CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-009433
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 26S protease regulatory subunit 4 
Protein Synonyms/Alias
 P26s4; 26S proteasome AAA-ATPase subunit RPT2; Proteasome 26S subunit ATPase 1 
Gene Name
 PSMC1 
Gene Synonyms/Alias
  
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
23KDDKDKKKKYEPPVPubiquitination[1, 2]
24DDKDKKKKYEPPVPTubiquitination[1, 2, 3]
41GKKKKKTKGPDAASKubiquitination[1]
48KGPDAASKLPLVTPHubiquitination[1, 2, 4, 5, 6]
61PHTQCRLKLLKLERIubiquitination[1]
64QCRLKLLKLERIKDYubiquitination[1, 3]
69LLKLERIKDYLLMEEubiquitination[1, 2, 3, 4, 6, 7, 8, 9]
86IRNQEQMKPLEEKQEubiquitination[1, 7]
91QMKPLEEKQEEERSKubiquitination[1, 7, 9]
98KQEEERSKVDDLRGTubiquitination[1, 4, 5, 6, 7, 9]
178VTVMKVEKAPQETYAubiquitination[1, 7, 9]
198DNQIQEIKESVELPLubiquitination[7]
217YYEEMGIKPPKGVILubiquitination[1, 7, 9]
220EMGIKPPKGVILYGPubiquitination[1]
232YGPPGTGKTLLAKAVubiquitination[1, 4, 5, 6, 7, 9]
237TGKTLLAKAVANQTSubiquitination[1, 5, 6, 7, 9, 10]
258VGSELIQKYLGDGPKacetylation[11]
258VGSELIQKYLGDGPKubiquitination[1, 3, 4, 5, 6, 7, 9, 10, 12]
265KYLGDGPKLVRELFRubiquitination[1, 3, 7, 9]
293EIDAIGTKRYDSNSGubiquitination[1, 3, 7, 9]
326FDSRGDVKVIMATNRubiquitination[1, 7]
350RPGRIDRKIEFPLPDubiquitination[1]
359EFPLPDEKTKKRIFQubiquitination[1, 7, 9]
387LDDLIMAKDDLSGADubiquitination[1, 7]
396DLSGADIKAICTEAGubiquitination[1]
413ALRERRMKVTNEDFKubiquitination[1, 7]
420KVTNEDFKKSKENVLubiquitination[1, 4, 6, 7]
421VTNEDFKKSKENVLYubiquitination[1]
423NEDFKKSKENVLYKKubiquitination[1]
430KENVLYKKQEGTPEGubiquitination[1, 7, 9]
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] 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]
 [3] 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]
 [4] 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]
 [5] 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]
 [6] 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]
 [7] 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]
 [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] 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]
 [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]
 [11] 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]
 [12] 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] 
Functional Description
 The 26S protease is involved in the ATP-dependent degradation of ubiquitinated proteins. The regulatory (or ATPase) complex confers ATP dependency and substrate specificity to the 26S complex. 
Sequence Annotation
 NP_BIND 226 233 ATP (Potential).
 MOD_RES 4 4 Phosphoserine.
 MOD_RES 258 258 N6-acetyllysine.
 MOD_RES 439 439 Phosphotyrosine.
 LIPID 2 2 N-myristoyl glycine (By similarity).
 CROSSLNK 237 237 Glycyl lysine isopeptide (Lys-Gly)  
Keyword
 Acetylation; ATP-binding; Complete proteome; Cytoplasm; Direct protein sequencing; Isopeptide bond; Lipoprotein; Myristate; Nucleotide-binding; Nucleus; Phosphoprotein; Proteasome; Reference proteome; Ubl conjugation. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 440 AA 
Protein Sequence
MGQSQSGGHG PGGGKKDDKD KKKKYEPPVP TRVGKKKKKT KGPDAASKLP LVTPHTQCRL 60
KLLKLERIKD YLLMEEEFIR NQEQMKPLEE KQEEERSKVD DLRGTPMSVG TLEEIIDDNH 120
AIVSTSVGSE HYVSILSFVD KDLLEPGCSV LLNHKVHAVI GVLMDDTDPL VTVMKVEKAP 180
QETYADIGGL DNQIQEIKES VELPLTHPEY YEEMGIKPPK GVILYGPPGT GKTLLAKAVA 240
NQTSATFLRV VGSELIQKYL GDGPKLVREL FRVAEEHAPS IVFIDEIDAI GTKRYDSNSG 300
GEREIQRTML ELLNQLDGFD SRGDVKVIMA TNRIETLDPA LIRPGRIDRK IEFPLPDEKT 360
KKRIFQIHTS RMTLADDVTL DDLIMAKDDL SGADIKAICT EAGLMALRER RMKVTNEDFK 420
KSKENVLYKK QEGTPEGLYL 440 
Gene Ontology
 GO:0005829; C:cytosol; TAS:Reactome.
 GO:0005654; C:nucleoplasm; TAS:Reactome.
 GO:0022624; C:proteasome accessory complex; ISS:UniProtKB.
 GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
 GO:0016887; F:ATPase activity; ISS:UniProtKB.
 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: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:0016032; P:viral reproduction; TAS:Reactome. 
Interpro
 IPR005937; 26S_Psome_P45.
 IPR003593; AAA+_ATPase.
 IPR003959; ATPase_AAA_core.
 IPR003960; ATPase_AAA_CS.
 IPR027417; P-loop_NTPase. 
Pfam
 PF00004; AAA 
SMART
 SM00382; AAA 
PROSITE
 PS00674; AAA 
PRINTS