CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-023248
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 26S proteasome non-ATPase regulatory subunit 13 
Protein Synonyms/Alias
 26S proteasome regulatory subunit RPN9; 26S proteasome regulatory subunit S11; 26S proteasome regulatory subunit p40.5 
Gene Name
 PSMD13 
Gene Synonyms/Alias
  
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
2******MKDVPGFLQubiquitination[1]
31RLEELYTKKLWHQLTubiquitination[2, 3]
32LEELYTKKLWHQLTLubiquitination[3]
99VALTFLEKTREKVKSubiquitination[1, 2, 3, 4]
105EKTREKVKSSDEAVIubiquitination[3]
115DEAVILCKTAIGALKubiquitination[1, 3, 4, 5]
122KTAIGALKLNIGDLQubiquitination[1, 2, 3, 4]
132IGDLQVTKETIEDVEubiquitination[2]
161RFYDLSSKYYQTIGNubiquitination[1, 2, 3, 4]
174GNHASYYKDALRFLGubiquitination[1, 2, 3, 4]
186FLGCVDIKDLPVSEQubiquitination[2, 3, 4, 6]
252VERFQTLKTAWGQQPubiquitination[2, 3, 5]
298LTFEEIAKSAKITVNacetylation[7]
298LTFEEIAKSAKITVNubiquitination[2, 3]
301EEIAKSAKITVNEVEubiquitination[3]
321ALSVGLVKGSIDEVDubiquitination[1, 2, 3]
329GSIDEVDKRVHMTWVubiquitination[3]
347VLDLQQIKGMKDRLEubiquitination[1, 2, 3]
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] 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]
 [4] 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]
 [5] 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]
 [6] 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]
 [7] 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] 
Functional Description
 Acts as a regulatory subunit of the 26S proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins. 
Sequence Annotation
 DOMAIN 239 335 PCI.
 MOD_RES 298 298 N6-acetyllysine.  
Keyword
 Acetylation; Alternative splicing; Complete proteome; Polymorphism; Proteasome; Reference proteome. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 376 AA 
Protein Sequence
MKDVPGFLQQ SQNSGPGQPA VWHRLEELYT KKLWHQLTLQ VLDFVQDPCF AQGDGLIKLY 60
ENFISEFEHR VNPLSLVEII LHVVRQMTDP NVALTFLEKT REKVKSSDEA VILCKTAIGA 120
LKLNIGDLQV TKETIEDVEE MLNNLPGVTS VHSRFYDLSS KYYQTIGNHA SYYKDALRFL 180
GCVDIKDLPV SEQQERAFTL GLAGLLGEGV FNFGELLMHP VLESLRNTDR QWLIDTLYAF 240
NSGNVERFQT LKTAWGQQPD LAANEAQLLR KIQLLCLMEM TFTRPANHRQ LTFEEIAKSA 300
KITVNEVELL VMKALSVGLV KGSIDEVDKR VHMTWVQPRV LDLQQIKGMK DRLEFWCTDV 360
KSMEMLVEHQ AHDILT 376 
Gene Ontology
 GO:0005829; C:cytosol; TAS:Reactome.
 GO:0005654; C:nucleoplasm; TAS:Reactome.
 GO:0005838; C:proteasome regulatory particle; TAS:ProtInc.
 GO:0031145; P:anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process; TAS:Reactome.
 GO:0002479; P:antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent; TAS:Reactome.
 GO:0006915; P:apoptotic process; TAS:Reactome.
 GO:0006977; P:DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest; TAS:Reactome.
 GO:0000082; P:G1/S transition of mitotic cell cycle; TAS:Reactome.
 GO:0010467; P:gene expression; TAS:Reactome.
 GO:0007127; P:meiosis I; IEA:Compara.
 GO:0016071; P:mRNA metabolic process; TAS:Reactome.
 GO:0051436; P:negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle; TAS:Reactome.
 GO:0051437; P:positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle; TAS:Reactome.
 GO:0000209; P:protein polyubiquitination; TAS:Reactome.
 GO:0042981; P:regulation of apoptotic process; TAS:Reactome.
 GO:0006521; P:regulation of cellular amino acid metabolic process; TAS:Reactome.
 GO:0044281; P:small molecule metabolic process; TAS:Reactome.
 GO:0016032; P:viral reproduction; TAS:Reactome. 
Interpro
 IPR000717; PCI_dom. 
Pfam
 PF01399; PCI 
SMART
 SM00088; PINT 
PROSITE
  
PRINTS