CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-037347
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
  
Protein Name
 Ribonucleoside-diphosphate reductase 
Protein Synonyms/Alias
  
Gene Name
 RRM1 
Gene Synonyms/Alias
  
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
21KHSPMVAKSTLDIVLubiquitination[1]
31LDIVLANKDRLNSAIubiquitination[1, 2, 3]
52SYNYFGFKTLERSYLubiquitination[1, 2, 3, 4, 5, 6]
61LERSYLLKINGKVAEubiquitination[1, 2, 3, 4, 6, 7]
65YLLKINGKVAERPQHubiquitination[1, 3]
83RVSVGIHKEDIDAAIubiquitination[1, 2]
139EGIYDTLKQCALISKubiquitination[1, 2, 5]
146KQCALISKSAGGIGVubiquitination[1, 5]
223DLKKNTGKEEQRARDmethylation[8]
279KLYASYEKQGRVRKVacetylation[9]
279KLYASYEKQGRVRKVubiquitination[1, 2, 3, 4, 5, 6, 7]
311GTPYMLYKDSCNRKSubiquitination[5]
317YKDSCNRKSNQQNLGubiquitination[1, 2, 3, 7]
368EHTYDFKKLAEVTKVubiquitination[1, 2, 10]
374KKLAEVTKVVVRNLNubiquitination[1, 2, 3, 4, 5, 6, 7]
382VVVRNLNKIIDINYYubiquitination[1, 3, 5]
399PEACLSNKRHRPIGIacetylation[3, 11]
399PEACLSNKRHRPIGIubiquitination[1, 2, 3, 5, 7]
490DWKVLKEKIAKYGIRubiquitination[1]
493VLKEKIAKYGIRNSLubiquitination[1, 4]
546IVNPHLLKDLTERGLubiquitination[1, 2, 3, 4, 5, 6, 12]
559GLWHEEMKNQIIACNubiquitination[1]
580PEIPDDLKQLYKTVWubiquitination[1]
584DDLKQLYKTVWEISQubiquitination[4]
592TVWEISQKTVLKMAAubiquitination[1, 3, 4, 5, 6]
596ISQKTVLKMAAERGAubiquitination[1, 4, 5]
632SMHFYGWKQGLKTGMubiquitination[1]
636YGWKQGLKTGMYYLRubiquitination[1]
657PIQFTLNKEKLKDKEubiquitination[1, 2, 3, 4, 5, 6, 12]
659QFTLNKEKLKDKEKVubiquitination[1, 3]
Reference
 [1] 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]
 [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] 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]
 [4] 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]
 [5] 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]
 [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] 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]
 [8] Large-scale global identification of protein lysine methylation in vivo.
 Cao XJ, Arnaudo AM, Garcia BA.
 Epigenetics. 2013 May 1;8(5):477-85. [PMID: 23644510]
 [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] 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]
 [11] 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]
 [12] 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] 
Functional Description
 Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides (By similarity). 
Sequence Annotation
  
Keyword
 Complete proteome; DNA replication; Oxidoreductase; Reference proteome. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 695 AA 
Protein Sequence
MEDLYNYINP HNGKHSPMVA KSTLDIVLAN KDRLNSAIIY DRDFSYNYFG FKTLERSYLL 60
KINGKVAERP QHMLMRVSVG IHKEDIDAAI ETYNLLSERW FTHASPTLFN AGTNRPQLSS 120
CFLLSMKDDS IEGIYDTLKQ CALISKSAGG IGVAVSCIRA TGSYIAGTNG NSNGLVPMLR 180
VYNNTARYVD QGGNKRPGAF AIYLEPWHLD IFEFLDLKKN TGKEEQRARD LFFALWIPDL 240
FMKRVETNQD WSLMCPNECP GLDEVWGEEF EKLYASYEKQ GRVRKVVKAQ QLWYAIIESQ 300
TETGTPYMLY KDSCNRKSNQ QNLGTIKCSN LCTEIVEYTS KDEVAVCNLA SLALNMYVTS 360
EHTYDFKKLA EVTKVVVRNL NKIIDINYYP VPEACLSNKR HRPIGIGVQG LADAFILMRY 420
PFESAEAQLL NKQIFETIYY GALEASCDLA KEQGPYETYE GSPVSKGILQ YDMWNVTPTD 480
LWDWKVLKEK IAKYGIRNSL LIAPMPTAST AQILGNNESI EPYTSNIYTR RVLSGEFQIV 540
NPHLLKDLTE RGLWHEEMKN QIIACNGSIQ SIPEIPDDLK QLYKTVWEIS QKTVLKMAAE 600
RGAFIDQSQS LNIHIAEPNY GKLTSMHFYG WKQGLKTGMY YLRTRPAANP IQFTLNKEKL 660
KDKEKVSKEE EEKERNTAAM VCSLENRDEC LMCGS 695 
Gene Ontology
 GO:0005971; C:ribonucleoside-diphosphate reductase complex; IEA:InterPro.
 GO:0005524; F:ATP binding; IEA:InterPro.
 GO:0004748; F:ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor; IEA:EC.
 GO:0009263; P:deoxyribonucleotide biosynthetic process; IEA:Compara.
 GO:0006260; P:DNA replication; IEA:UniProtKB-UniPathway.
 GO:0051290; P:protein heterotetramerization; IEA:Compara. 
Interpro
 IPR013346; NrdE_NrdA.
 IPR000788; RNR_lg_C.
 IPR013509; RNR_lsu_N.
 IPR008926; RNR_R1-su_N. 
Pfam
 PF02867; Ribonuc_red_lgC
 PF00317; Ribonuc_red_lgN 
SMART
  
PROSITE
 PS00089; RIBORED_LARGE 
PRINTS
 PR01183; RIBORDTASEM1.