CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-042360
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
  
Protein Name
 Nuclease-sensitive element-binding protein 1 
Protein Synonyms/Alias
  
Gene Name
 YBX1 
Gene Synonyms/Alias
  
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
131KDSWNDTKEDVFVHQacetylation[1, 2]
131KDSWNDTKEDVFVHQubiquitination[2, 3, 4]
142FVHQTAIKKNNPRKYubiquitination[2, 3, 4, 5, 6, 7, 8, 9, 10]
143VHQTAIKKNNPRKYLubiquitination[2, 3, 4, 6, 7, 8, 10]
168FDVVEGEKGAEAANVubiquitination[2, 6, 7, 10]
187GVPVQGSKYAADRNHubiquitination[6, 7]
314EDGNEEDKENQGDETubiquitination[2, 6, 10, 11]
346RRRPENPKPQDGKETubiquitination[7]
351NPKPQDGKETKAADPubiquitination[6, 7]
354PQDGKETKAADPPAEubiquitination[2, 6, 7, 10]
Reference
 [1] 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]
 [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] 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] 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]
 [5] 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]
 [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] 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]
 [8] 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]
 [9] 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]
 [10] 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]
 [11] 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
Functional Description
  
Sequence Annotation
  
Keyword
 Complete proteome; Reference proteome. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 374 AA 
Protein Sequence
XRVRRGPLPA DRPRALGPAR RCSRHPHPAP FRVCSEGAAH RLRRPERLPL PSRALRPRPA 60
HTPILGPAPR ACPGAPRASD SPTCAAAAAT AWPRTRAVER KGCQVAAAAG VRGTGCPSRA 120
DLEKDSWNDT KEDVFVHQTA IKKNNPRKYL RSVGDGETVE FDVVEGEKGA EAANVTGPGG 180
VPVQGSKYAA DRNHYRRYPR RRGPPRNYQQ NYQNSESGEK NEGSESAPEG QAQQRRPYRR 240
RRFPPYYMRR PYGRRPQYSN PPVQGEVMEG ADNQGAGEQG RPVRQNMYRG YRPRFRRGPP 300
RQRQPREDGN EEDKENQGDE TQGQQPPQRR YRRNFNYRRR RPENPKPQDG KETKAADPPA 360
ENSSAPEAEQ GGAE 374 
Gene Ontology
 GO:0005737; C:cytoplasm; IDA:HPA.
 GO:0043231; C:intracellular membrane-bounded organelle; IDA:HPA.
 GO:0003677; F:DNA binding; IEA:InterPro.
 GO:0006355; P:regulation of transcription, DNA-dependent; IEA:InterPro. 
Interpro
 IPR011129; Cold_shock_prot.
 IPR002059; CSP_DNA-bd.
 IPR012340; NA-bd_OB-fold. 
Pfam
 PF00313; CSD 
SMART
 SM00357; CSP 
PROSITE
  
PRINTS
 PR00050; COLDSHOCK.