CPLM 1.0 - Compendium of Protein Lysine Modification
TagContent
CPLM ID CPLM-009867
UniProt Accession
Genbank Protein ID
Genbank Nucleotide ID
Protein Name
 Histone H3.1 
Protein Synonyms/Alias
 Histone H3/a; Histone H3/b; Histone H3/c; Histone H3/d; Histone H3/f; Histone H3/h; Histone H3/i; Histone H3/j; Histone H3/k; Histone H3/l 
Gene Name
 HIST1H3A; HIST1H3B; HIST1H3C; HIST1H3D; HIST1H3E; HIST1H3F; HIST1H3G; HIST1H3H; HIST1H3I; HIST1H3J 
Gene Synonyms/Alias
 H3FA; H3FL; H3FC; H3FB; H3FD; H3FI; H3FH; H3FK; H3FF; H3FJ 
Created Date
 July 27, 2013 
Organism
 Homo sapiens (Human) 
NCBI Taxa ID
 9606 
Lysine Modification
Position
Peptide
Type
References
5***MARTKQTARKSTacetylation[1, 2, 3, 4]
5***MARTKQTARKSTcrotonylation[5]
5***MARTKQTARKSTmethylation[6, 7, 8]
10RTKQTARKSTGGKAPacetylation[1, 2, 3, 4, 9, 10, 11, 12, 13]
10RTKQTARKSTGGKAPcrotonylation[5]
10RTKQTARKSTGGKAPmethylation[6, 7, 8, 14, 15]
15ARKSTGGKAPRKQLAacetylation[1, 2, 3, 4, 9, 10, 12, 16, 17, 18, 19]
19TGGKAPRKQLATKAAacetylation[1, 2, 3, 4, 9, 10, 12, 19, 20]
19TGGKAPRKQLATKAAcrotonylation[5]
19TGGKAPRKQLATKAAmethylation[8]
19TGGKAPRKQLATKAAsumoylation[21]
19TGGKAPRKQLATKAAubiquitination[22]
23APRKQLATKAARKSApropionylation[23]
24PRKQLATKAARKSAPacetylation[1, 2, 3, 4, 9, 10, 12, 19]
24PRKQLATKAARKSAPcrotonylation[5]
24PRKQLATKAARKSAPmethylation[8, 15]
24PRKQLATKAARKSAPsumoylation[24]
24PRKQLATKAARKSAPubiquitination[22]
28LATKAARKSAPATGGacetylation[4, 9, 10, 12, 13, 25, 26]
28LATKAARKSAPATGGcrotonylation[5]
28LATKAARKSAPATGGmethylation[8, 14, 15, 27]
28LATKAARKSAPATGGubiquitination[28, 29]
37APATGGVKKPHRYRPacetylation[2, 3, 4, 10, 13, 25, 26]
37APATGGVKKPHRYRPmethylation[8, 14, 15, 27]
37APATGGVKKPHRYRPubiquitination[22, 28, 29, 30]
38PATGGVKKPHRYRPGmethylation[8, 15, 27]
38PATGGVKKPHRYRPGubiquitination[30]
57REIRRYQKSTELLIRacetylation[2, 3, 4, 11, 12, 31]
57REIRRYQKSTELLIRcrotonylation[5]
57REIRRYQKSTELLIRmethylation[8]
57REIRRYQKSTELLIRubiquitination[22, 30, 32]
65STELLIRKLPFQRLVmethylation[8]
65STELLIRKLPFQRLVubiquitination[30]
80REIAQDFKTDLRFQSacetylation[2, 3, 4, 12, 33]
80REIAQDFKTDLRFQSmethylation[8, 34]
80REIAQDFKTDLRFQSubiquitination[22, 30, 32]
116NLCAIHAKRVTIMPKacetylation[35]
116NLCAIHAKRVTIMPKubiquitination[32]
123KRVTIMPKDIQLARRacetylation[12, 35]
123KRVTIMPKDIQLARRmethylation[8, 14]
123KRVTIMPKDIQLARRubiquitination[22, 30]
Reference
 [1] Patterns of histone acetylation.
 Thorne AW, Kmiciek D, Mitchelson K, Sautiere P, Crane-Robinson C.
 Eur J Biochem. 1990 Nov 13;193(3):701-13. [PMID: 2249688]
 [2] Human spleen histone H3. Isolation and amino acid sequence.
 Ohe Y, Iwai K.
 J Biochem. 1981 Oct;90(4):1205-11. [PMID: 7309716]
 [3] Organismal differences in post-translational modifications in histones H3 and H4.
 Garcia BA, Hake SB, Diaz RL, Kauer M, Morris SA, Recht J, Shabanowitz J, Mishra N, Strahl BD, Allis CD, Hunt DF.
 J Biol Chem. 2007 Mar 9;282(10):7641-55. [PMID: 17194708]
 [4] Proteome-wide prediction of acetylation substrates.
 Basu A, Rose KL, Zhang J, Beavis RC, Ueberheide B, Garcia BA, Chait B, Zhao Y, Hunt DF, Segal E, Allis CD, Hake SB.
 Proc Natl Acad Sci U S A. 2009 Aug 18;106(33):13785-90. [PMID: 19666589]
 [5] Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification.
 Tan M, Luo H, Lee S, Jin F, Yang JS, Montellier E, Buchou T, Cheng Z, Rousseaux S, Rajagopal N, Lu Z, Ye Z, Zhu Q, Wysocka J, Ye Y, Khochbin S, Ren B, Zhao Y.
 Cell. 2011 Sep 16;146(6):1016-28. [PMID: 21925322]
 [6] Identification of novel histone post-translational modifications by peptide mass fingerprinting.
 Zhang L, Eugeni EE, Parthun MR, Freitas MA.
 Chromosoma. 2003 Aug;112(2):77-86. [PMID: 12937907]
 [7] CpG-binding protein (CXXC finger protein 1) is a component of the mammalian Set1 histone H3-Lys4 methyltransferase complex, the analogue of the yeast Set1/COMPASS complex.
 Lee JH, Skalnik DG.
 J Biol Chem. 2005 Dec 16;280(50):41725-31. [PMID: 16253997]
 [8] Update on activities at the Universal Protein Resource (UniProt) in 2013.
 e="String">UniProt Consortium.
 Nucleic Acids Res. 2013 Jan;41(Database issue):D43-7. [PMID: 23161681]
 [9] Quantitative proteomic analysis of post-translational modifications of human histones.
 Beck HC, Nielsen EC, Matthiesen R, Jensen LH, Sehested M, Finn P, Grauslund M, Hansen AM, Jensen ON.
 Mol Cell Proteomics. 2006 Jul;5(7):1314-25. [PMID: 16627869]
 [10] Substrate and functional diversity of lysine acetylation revealed by a proteomics survey.
 Kim SC, Sprung R, Chen Y, Xu Y, Ball H, Pei J, Cheng T, Kho Y, Xiao H, Xiao L, Grishin NV, White M, Yang XJ, Zhao Y.
 Mol Cell. 2006 Aug;23(4):607-18. [PMID: 16916647]
 [11] Screen for DNA-damage-responsive histone modifications identifies H3K9Ac and H3K56Ac in human cells.
 Tjeertes JV, Miller KM, Jackson SP.
 EMBO J. 2009 Jul 8;28(13):1878-89. [PMID: 19407812]
 [12] 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]
 [13] Activator-dependent p300 acetylation of chromatin in vitro: enhancement of transcription by disruption of repressive nucleosome-nucleosome interactions.
 Szerlong HJ, Prenni JE, Nyborg JK, Hansen JC.
 J Biol Chem. 2010 Oct 15;285(42):31954-64. [PMID: 20720004]
 [14] Identification of methylation and acetylation sites on mouse histone H3 using matrix-assisted laser desorption/ionization time-of-flight and nanoelectrospray ionization tandem mass spectrometry.
 Cocklin RR, Wang M.
 J Protein Chem. 2003 May;22(4):327-34. [PMID: 13678296]
 [15] Mass spectrometry-based identification and characterisation of lysine and arginine methylation in the human proteome.
 Bremang M, Cuomo A, Agresta AM, Stugiewicz M, Spadotto V, Bonaldi T.
 Mol Biosyst. 2013 Jul 30;9(9):2231-47. [PMID: 23748837]
 [16] Overlapping but distinct patterns of histone acetylation by the human coactivators p300 and PCAF within nucleosomal substrates.
 Schiltz RL, Mizzen CA, Vassilev A, Cook RG, Allis CD, Nakatani Y.
 J Biol Chem. 1999 Jan 15;274(3):1189-92. [PMID: 9880483]
 [17] Tip60 acetylates six lysines of a specific class in core histones in vitro.
 Kimura A, Horikoshi M.
 Genes Cells. 1998 Dec;3(12):789-800. [PMID: 10096020]
 [18] Elongator is a histone H3 and H4 acetyltransferase important for normal histone acetylation levels in vivo.
 Winkler GS, Kristjuhan A, Erdjument-Bromage H, Tempst P, Svejstrup JQ.
 Proc Natl Acad Sci U S A. 2002 Mar 19;99(6):3517-22. [PMID: 11904415]
 [19] Analysis of dynamic changes in post-translational modifications of human histones during cell cycle by mass spectrometry.
 Bonenfant D, Towbin H, Coulot M, Schindler P, Mueller DR, van Oostrum J.
 Mol Cell Proteomics. 2007 Nov;6(11):1917-32. [PMID: 17644761]
 [20] Akt kinase targets the association of CBP with histone H3 to regulate the acetylation of lysine K18.
 Liu Y, Xing ZB, Zhang JH, Fang Y.
 FEBS Lett. 2013 Apr 2;587(7):847-53. [PMID: 23434580]
 [21] Targeted identification of SUMOylation sites in human proteins using affinity enrichment and paralog-specific reporter ions.
 Lamoliatte F, Bonneil E, Durette C, Caron-Lizotte O, Wildemann D, Zerweck J, Wenschuh H, Thibault P.
 Mol Cell Proteomics. 2013 Jun 7;. [PMID: 23750026]
 [22] 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]
 [23] Identification and characterization of propionylation at histone H3 lysine 23 in mammalian cells.
 Liu B, Lin Y, Darwanto A, Song X, Xu G, Zhang K.
 J Biol Chem. 2009 Nov 20;284(47):32288-95. [PMID: 19801601]
 [24] A novel proteomics approach to identify SUMOylated proteins and their modification sites in human cells.
 Galisson F, Mahrouche L, Courcelles M, Bonneil E, Meloche S, Chelbi-Alix MK, Thibault P.
 Mol Cell Proteomics. 2011 Feb;10(2):M110.004796. [PMID: 21098080]
 [25] 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]
 [26] 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]
 [27] Large-scale global identification of protein lysine methylation in vivo.
 Cao XJ, Arnaudo AM, Garcia BA.
 Epigenetics. 2013 May 1;8(5):477-85. [PMID: 23644510]
 [28] 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]
 [29] 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]
 [30] 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]
 [31] The type III histone deacetylase Sirt1 protein suppresses p300-mediated histone H3 lysine 56 acetylation at Bclaf1 promoter to inhibit T cell activation.
 Kong S, Kim SJ, Sandal B, Lee SM, Gao B, Zhang DD, Fang D.
 J Biol Chem. 2011 May 13;286(19):16967-75. [PMID: 21454709]
 [32] Ubiquitin ligase substrate identification through quantitative proteomics at both the protein and peptide levels.
 Lee KA, Hammerle LP, Andrews PS, Stokes MP, Mustelin T, Silva JC, Black RA, Doedens JR.
 J Biol Chem. 2011 Dec 2;286(48):41530-8. [PMID: 21987572]
 [33] Regulation of cellular metabolism by protein lysine acetylation.
 Zhao S, Xu W, Jiang W, Yu W, Lin Y, Zhang T, Yao J, Zhou L, Zeng Y, Li H, Li Y, Shi J, An W, Hancock SM, He F, Qin L, Chin J, Yang P, Chen X, Lei Q, Xiong Y, Guan KL.
 Science. 2010 Feb 19;327(5968):1000-4. [PMID: 20167786]
 [34] Histone H2B ubiquitylation controls processive methylation but not monomethylation by Dot1 and Set1.
 Shahbazian MD, Zhang K, Grunstein M.
 Mol Cell. 2005 Jul 22;19(2):271-7. [PMID: 16039595]
 [35] Acetylation of histone H3 at the nucleosome dyad alters DNA-histone binding.
 Manohar M, Mooney AM, North JA, Nakkula RJ, Picking JW, Edon A, Fishel R, Poirier MG, Ottesen JJ.
 J Biol Chem. 2009 Aug 28;284(35):23312-21. [PMID: 19520870
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. 
Sequence Annotation
 MOD_RES 3 3 Asymmetric dimethylarginine; by PRMT6.
 MOD_RES 4 4 Phosphothreonine; by GSG2.
 MOD_RES 5 5 Allysine; alternate.
 MOD_RES 5 5 N6,N6,N6-trimethyllysine; alternate.
 MOD_RES 5 5 N6,N6-dimethyllysine; alternate.
 MOD_RES 5 5 N6-acetyllysine; alternate.
 MOD_RES 5 5 N6-crotonyl-L-lysine; alternate.
 MOD_RES 5 5 N6-methyllysine; alternate.
 MOD_RES 7 7 Phosphothreonine; by PKC.
 MOD_RES 9 9 Citrulline; alternate.
 MOD_RES 9 9 Symmetric dimethylarginine; by PRMT5;
 MOD_RES 10 10 N6,N6,N6-trimethyllysine; alternate.
 MOD_RES 10 10 N6,N6-dimethyllysine; alternate.
 MOD_RES 10 10 N6-acetyllysine; alternate.
 MOD_RES 10 10 N6-crotonyl-L-lysine; alternate.
 MOD_RES 10 10 N6-methyllysine; alternate.
 MOD_RES 11 11 Phosphoserine; by AURKB, AURKC, RPS6KA3,
 MOD_RES 12 12 Phosphothreonine; by PKC and CHEK1.
 MOD_RES 15 15 N6-acetyllysine.
 MOD_RES 18 18 Asymmetric dimethylarginine; by CARM1;
 MOD_RES 18 18 Citrulline; alternate.
 MOD_RES 19 19 N6-acetyllysine; alternate.
 MOD_RES 19 19 N6-crotonyl-L-lysine; alternate.
 MOD_RES 19 19 N6-methyllysine; alternate.
 MOD_RES 24 24 N6-acetyllysine; alternate.
 MOD_RES 24 24 N6-crotonyl-L-lysine; alternate.
 MOD_RES 24 24 N6-methyllysine; alternate.
 MOD_RES 28 28 N6,N6,N6-trimethyllysine; alternate.
 MOD_RES 28 28 N6,N6-dimethyllysine; alternate.
 MOD_RES 28 28 N6-acetyllysine; alternate.
 MOD_RES 28 28 N6-crotonyl-L-lysine; alternate.
 MOD_RES 28 28 N6-methyllysine; alternate.
 MOD_RES 29 29 Phosphoserine; by AURKB, AURKC and
 MOD_RES 37 37 N6,N6,N6-trimethyllysine; alternate.
 MOD_RES 37 37 N6,N6-dimethyllysine; alternate.
 MOD_RES 37 37 N6-acetyllysine; alternate.
 MOD_RES 37 37 N6-methyllysine; alternate.
 MOD_RES 38 38 N6-methyllysine.
 MOD_RES 42 42 Phosphotyrosine.
 MOD_RES 57 57 N6,N6,N6-trimethyllysine; alternate.
 MOD_RES 57 57 N6-acetyllysine; alternate.
 MOD_RES 57 57 N6-crotonyl-L-lysine; alternate.
 MOD_RES 57 57 N6-methyllysine; by EHMT2; alternate.
 MOD_RES 58 58 Phosphoserine.
 MOD_RES 65 65 N6-methyllysine.
 MOD_RES 80 80 N6,N6,N6-trimethyllysine; alternate (By
 MOD_RES 80 80 N6,N6-dimethyllysine; alternate.
 MOD_RES 80 80 N6-acetyllysine; alternate.
 MOD_RES 80 80 N6-methyllysine; alternate.
 MOD_RES 81 81 Phosphothreonine.
 MOD_RES 108 108 Phosphothreonine (By similarity).
 MOD_RES 123 123 N6-methyllysine.  
Keyword
 3D-structure; Acetylation; Chromosome; Citrullination; Complete proteome; Direct protein sequencing; DNA-binding; Methylation; Nucleosome core; Nucleus; Phosphoprotein; Reference proteome; Ubl conjugation. 
Sequence Source
 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 
Protein Length
 136 AA 
Protein Sequence
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE 60
LLIRKLPFQR LVREIAQDFK TDLRFQSSAV MALQEACEAY LVGLFEDTNL CAIHAKRVTI 120
MPKDIQLARR IRGERA 136 
Gene Ontology
 GO:0005576; C:extracellular region; TAS:Reactome.
 GO:0005654; C:nucleoplasm; TAS:Reactome.
 GO:0000786; C:nucleosome; IEA:UniProtKB-KW.
 GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
 GO:0007596; P:blood coagulation; TAS:Reactome.
 GO:0006334; P:nucleosome assembly; IEA:InterPro.
 GO:0060968; P:regulation of gene silencing; IDA:BHF-UCL.
 GO:0051320; P:S phase; NAS:BHF-UCL. 
Interpro
 IPR009072; Histone-fold.
 IPR007125; Histone_core_D.
 IPR000164; Histone_H3. 
Pfam
 PF00125; Histone 
SMART
 SM00428; H3 
PROSITE
 PS00322; HISTONE_H3_1
 PS00959; HISTONE_H3_2 
PRINTS
 PR00622; HISTONEH3.