CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-037270
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
  
Protein Name
 THO complex subunit 4 
Protein Synonyms/Alias
  
Gene Name
 ALYREF 
Gene Synonyms/Alias
  
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
11SAPAMADKMDMSLDDubiquitination[1]
21MSLDDIIKLNRSQRGubiquitination[1, 2]
88PAPYSRPKQLPDKWQubiquitination[1, 3, 4]
93RPKQLPDKWQHDLFDacetylation[5, 6]
93RPKQLPDKWQHDLFDubiquitination[1, 2, 3, 4, 6, 7, 8, 9]
171ADALKAMKQYNGVPLubiquitination[1, 2, 3, 4, 6, 7, 8, 9]
242RGAGRNSKQQLSAEEacetylation[5, 6]
242RGAGRNSKQQLSAEEubiquitination[1, 2, 6, 7, 8, 9, 10, 11]
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] 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]
 [4] 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]
 [5] 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]
 [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] 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] 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] 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]
 [10] 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]
 [11] 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
  
Sequence Annotation
  
Keyword
 Complete proteome; Reference proteome. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 264 AA 
Protein Sequence
MPDSAPAMAD KMDMSLDDII KLNRSQRGGR GGGRGRGRAG SQGGRGGGAQ AAARVNRGGG 60
PIRNRPAIAR GAAGGGGRNR PAPYSRPKQL PDKWQHDLFD SGFGGGAGVE TGGKLLVSNL 120
DFGVSDADIQ ELFAEFGTLK KAAVHYDRSG RSLGTADVHF ERKADALKAM KQYNGVPLDG 180
RPMNIQLVTS QIDAQRRPAQ SVNRGGMTRN RGAGGFGGGG GTRRGTRGGA RGRGRGAGRN 240
SKQQLSAEEL DAQLDAYNAR MDTS 264 
Gene Ontology
 GO:0005634; C:nucleus; IDA:HPA.
 GO:0003676; F:nucleic acid binding; IEA:InterPro.
 GO:0000166; F:nucleotide binding; IEA:InterPro. 
Interpro
 IPR025715; FoP_duplication.
 IPR012677; Nucleotide-bd_a/b_plait.
 IPR000504; RRM_dom. 
Pfam
 PF13865; FoP_duplication
 PF00076; RRM_1 
SMART
 SM00360; RRM 
PROSITE
 PS50102; RRM 
PRINTS