CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-022188
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 tRNA wybutosine-synthesizing protein 1 homolog 
Protein Synonyms/Alias
 Radical S-adenosyl methionine and flavodoxin domain-containing protein 1; tRNA-yW-synthesizing protein 
Gene Name
 TYW1 
Gene Synonyms/Alias
 RSAFD1 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
52QGKNLQEKSVPKAAQubiquitination[1]
166SIDFRFGKTYLKGMRubiquitination[1]
221DCDVVKSKHGSIEADubiquitination[1]
235DFRAWKTKFISQLQAubiquitination[1]
245SQLQALQKGERKKSCubiquitination[1]
337EKEQQEEKSGLFRNMubiquitination[1]
366ALREALTKQGYQLIGubiquitination[1, 2]
385VKLCRWTKSMLRGRGubiquitination[1]
396RGRGGCYKHTFYGIEacetylation[3]
396RGRGGCYKHTFYGIEubiquitination[1]
438VGTEWRWKMDQPEMIubiquitination[1]
447DQPEMILKEAIENHQubiquitination[1]
458ENHQNMIKQFKGVPGubiquitination[1, 4, 5]
461QNMIKQFKGVPGVKAubiquitination[1]
467FKGVPGVKAERFEEGubiquitination[1]
499PEINRFLKLLHQCKIubiquitination[1]
505LKLLHQCKISSFLVTubiquitination[1]
543STKDSLKKIDRPLFKubiquitination[1]
550KIDRPLFKDFWQRFLubiquitination[1, 4, 5, 6]
561QRFLDSLKALAVKQQubiquitination[1]
689YEDSGGSKTFSAKDYubiquitination[1, 6]
694GSKTFSAKDYMARTPubiquitination[1, 7]
716SERGFDPKDTRHQRKubiquitination[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] 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]
 [3] 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]
 [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] 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]
 [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
Functional Description
 Probable component of the wybutosine biosynthesis pathway. Wybutosine is a hyper modified guanosine with a tricyclic base found at the 3'-position adjacent to the anticodon of eukaryotic phenylalanine tRNA (By similarity). 
Sequence Annotation
 DOMAIN 79 237 Flavodoxin-like.
 NP_BIND 85 89 FMN (By similarity).
 NP_BIND 176 208 FMN (By similarity).
 METAL 416 416 Iron-sulfur (4Fe-4S-S-AdoMet)
 METAL 420 420 Iron-sulfur (4Fe-4S-S-AdoMet)
 METAL 423 423 Iron-sulfur (4Fe-4S-S-AdoMet)  
Keyword
 4Fe-4S; Alternative splicing; Complete proteome; Iron; Iron-sulfur; Metal-binding; Nucleotide-binding; Polymorphism; Reference proteome; S-adenosyl-L-methionine; tRNA processing. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 732 AA 
Protein Sequence
MDPSADTWDL FSPLISLWIN RFYIYLGFAV SISLWICVQI VIKTQGKNLQ EKSVPKAAQD 60
LMTNGYVSLQ EKDIFVSGVK IFYGSQTGTA KGFATVLAEA VTSLDLPVAI INLKEYDPDD 120
HLIEEVTSKN VCVFLVATYT DGLPTESAEW FCKWLEEASI DFRFGKTYLK GMRYAVFGLG 180
NSAYASHFNK VGKNVDKWLW MLGAHRVMSR GEGDCDVVKS KHGSIEADFR AWKTKFISQL 240
QALQKGERKK SCGGHCKKGK CESHQHGSEE REEGSHEQDE LHHRDTEEEE PFESSSEEEF 300
GGEDHQSLNS IVDVEDLGKI MDHVKKEKRE KEQQEEKSGL FRNMGRNEDG ERRAMITPAL 360
REALTKQGYQ LIGSHSGVKL CRWTKSMLRG RGGCYKHTFY GIESHRCMET TPSLACANKC 420
VFCWRHHTNP VGTEWRWKMD QPEMILKEAI ENHQNMIKQF KGVPGVKAER FEEGMTVKHC 480
ALSLVGEPIM YPEINRFLKL LHQCKISSFL VTNAQFPAEI RNLEPVTQLY VSVDASTKDS 540
LKKIDRPLFK DFWQRFLDSL KALAVKQQRT VYRLTLVKAW NVDELQAYAQ LVSLGNPDFI 600
EVKGVTYCGE SSASSLTMAH VPWHEEVVQF VHELVDLIPE YEIACEHEHS NCLLIAHRKF 660
KIGGEWWTWI DYNRFQELIQ EYEDSGGSKT FSAKDYMART PHWALFGASE RGFDPKDTRH 720
QRKNKSKAIS GC 732 
Gene Ontology
 GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
 GO:0010181; F:FMN binding; IEA:InterPro.
 GO:0005506; F:iron ion binding; IEA:InterPro.
 GO:0016491; F:oxidoreductase activity; IEA:InterPro.
 GO:0008033; P:tRNA processing; IEA:UniProtKB-KW. 
Interpro
 IPR013785; Aldolase_TIM.
 IPR001094; Flavdoxin.
 IPR008254; Flavodoxin/NO_synth.
 IPR007197; rSAM.
 IPR013917; tRNA_wybutosine-synth. 
Pfam
 PF00258; Flavodoxin_1
 PF04055; Radical_SAM
 PF08608; Wyosine_form 
SMART
  
PROSITE
 PS50902; FLAVODOXIN_LIKE 
PRINTS
 PR00369; FLAVODOXIN.