CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-015079
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 tRNA wybutosine-synthesizing protein 1 homolog B 
Protein Synonyms/Alias
 Radical S-adenosyl methionine and flavodoxin domain-containing protein 2 
Gene Name
 TYW1B 
Gene Synonyms/Alias
 RSAFD2 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
120SIDFRFGKTYLKGMRubiquitination[1]
189NFRAWKTKFISQLQAubiquitination[1]
199SQLQALQKGERKKSCubiquitination[1]
291EKEQQEEKSGLFRNMubiquitination[1]
374VGTEWLWKMDQPEMIubiquitination[1]
383DQPEMILKEAIENHQubiquitination[1]
394ENHQNMIKQFKGVPGubiquitination[1, 2, 3]
397QNMIKQFKGVPGVKAubiquitination[1]
403FKGVPGVKAERFEEGubiquitination[1, 3]
435PEINRFLKLLHQCKIubiquitination[1]
441LKLLHQCKISSFLVTubiquitination[1]
479STKDSLKKIDRPLFKubiquitination[1]
497QQFLDSLKALAVKQQubiquitination[1]
625YEDSGGSKTFSAKDYubiquitination[1, 4]
630GSKTFSAKDYMARTPubiquitination[1, 3, 5]
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] 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]
 [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] 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]
 [5] 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 37 191 Flavodoxin-like.
 NP_BIND 43 47 FMN (By similarity).
 NP_BIND 130 162 FMN (By similarity).
 METAL 352 352 Iron-sulfur (4Fe-4S-S-AdoMet)
 METAL 356 356 Iron-sulfur (4Fe-4S-S-AdoMet)
 METAL 359 359 Iron-sulfur (4Fe-4S-S-AdoMet)  
Keyword
 4Fe-4S; Complete proteome; Iron; Iron-sulfur; Metal-binding; Nucleotide-binding; Reference proteome; S-adenosyl-L-methionine; tRNA processing. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 668 AA 
Protein Sequence
MDPSADTWDL SSPLISLWIN RFYIYLGFAV SISLWICVQI VIEMQGFATV LAEAVTSLDL 60
PVAIINLKEY DPDDHLIEEV TSKNVCVFLV ATYTDGLPTE SAEWFCKWLE EASIDFRFGK 120
TYLKGMRDAV FGLGNSAYAS HFNKVGKNVD KWLWMLGVHR VMSRGEGDCD VVKSKHGSIE 180
ANFRAWKTKF ISQLQALQKG ERKKSCGGHC KKGKCESHQH GSEEREEGSQ EQDELHHRDT 240
KEEEPFESSS EEEFGGEDHQ SLNSIVDVED LGKIMDHVKK EKREKEQQEE KSGLFRNMGR 300
NEDGERRAMI TPALREALTK QVDAPRERSL LQTHILWNES HRCMETTPSL ACANKCVFCW 360
WHHNNPVGTE WLWKMDQPEM ILKEAIENHQ NMIKQFKGVP GVKAERFEEG MTVKHCALSL 420
VGEPIMYPEI NRFLKLLHQC KISSFLVTNA QFPAEIRNLE PVTQLYVSVD ASTKDSLKKI 480
DRPLFKDFWQ QFLDSLKALA VKQQRTVYRL MLVKAWNVDE LQAYAQLVSL GNPDFIEVKG 540
VTYCRESSAS SLTMAHVPWH EEVVQFVREL VDLIPEYEIA CEHEHSNCLL IAHRKFKIGG 600
EWWTWIDYNR FQELIQEYED SGGSKTFSAK DYMARTPHWA LFGANERSFD PKDTRHQRKN 660
KSKAISGC 668 
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.