CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-019710
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 26S proteasome non-ATPase regulatory subunit 1 
Protein Synonyms/Alias
 26S proteasome regulatory subunit RPN2; 26S proteasome regulatory subunit S1; 26S proteasome subunit p112 
Gene Name
 PSMD1 
Gene Synonyms/Alias
  
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
20DEDEPQLKEFALHKLubiquitination[1, 2]
123ADLPEGEKKPIDQRLubiquitination[2]
124DLPEGEKKPIDQRLEubiquitination[1, 2]
136RLEGIVNKMFQRCLDubiquitination[1, 2, 3, 4]
292GTVPGSEKDSDSMETubiquitination[1, 2, 5]
302DSMETEEKTSSAFVGubiquitination[1, 2, 3, 4]
310TSSAFVGKTPEASPEacetylation[6, 7, 8, 9]
310TSSAFVGKTPEASPEubiquitination[1, 2, 3, 4, 5, 9, 10, 11, 12, 13, 14, 15]
319PEASPEPKDQTLKMIubiquitination[1, 2]
324EPKDQTLKMIKILSGubiquitination[1]
354NTDLMILKNTKDAVRubiquitination[1, 2]
543AQETQHEKILRGLAVubiquitination[1, 2]
574IESLCRDKDPILRRSubiquitination[2]
597YCGSGNNKAIRRLLHubiquitination[2]
715QFRQLYSKVINDKHDubiquitination[2]
720YSKVINDKHDDVMAKacetylation[8, 9]
720YSKVINDKHDDVMAKubiquitination[1, 2, 9]
803KMPKVQYKSNCKPSTubiquitination[2]
807VQYKSNCKPSTFAYPubiquitination[2]
821PAPLEVPKEKEKEKVubiquitination[3, 4]
825EVPKEKEKEKVSTAVubiquitination[9]
827PKEKEKEKVSTAVLSubiquitination[1, 9]
838AVLSITAKAKKKEKEubiquitination[1, 2, 9, 12, 14, 15]
840LSITAKAKKKEKEKEubiquitination[2]
853KEKKEEEKMEVDEAEubiquitination[1]
861MEVDEAEKKEEKEKKubiquitination[1, 9, 15]
862EVDEAEKKEEKEKKKubiquitination[1, 9]
865EAEKKEEKEKKKEPEubiquitination[1, 15]
868KKEEKEKKKEPEPNFubiquitination[1, 2, 9]
869KEEKEKKKEPEPNFQubiquitination[1, 2]
890RVMPAQLKVLTMPETubiquitination[1, 2, 3, 4, 9, 12, 14, 15]
904TCRYQPFKPLSIGGIubiquitination[1, 9]
934PVAAHGPKIEEEEQEubiquitination[1, 15]
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] 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]
 [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] 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]
 [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] 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]
 [7] 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]
 [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] 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]
 [10] 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]
 [11] 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]
 [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]
 [13] 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]
 [14] 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]
 [15] 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] 
Functional Description
 Acts as a regulatory subunit of the 26 proteasome which is involved in the ATP-dependent degradation of ubiquitinated proteins. 
Sequence Annotation
 REPEAT 403 436 PC 1.
 REPEAT 441 474 PC 2.
 REPEAT 476 510 PC 3.
 REPEAT 511 545 PC 4.
 REPEAT 547 580 PC 5.
 REPEAT 581 616 PC 6.
 REPEAT 617 649 PC 7.
 REPEAT 651 685 PC 8.
 REPEAT 686 726 PC 9.
 REPEAT 729 761 PC 10.
 MOD_RES 1 1 N-acetylmethionine.
 MOD_RES 273 273 Phosphothreonine.
 MOD_RES 290 290 Phosphoserine.
 MOD_RES 310 310 N6-acetyllysine.
 MOD_RES 311 311 Phosphothreonine.
 MOD_RES 315 315 Phosphoserine.  
Keyword
 Acetylation; Alternative splicing; Complete proteome; Phosphoprotein; Proteasome; Reference proteome; Repeat. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 953 AA 
Protein Sequence
MITSAAGIIS LLDEDEPQLK EFALHKLNAV VNDFWAEISE SVDKIEVLYE DEGFRSRQFA 60
ALVASKVFYH LGAFEESLNY ALGAGDLFNV NDNSEYVETI IAKCIDHYTK QCVENADLPE 120
GEKKPIDQRL EGIVNKMFQR CLDDHKYKQA IGIALETRRL DVFEKTILES NDVPGMLAYS 180
LKLCMSLMQN KQFRNKVLRV LVKIYMNLEK PDFINVCQCL IFLDDPQAVS DILEKLVKED 240
NLLMAYQICF DLYESASQQF LSSVIQNLRT VGTPIASVPG STNTGTVPGS EKDSDSMETE 300
EKTSSAFVGK TPEASPEPKD QTLKMIKILS GEMAIELHLQ FLIRNNNTDL MILKNTKDAV 360
RNSVCHTATV IANSFMHCGT TSDQFLRDNL EWLARATNWA KFTATASLGV IHKGHEKEAL 420
QLMATYLPKD TSPGSAYQEG GGLYALGLIH ANHGGDIIDY LLNQLKNASN DIVRHGGSLG 480
LGLAAMGTAR QDVYDLLKTN LYQDDAVTGE AAGLALGLVM LGSKNAQAIE DMVGYAQETQ 540
HEKILRGLAV GIALVMYGRM EEADALIESL CRDKDPILRR SGMYTVAMAY CGSGNNKAIR 600
RLLHVAVSDV NDDVRRAAVE SLGFILFRTP EQCPSVVSLL SESYNPHVRY GAAMALGICC 660
AGTGNKEAIN LLEPMTNDPV NYVRQGALIA SALIMIQQTE ITCPKVNQFR QLYSKVINDK 720
HDDVMAKFGA ILAQGILDAG GHNVTISLQS RTGHTHMPSV VGVLVFTQFW FWFPLSHFLS 780
LAYTPTCVIG LNKDLKMPKV QYKSNCKPST FAYPAPLEVP KEKEKEKVST AVLSITAKAK 840
KKEKEKEKKE EEKMEVDEAE KKEEKEKKKE PEPNFQLLDN PARVMPAQLK VLTMPETCRY 900
QPFKPLSIGG IIILKDTSED IEELVEPVAA HGPKIEEEEQ EPEPPEPFEY IDD 953 
Gene Ontology
 GO:0005829; C:cytosol; TAS:Reactome.
 GO:0005654; C:nucleoplasm; TAS:Reactome.
 GO:0005838; C:proteasome regulatory particle; TAS:ProtInc.
 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
 IPR016642; 26S_Psome_Rpn2.
 IPR002015; APC_proteasome.
 IPR011989; ARM-like.
 IPR016024; ARM-type_fold. 
Pfam
 PF01851; PC_rep 
SMART
  
PROSITE
  
PRINTS