CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-031142
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Histone H2B 
Protein Synonyms/Alias
  
Gene Name
 HIST2H2BF 
Gene Synonyms/Alias
  
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
6**MPDPAKSAPAPKKacetylation[1, 2]
6**MPDPAKSAPAPKKubiquitination[2, 3, 4]
12AKSAPAPKKGSKKAVacetylation[1, 2, 5]
13KSAPAPKKGSKKAVTacetylation[1, 2, 5]
16PAPKKGSKKAVTKVQacetylation[1, 5]
17APKKGSKKAVTKVQKacetylation[1, 2, 5]
21GSKKAVTKVQKKDGKacetylation[1, 2]
24KAVTKVQKKDGKKRKacetylation[2]
35KKRKRSRKESYSVYVubiquitination[2, 3, 4, 6, 7]
44SYSVYVYKVLKQVHPubiquitination[2, 3, 4, 6, 7]
47VYVYKVLKQVHPDTGacetylation[2]
47VYVYKVLKQVHPDTGubiquitination[2, 3, 4, 6, 7, 8, 9, 10]
58PDTGISSKAMGIMNSubiquitination[2, 4, 7, 9]
86SRLAHYNKRSTITSRacetylation[2]
86SRLAHYNKRSTITSRubiquitination[3, 11]
109LLPGELAKHAVSEGTacetylation[1, 2, 12]
109LLPGELAKHAVSEGTubiquitination[2, 3, 4, 6, 7, 8, 9, 10, 13]
117HAVSEGTKAVTKYTSacetylation[2, 5]
117HAVSEGTKAVTKYTSubiquitination[2, 3, 4, 6, 7, 8, 9, 10]
121EGTKAVTKYTSSNPRubiquitination[4]
Reference
 [1] Monoclonal antibody cocktail as an enrichment tool for acetylome analysis.
 Shaw PG, Chaerkady R, Zhang Z, Davidson NE, Pandey A.
 Anal Chem. 2011 May 15;83(10):3623-6. [PMID: 21466224]
 [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] 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]
 [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] 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]
 [6] 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]
 [7] 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]
 [8] 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]
 [9] 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]
 [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]
 [12] 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]
 [13] Proteomic snapshot of the EGF-induced ubiquitin network.
 Argenzio E, Bange T, Oldrini B, Bianchi F, Peesari R, Mari S, Di Fiore PP, Mann M, Polo S.
 Mol Syst Biol. 2011 Jan 18;7:462. [PMID: 21245847
Functional Description
 Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling (By similarity). 
Sequence Annotation
  
Keyword
 Chromosome; Complete proteome; DNA-binding; Isopeptide bond; Nucleosome core; Nucleus; Reference proteome. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 166 AA 
Protein Sequence
MPDPAKSAPA PKKGSKKAVT KVQKKDGKKR KRSRKESYSV YVYKVLKQVH PDTGISSKAM 60
GIMNSFVNDI FERIAGEASR LAHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT 120
KYTSSNPRNL SPTKPGGSED RQPPPSQLSA IPPFCLVLRA GIAGQV 166 
Gene Ontology
 GO:0000786; C:nucleosome; IEA:UniProtKB-KW.
 GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
 GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
 GO:0006334; P:nucleosome assembly; IEA:InterPro. 
Interpro
 IPR009072; Histone-fold.
 IPR007125; Histone_core_D.
 IPR000558; Histone_H2B. 
Pfam
 PF00125; Histone 
SMART
 SM00427; H2B 
PROSITE
 PS00357; HISTONE_H2B 
PRINTS
 PR00621; HISTONEH2B.