CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-008883
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 UV excision repair protein RAD23 homolog A 
Protein Synonyms/Alias
 HR23A; hHR23A 
Gene Name
 RAD23A 
Gene Synonyms/Alias
  
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
8MAVTITLKTLQQQTFubiquitination[1]
16TLQQQTFKIRMEPDEubiquitination[1, 2, 3, 4, 5]
26MEPDETVKVLKEKIEubiquitination[1, 2, 4, 5]
29DETVKVLKEKIEAEKubiquitination[4]
31TVKVLKEKIEAEKGRubiquitination[4]
36KEKIEAEKGRDAFPVubiquitination[4]
47AFPVAGQKLIYAGKIacetylation[6]
47AFPVAGQKLIYAGKIubiquitination[1, 2, 4, 5, 7]
53QKLIYAGKILSDDVPubiquitination[1, 2, 3, 4, 5, 7, 8, 9, 10]
69RDYRIDEKNFVVVMVubiquitination[1, 2, 4]
78FVVVMVTKTKAGQGTubiquitination[2, 3, 4, 5, 7]
80VVMVTKTKAGQGTSAubiquitination[2, 3, 4, 5]
122PPAAREDKSPSEESAubiquitination[2, 3, 4, 5, 7, 11, 12, 13, 14]
321IQVTPQEKEAIERLKubiquitination[2, 5]
Reference
 [1] 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]
 [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] 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] 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] 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]
 [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] 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]
 [8] 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]
 [9] 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]
 [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] Quantitative analysis of global ubiquitination in HeLa cells by mass spectrometry.
 Meierhofer D, Wang X, Huang L, Kaiser P.
 J Proteome Res. 2008 Oct;7(10):4566-76. [PMID: 18781797]
 [12] A data set of human endogenous protein ubiquitination sites.
 Shi Y, Chan DW, Jung SY, Malovannaya A, Wang Y, Qin J.
 Mol Cell Proteomics. 2011 May;10(5):M110.002089. [PMID: 20972266]
 [13] 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]
 [14] 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
Functional Description
 Multiubiquitin chain receptor involved in modulation of proteasomal degradation. Binds to 'Lys-48'-linked polyubiquitin chains in a length-dependent manner and with a lower affinity to 'Lys-63'-linked polyubiquitin chains. Proposed to be capable to bind simultaneously to the 26S proteasome and to polyubiquitinated substrates and to deliver ubiquitinated proteins to the proteasome. 
Sequence Annotation
 DOMAIN 1 81 Ubiquitin-like.
 DOMAIN 161 201 UBA 1.
 DOMAIN 318 358 UBA 2.
 REGION 319 363 HIV-1 vpr binding.
 MOD_RES 123 123 Phosphoserine.
 MOD_RES 133 133 Phosphoserine.
 MOD_RES 205 205 Phosphoserine.
 MOD_RES 295 295 Phosphoserine.
 MOD_RES 357 357 Phosphoserine.
 CROSSLNK 122 122 Glycyl lysine isopeptide (Lys-Gly)  
Keyword
 3D-structure; Alternative splicing; Complete proteome; DNA damage; DNA repair; Host-virus interaction; Isopeptide bond; Nucleus; Phosphoprotein; Polymorphism; Proteasome; Reference proteome; Repeat; Ubl conjugation. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 363 AA 
Protein Sequence
MAVTITLKTL QQQTFKIRME PDETVKVLKE KIEAEKGRDA FPVAGQKLIY AGKILSDDVP 60
IRDYRIDEKN FVVVMVTKTK AGQGTSAPPE ASPTAAPESS TSFPPAPTSG MSHPPPAARE 120
DKSPSEESAP TTSPESVSGS VPSSGSSGRE EDAASTLVTG SEYETMLTEI MSMGYERERV 180
VAALRASYNN PHRAVEYLLT GIPGSPEPEH GSVQESQVSE QPATEAAGEN PLEFLRDQPQ 240
FQNMRQVIQQ NPALLPALLQ QLGQENPQLL QQISRHQEQF IQMLNEPPGE LADISDVEGE 300
VGAIGEEAPQ MNYIQVTPQE KEAIERLKAL GFPESLVIQA YFACEKNENL AANFLLSQNF 360
DDE 363 
Gene Ontology
 GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
 GO:0000502; C:proteasome complex; IEA:UniProtKB-KW.
 GO:0003684; F:damaged DNA binding; IEA:InterPro.
 GO:0031593; F:polyubiquitin binding; IDA:UniProtKB.
 GO:0003697; F:single-stranded DNA binding; TAS:ProtInc.
 GO:0006289; P:nucleotide-excision repair; IDA:UniProtKB.
 GO:0045070; P:positive regulation of viral genome replication; IMP:UniProtKB.
 GO:0043161; P:proteasomal ubiquitin-dependent protein catabolic process; IEA:InterPro.
 GO:0032434; P:regulation of proteasomal ubiquitin-dependent protein catabolic process; IDA:UniProtKB.
 GO:0019048; P:virus-host interaction; IEA:UniProtKB-KW. 
Interpro
 IPR004806; Rad23.
 IPR006636; STI1_HS-bd.
 IPR009060; UBA-like.
 IPR000449; UBA/transl_elong_EF1B_N.
 IPR015940; UBA/transl_elong_EF1B_N_euk.
 IPR000626; Ubiquitin.
 IPR019955; Ubiquitin_supergroup.
 IPR015360; XPC-bd. 
Pfam
 PF00627; UBA
 PF00240; ubiquitin
 PF09280; XPC-binding 
SMART
 SM00727; STI1
 SM00165; UBA
 SM00213; UBQ 
PROSITE
 PS50030; UBA
 PS00299; UBIQUITIN_1
 PS50053; UBIQUITIN_2 
PRINTS
 PR01839; RAD23PROTEIN.