CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-008870
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Tyrosine--tRNA ligase, cytoplasmic 
Protein Synonyms/Alias
 Tyrosyl-tRNA synthetase; TyrRS; Tyrosine--tRNA ligase, cytoplasmic, N-terminally processed 
Gene Name
 YARS 
Gene Synonyms/Alias
  
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
10DAPSPEEKLHLITRNubiquitination[1]
26QEVLGEEKLKEILKEacetylation[2]
26QEVLGEEKLKEILKEubiquitination[1, 3]
28VLGEEKLKEILKEREubiquitination[1]
114SIGVPLEKLKFIKGTubiquitination[3]
119LEKLKFIKGTDYQLSubiquitination[1, 3, 4, 5, 6]
127GTDYQLSKEYTLDVYubiquitination[1, 3, 6, 7, 8]
146VVTQHDSKKAGAEVVacetylation[2, 9]
147VTQHDSKKAGAEVVKubiquitination[1, 10]
190FGGIDQRKIFTFAEKacetylation[11]
190FGGIDQRKIFTFAEKubiquitination[1]
197KIFTFAEKYLPALGYacetylation[2, 9, 11]
197KIFTFAEKYLPALGYubiquitination[1, 4, 5, 8]
206LPALGYSKRVHLMNPacetylation[9, 11]
206LPALGYSKRVHLMNPubiquitination[1, 4, 5]
231SSSEEESKIDLLDRKacetylation[2]
247DVKKKLKKAFCEPGNubiquitination[1, 8]
272KHVLFPLKSEFVILRacetylation[9]
282FVILRDEKWGGNKTYubiquitination[8]
319SVEVALNKLLDPIREacetylation[2]
334KFNTPALKKLASAAYubiquitination[1]
335FNTPALKKLASAAYPubiquitination[1, 3]
356PMAKGPAKNSEPEEVubiquitination[1, 6, 12]
374RLDIRVGKIITVEKHubiquitination[1]
380GKIITVEKHPDADSLubiquitination[8]
391ADSLYVEKIDVGEAEubiquitination[1, 7]
412GLVQFVPKEELQDRLubiquitination[1, 7, 13]
427VVVLCNLKPQKMRGVubiquitination[1]
430LCNLKPQKMRGVESQubiquitination[1]
470PGEHVFVKGYEKGQPacetylation[2]
470PGEHVFVKGYEKGQPubiquitination[1, 7, 12]
474VFVKGYEKGQPDEELacetylation[6, 9]
474VFVKGYEKGQPDEELubiquitination[1]
482GQPDEELKPKKKVFEacetylation[6, 9]
482GQPDEELKPKKKVFEubiquitination[1]
490PKKKVFEKLQADFKIacetylation[2, 9]
490PKKKVFEKLQADFKIubiquitination[1, 8]
506EECIAQWKQTNFMTKubiquitination[1]
513KQTNFMTKLGSISCKubiquitination[1, 3, 4, 5, 6, 7, 8, 12, 13, 14, 15]
520KLGSISCKSLKGGNIubiquitination[1]
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] 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]
 [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] 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] 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]
 [6] 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]
 [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] 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]
 [9] 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]
 [10] 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]
 [11] 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]
 [12] 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]
 [13] 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]
 [14] 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]
 [15] 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
 Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction: tyrosine is first activated by ATP to form Tyr- AMP and then transferred to the acceptor end of tRNA(Tyr) (By similarity). 
Sequence Annotation
 DOMAIN 364 468 tRNA-binding.
 MOTIF 44 52 "HIGH" region.
 MOTIF 222 226 "KMSKS" region.
 BINDING 39 39 Tyrosine.
 BINDING 166 166 Tyrosine.
 BINDING 170 170 Tyrosine.
 BINDING 173 173 Tyrosine.
 BINDING 188 188 Tyrosine.
 MOD_RES 1 1 N-acetylmethionine.
 MOD_RES 2 2 N-acetylglycine; in Tyrosine--tRNA
 MOD_RES 197 197 N6-acetyllysine.
 MOD_RES 206 206 N6-acetyllysine.
 MOD_RES 474 474 N6-acetyllysine.
 MOD_RES 482 482 N6-acetyllysine.
 MOD_RES 490 490 N6-acetyllysine.  
Keyword
 3D-structure; Acetylation; Aminoacyl-tRNA synthetase; ATP-binding; Charcot-Marie-Tooth disease; Complete proteome; Cytoplasm; Direct protein sequencing; Disease mutation; Ligase; Neuropathy; Nucleotide-binding; Polymorphism; Protein biosynthesis; Reference proteome; RNA-binding; tRNA-binding. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 528 AA 
Protein Sequence
MGDAPSPEEK LHLITRNLQE VLGEEKLKEI LKERELKIYW GTATTGKPHV AYFVPMSKIA 60
DFLKAGCEVT ILFADLHAYL DNMKAPWELL ELRVSYYENV IKAMLESIGV PLEKLKFIKG 120
TDYQLSKEYT LDVYRLSSVV TQHDSKKAGA EVVKQVEHPL LSGLLYPGLQ ALDEEYLKVD 180
AQFGGIDQRK IFTFAEKYLP ALGYSKRVHL MNPMVPGLTG SKMSSSEEES KIDLLDRKED 240
VKKKLKKAFC EPGNVENNGV LSFIKHVLFP LKSEFVILRD EKWGGNKTYT AYVDLEKDFA 300
AEVVHPGDLK NSVEVALNKL LDPIREKFNT PALKKLASAA YPDPSKQKPM AKGPAKNSEP 360
EEVIPSRLDI RVGKIITVEK HPDADSLYVE KIDVGEAEPR TVVSGLVQFV PKEELQDRLV 420
VVLCNLKPQK MRGVESQGML LCASIEGINR QVEPLDPPAG SAPGEHVFVK GYEKGQPDEE 480
LKPKKKVFEK LQADFKISEE CIAQWKQTNF MTKLGSISCK SLKGGNIS 528 
Gene Ontology
 GO:0005829; C:cytosol; TAS:Reactome.
 GO:0005615; C:extracellular space; TAS:ProtInc.
 GO:0005634; C:nucleus; IDA:HPA.
 GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
 GO:0005153; F:interleukin-8 receptor binding; TAS:ProtInc.
 GO:0004871; F:signal transducer activity; NAS:ProtInc.
 GO:0000049; F:tRNA binding; IEA:UniProtKB-KW.
 GO:0004831; F:tyrosine-tRNA ligase activity; TAS:Reactome.
 GO:0006915; P:apoptotic process; TAS:ProtInc.
 GO:0006437; P:tyrosyl-tRNA aminoacylation; TAS:ProtInc. 
Interpro
 IPR002305; aa-tRNA-synth_Ic.
 IPR012340; NA-bd_OB-fold.
 IPR014729; Rossmann-like_a/b/a_fold.
 IPR002547; tRNA-bd_dom.
 IPR002307; Tyr-tRNA-ligase.
 IPR023617; Tyr-tRNA-ligase_arc/euk-type. 
Pfam
 PF00579; tRNA-synt_1b
 PF01588; tRNA_bind 
SMART
  
PROSITE
 PS00178; AA_TRNA_LIGASE_I
 PS50886; TRBD 
PRINTS
 PR01040; TRNASYNTHTYR.