CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-014027
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Protein DDI1 homolog 2 
Protein Synonyms/Alias
  
Gene Name
 DDI2 
Gene Synonyms/Alias
  
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
67SLASYGLKDGDVVILubiquitination[1, 2, 3, 4, 5, 6, 7]
77DVVILRQKENADPRPubiquitination[1, 2, 5, 6, 7]
153PHELSLLKERNPPLAubiquitination[1, 2, 3, 4, 5, 6, 8]
170LLSGDLEKFSRVLVEubiquitination[1, 2, 4, 5, 6, 8]
205FDLEAQAKIEEDIRQubiquitination[2, 3]
283RRWAGIAKGVGTQKIubiquitination[1, 2, 4, 5, 6, 7, 9, 10]
289AKGVGTQKIIGRVHLubiquitination[1, 2, 4, 5, 6, 7]
337HQCSIDLKKNVLVIGubiquitination[5]
338QCSIDLKKNVLVIGTubiquitination[5, 7]
389ELAEALQKSAEDAERubiquitination[2, 4, 5, 6, 7, 9]
Reference
 [1] 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]
 [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]
 [3] 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]
 [4] 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]
 [5] 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]
 [6] 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]
 [7] 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]
 [8] Global analysis of lysine ubiquitination by ubiquitin remnant immunoaffinity profiling.
 Xu G, Paige JS, Jaffrey SR.
 Nat Biotechnol. 2010 Aug;28(8):868-73. [PMID: 20639865]
 [9] 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]
 [10] 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
Functional Description
  
Sequence Annotation
 DOMAIN 1 81 Ubiquitin-like.
 MOD_RES 106 106 Phosphoserine.
 MOD_RES 120 120 Phosphoserine (By similarity).
 MOD_RES 121 121 Phosphoserine (By similarity).
 MOD_RES 128 128 Phosphoserine.
 MOD_RES 194 194 Phosphoserine.  
Keyword
 Alternative splicing; Complete proteome; Phosphoprotein; Reference proteome. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 399 AA 
Protein Sequence
MLLTVYCVRR DLSEVTFSLQ VDADFELHNF RALCELESGI PAAESQIVYA ERPLTDNHRS 60
LASYGLKDGD VVILRQKENA DPRPPVQFPN LPRIDFSSIA VPGTSSPRQR QPPGTQQSHS 120
SPGEITSSPQ GLDNPALLRD MLLANPHELS LLKERNPPLA EALLSGDLEK FSRVLVEQQQ 180
DRARREQERI RLFSADPFDL EAQAKIEEDI RQQNIEENMT IAMEEAPESF GQVVMLYINC 240
KVNGHPVKAF VDSGAQMTIM SQACAERCNI MRLVDRRWAG IAKGVGTQKI IGRVHLAQVQ 300
IEGDFLPCSF SILEEQPMDM LLGLDMLKRH QCSIDLKKNV LVIGTTGSQT TFLPEGELPE 360
CARLAYGAGR EDVRPEEIAD QELAEALQKS AEDAERQKP 399 
Gene Ontology
 GO:0004190; F:aspartic-type endopeptidase activity; IEA:InterPro.
 GO:0006508; P:proteolysis; IEA:InterPro. 
Interpro
 IPR021109; Peptidase_aspartic.
 IPR019103; Peptidase_aspartic_DDI1-type.
 IPR000626; Ubiquitin.
 IPR019955; Ubiquitin_supergroup. 
Pfam
 PF09668; Asp_protease
 PF00240; ubiquitin 
SMART
  
PROSITE
 PS50053; UBIQUITIN_2 
PRINTS