEAD
 PF00271; Helicase_C 
SMART
 SM00487; DEXDc
 SM00490; HELICc 
PROSITE
 PS51192; HELICASE_ATP_BIND_1
 PS51194; HELICASE_CTER
 PS51195; Q_MOTIF 
PRINTS