CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-007718
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 26S protease regulatory subunit 6B 
Protein Synonyms/Alias
 26S proteasome AAA-ATPase subunit RPT3; MB67-interacting protein; MIP224; Proteasome 26S subunit ATPase 4; Tat-binding protein 7; TBP-7 
Gene Name
 PSMC4 
Gene Synonyms/Alias
 MIP224; TBP7 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
46DLYSRYKKLQQELEFubiquitination[1, 2]
62EVQEEYIKDEQKNLKubiquitination[1]
70DEQKNLKKEFLHAQEubiquitination[2, 3, 4]
80LHAQEEVKRIQSIPLubiquitination[1, 2, 4]
125TIDRELLKPNASVALubiquitination[1, 2, 3, 4, 5, 6]
192LTHFELYKQIGIDPPubiquitination[1, 2, 3, 4, 6]
212YGPPGCGKTMLAKAVubiquitination[1, 4]
217CGKTMLAKAVAHHTTubiquitination[2, 4, 6]
238VGSEFVQKYLGEGPRacetylation[2, 7, 8, 9, 10]
238VGSEFVQKYLGEGPRubiquitination[1, 2, 3, 4, 5, 6]
255RDVFRLAKENAPAIIubiquitination[4, 6, 11]
273EIDAIATKRFDAQTGubiquitination[1, 4, 6, 12]
397NRYIVLAKDFEKAYKacetylation[2, 7, 9, 10]
397NRYIVLAKDFEKAYKubiquitination[1, 4, 6]
401VLAKDFEKAYKTVIKacetylation[7]
401VLAKDFEKAYKTVIKubiquitination[1]
408KAYKTVIKKDEQEHEubiquitination[4]
409AYKTVIKKDEQEHEFubiquitination[1, 6]
418EQEHEFYK*******ubiquitination[1, 2]
Reference
 [1] 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]
 [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] 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]
 [4] 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]
 [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] 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] 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]
 [8] Monoclonal antibody cocktail as an enrichment tool for acetylome analysis.
 Shaw PG, Chaerkady R, Zhang Z, Davidson NE, Pandey A.
 Anal Chem. 2011 May 15;83(10):3623-6. [PMID: 21466224]
 [9] Proteomic investigations reveal a role for RNA processing factor THRAP3 in the DNA damage response.
 Beli P, Lukashchuk N, Wagner SA, Weinert BT, Olsen JV, Baskcomb L, Mann M, Jackson SP, Choudhary C.
 Mol Cell. 2012 Apr 27;46(2):212-25. [PMID: 22424773]
 [10] 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]
 [11] 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]
 [12] 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
 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 206 213 ATP (Potential).
 MOD_RES 1 1 N-acetylmethionine.
 MOD_RES 21 21 Phosphoserine.
 MOD_RES 28 28 Phosphoserine.
 MOD_RES 397 397 N6-acetyllysine.
 MOD_RES 401 401 N6-acetyllysine.  
Keyword
 3D-structure; Acetylation; Alternative splicing; ATP-binding; Complete proteome; Cytoplasm; Direct protein sequencing; Nucleotide-binding; Nucleus; Phosphoprotein; Proteasome; Reference proteome. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 418 AA 
Protein Sequence
MEEIGILVEK AQDEIPALSV SRPQTGLSFL GPEPEDLEDL YSRYKKLQQE LEFLEVQEEY 60
IKDEQKNLKK EFLHAQEEVK RIQSIPLVIG QFLEAVDQNT AIVGSTTGSN YYVRILSTID 120
RELLKPNASV ALHKHSNALV DVLPPEADSS IMMLTSDQKP DVMYADIGGM DIQKQEVREA 180
VELPLTHFEL YKQIGIDPPR GVLMYGPPGC GKTMLAKAVA HHTTAAFIRV VGSEFVQKYL 240
GEGPRMVRDV FRLAKENAPA IIFIDEIDAI ATKRFDAQTG ADREVQRILL ELLNQMDGFD 300
QNVNVKVIMA TNRADTLDPA LLRPGRLDRK IEFPLPDRRQ KRLIFSTITS KMNLSEEVDL 360
EDYVARPDKI SGADINSICQ ESGMLAVREN RYIVLAKDFE KAYKTVIKKD EQEHEFYK 418 
Gene Ontology
 GO:0005829; C:cytosol; TAS:Reactome.
 GO:0005739; C:mitochondrion; IDA:HPA.
 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; 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:0001824; P:blastocyst development; IEA:Compara.
 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