CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-008933
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 26S proteasome non-ATPase regulatory subunit 4 
Protein Synonyms/Alias
 26S proteasome regulatory subunit RPN10; 26S proteasome regulatory subunit S5A; Antisecretory factor 1; AF; ASF; Multiubiquitin chain-binding protein 
Gene Name
 PSMD4 
Gene Synonyms/Alias
 MCB1 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
40VNIVCHSKTRSNPENubiquitination[1, 2, 3, 4, 5, 6, 7, 8, 9]
74DTGRILSKLHTVQPKubiquitination[2, 3, 4, 5, 6, 8, 9]
81KLHTVQPKGKITFCTubiquitination[2, 3, 6, 9]
83HTVQPKGKITFCTGIubiquitination[2, 3, 6, 7, 9]
98RVAHLALKHRQGKNHubiquitination[3]
122SPVEDNEKDLVKLAKubiquitination[1, 2, 3, 6, 7, 8, 9, 10]
126DNEKDLVKLAKRLKKubiquitination[2, 3, 7, 8, 9]
129KDLVKLAKRLKKEKVubiquitination[7]
135AKRLKKEKVNVDIINubiquitination[2, 3, 6, 8, 9]
152EEEVNTEKLTAFVNTubiquitination[3, 6, 8]
262DSDDALLKMTISQQEubiquitination[3, 6, 7, 8, 9, 10]
365SLASQATKDGKKDKKubiquitination[3, 7, 8]
369QATKDGKKDKKEEDKubiquitination[7]
Reference
 [1] 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]
 [2] 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]
 [3] 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]
 [4] 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]
 [5] 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]
 [6] 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]
 [7] 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]
 [8] 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]
 [9] 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]
 [10] Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level.
 Danielsen JM, Sylvestersen KB, Bekker-Jensen S, Szklarczyk D, Poulsen JW, Horn H, Jensen LJ, Mailand N, Nielsen ML.
 Mol Cell Proteomics. 2011 Mar;10(3):M110.003590. [PMID: 21139048] 
Functional Description
 Binds and presumably selects ubiquitin-conjugates for destruction. Displays selectivity for longer polyubiquitin chains. Modulates intestinal fluid secretion. 
Sequence Annotation
 DOMAIN 5 188 VWFA.
 REPEAT 211 230 UIM 1.
 REPEAT 282 301 UIM 2.
 REGION 216 220 Essential for ubiquitin-binding.
 REGION 287 291 Essential for ubiquitin-binding.
 MOD_RES 250 250 Phosphothreonine (By similarity).
 MOD_RES 253 253 Phosphothreonine (By similarity).
 MOD_RES 256 256 Phosphoserine (By similarity).
 MOD_RES 266 266 Phosphoserine.
 MOD_RES 358 358 Phosphoserine.
 MOD_RES 361 361 Phosphoserine.  
Keyword
 3D-structure; Alternative splicing; Complete proteome; Direct protein sequencing; Phosphoprotein; Proteasome; Reference proteome; Repeat. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 377 AA 
Protein Sequence
MVLESTMVCV DNSEYMRNGD FLPTRLQAQQ DAVNIVCHSK TRSNPENNVG LITLANDCEV 60
LTTLTPDTGR ILSKLHTVQP KGKITFCTGI RVAHLALKHR QGKNHKMRII AFVGSPVEDN 120
EKDLVKLAKR LKKEKVNVDI INFGEEEVNT EKLTAFVNTL NGKDGTGSHL VTVPPGPSLA 180
DALISSPILA GEGGAMLGLG ASDFEFGVDP SADPELALAL RVSMEEQRQR QEEEARRAAA 240
ASAAEAGIAT TGTEDSDDAL LKMTISQQEF GRTGLPDLSS MTEEEQIAYA MQMSLQGAEF 300
GQAESADIDA SSAMDTSEPA KEEDDYDVMQ DPEFLQSVLE NLPGVDPNNE AIRNAMGSLA 360
SQATKDGKKD KKEEDKK 377 
Gene Ontology
 GO:0005829; C:cytosol; TAS:Reactome.
 GO:0005654; C:nucleoplasm; TAS:Reactome.
 GO:0022624; C:proteasome accessory complex; ISS:UniProtKB.
 GO:0008540; C:proteasome regulatory particle, base subcomplex; 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:0044281; P:small molecule metabolic process; TAS:Reactome.
 GO:0016032; P:viral reproduction; TAS:Reactome. 
Interpro
 IPR027040; Proteasome_su_Rpn10.
 IPR003903; Ubiquitin-int_motif.
 IPR002035; VWF_A. 
Pfam
 PF02809; UIM 
SMART
 SM00726; UIM
 SM00327; VWA 
PROSITE
 PS50330; UIM
 PS50234; VWFA 
PRINTS