CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-000664
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 26S proteasome non-ATPase regulatory subunit 3 
Protein Synonyms/Alias
 26S proteasome regulatory subunit RPN3; 26S proteasome regulatory subunit S3; Proteasome subunit p58 
Gene Name
 PSMD3 
Gene Synonyms/Alias
  
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
14ARRRGADKAKPPPGGacetylation[1]
16RRGADKAKPPPGGGEubiquitination[2, 3]
38APQDVEMKEEAATGGubiquitination[2, 3, 4, 5]
54STGEADGKTAAAAAEubiquitination[2, 3, 4, 6, 7]
76TVTLEDIKEHVKQLEacetylation[8]
76TVTLEDIKEHVKQLEubiquitination[2, 4, 5, 6, 7]
84EHVKQLEKAVSGKEPubiquitination[4, 5]
194ISDDLMQKISTQNRRubiquitination[2]
209ALDLVAAKCYYYHARubiquitination[4]
223RVYEFLDKLDVVRSFubiquitination[2, 4, 6, 7, 9]
269SLYDQAEKLVSKSVFubiquitination[6, 7]
273QAEKLVSKSVFPEQAubiquitination[2, 3, 4, 6, 7, 9, 10]
296LYYTGRIKAIQLEYSubiquitination[2, 3, 4, 9]
374VRTGNLAKFNQVLDQubiquitination[2, 3, 6, 7]
404RLRHNVIKTGVRMISubiquitination[4]
425SLADIAQKLQLDSPEubiquitination[2, 3]
440DAEFIVAKAIRDGVIubiquitination[2, 3, 6, 7, 11]
455EASINHEKGYVQSKEubiquitination[2]
461EKGYVQSKEMIDIYSubiquitination[2, 6, 7]
492DIHNMSVKAMRFPPKubiquitination[4, 12]
503FPPKSYNKDLESAEEubiquitination[2, 4, 5]
Reference
 [1] 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]
 [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] 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]
 [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] 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]
 [6] 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]
 [7] 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]
 [8] 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]
 [9] 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]
 [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] 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] 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] 
Functional Description
 Acts as a regulatory subunit of the 26 proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins. 
Sequence Annotation
 DOMAIN 358 462 PCI.  
Keyword
 Complete proteome; Proteasome; Reference proteome. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 534 AA 
Protein Sequence
MKQEGSARRR GADKAKPPPG GGEQEPPPPP APQDVEMKEE AATGGGSTGE ADGKTAAAAA 60
EHSQRELDTV TLEDIKEHVK QLEKAVSGKE PRFVLRALRM LPSTSRRLNH YVLYKAVQGF 120
FTSNNATRDF LLPFLEEPMD TEADLQFRPR TGKAASTPLL PEVEAYLQLL VVIFMMNSKR 180
YKEAQKISDD LMQKISTQNR RALDLVAAKC YYYHARVYEF LDKLDVVRSF LHARLRTATL 240
RHDADGQATL LNLLLRNYLH YSLYDQAEKL VSKSVFPEQA NNNEWARYLY YTGRIKAIQL 300
EYSEARRTMT NALRKAPQHT AVGFKQTVHK LLIVVELLLG EIPDRLQFRQ PSLKRSLMPY 360
FLLTQAVRTG NLAKFNQVLD QFGEKFQADG TYTLIIRLRH NVIKTGVRMI SLSYSRISLA 420
DIAQKLQLDS PEDAEFIVAK AIRDGVIEAS INHEKGYVQS KEMIDIYSTR EPQLAFHQRI 480
SFCLDIHNMS VKAMRFPPKS YNKDLESAEE RREREQQDLE FAKEMAEDDD DSFP 534 
Gene Ontology
 GO:0005829; C:cytosol; TAS:Reactome.
 GO:0005654; C:nucleoplasm; TAS:Reactome.
 GO:0022624; C:proteasome accessory complex; ISS:UniProtKB.
 GO:0030234; F:enzyme regulator activity; IEA:InterPro.
 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:0042176; P:regulation of protein catabolic process; IEA:InterPro.
 GO:0044281; P:small molecule metabolic process; TAS:Reactome.
 GO:0016032; P:viral reproduction; TAS:Reactome. 
Interpro
 IPR013586; 26S_Psome_reg_C.
 IPR013143; PAM.
 IPR000717; PCI_dom.
 IPR011990; TPR-like_helical.
 IPR011991; WHTH_DNA-bd_dom. 
Pfam
 PF01399; PCI
 PF08375; Rpn3_C 
SMART
 SM00753; PAM
 SM00088; PINT 
PROSITE
  
PRINTS