UniProt Accession

 H3_YEAST; P61830; D6VQ11; E9PAG1; P02303; P13996; Q6B1U3; Q6Q7G9 

Genbank Protein ID

 X00724; X00725; Z35879; Z71306; Z71307; AY558343; AY692987; AY554000; AY554001; AY554002; AY554003; AY554004; AY554005; AY554006; AY554007; AY554008; BK006936; BK006947 

Genbank Nucleotide ID

 CAA25310.1; CAA25312.1; CAA84948.1; CAA95893.1; CAA95894.1; AAS56669.1; AAT93006.1; AAS64341.1; AAS64342.1; AAS64343.1; AAS64344.1; AAS64345.1; AAS64346.1; AAS64347.1; AAS64348.1; AAS64349.1; DAA07131.1; DAA10514.1 

Protein Name

 Histone H3 

Protein Synonyms/Alias

  

Gene Name

 HHT1; HHT2 

Gene Synonyms/Alias

 YBR010W; YBR0201; SIN2; YNL031C; N2749 

Created Date

 July 27, 2013 

Organism

 Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) 

NCBI Taxa ID

 559292 

Lysine Modification

Position	Peptide	Type	References
5	***MARTKQTARKST	methylation	[1]
10	RTKQTARKSTGGKAP	acetylation	[2, 3, 4, 5, 6, 7, 8]
10	RTKQTARKSTGGKAP	methylation	[1]
15	ARKSTGGKAPRKQLA	acetylation	[2, 4, 5, 6, 7, 8, 9, 10]
15	ARKSTGGKAPRKQLA	butyrylation	[11]
15	ARKSTGGKAPRKQLA	methylation	[1]
19	TGGKAPRKQLASKAA	acetylation	[2, 3, 4, 5, 7, 8, 12]
19	TGGKAPRKQLASKAA	methylation	[1]
24	PRKQLASKAARKSAP	acetylation	[2, 3, 4, 7, 8, 12]
24	PRKQLASKAARKSAP	methylation	[1]
24	PRKQLASKAARKSAP	propionylation	[11]
28	LASKAARKSAPSTGG	acetylation	[3, 4, 5, 7, 8, 12]
28	LASKAARKSAPSTGG	butyrylation	[11]
28	LASKAARKSAPSTGG	methylation	[1]
28	LASKAARKSAPSTGG	ubiquitination	[13]
37	APSTGGVKKPHRYKP	acetylation	[6, 7, 14]
37	APSTGGVKKPHRYKP	methylation	[1]
38	PSTGGVKKPHRYKPG	methylation	[1]
38	PSTGGVKKPHRYKPG	ubiquitination	[13]
57	REIRRFQKSTELLIR	acetylation	[5, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27]
57	REIRRFQKSTELLIR	malonylation	[28]
57	REIRRFQKSTELLIR	propionylation	[11]
57	REIRRFQKSTELLIR	ubiquitination	[13]
65	STELLIRKLPFQRLV	acetylation	[5]
80	REIAQDFKTDLRFQS	methylation	[1]
80	REIAQDFKTDLRFQS	succinylation	[28]
80	REIAQDFKTDLRFQS	ubiquitination	[13]

Reference

 [1] 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]
 [2] Identification of a non-basic domain in the histone H4 N-terminus required for repression of the yeast silent mating loci.
 Johnson LM, Fisher-Adams G, Grunstein M.
 EMBO J. 1992 Jun;11(6):2201-9. [PMID: 1600945]
 [3] Highly specific antibodies determine histone acetylation site usage in yeast heterochromatin and euchromatin.
 Suka N, Suka Y, Carmen AA, Wu J, Grunstein M.
 Mol Cell. 2001 Aug;8(2):473-9. [PMID: 11545749]
 [4] Redundant roles for histone H3 N-terminal lysine residues in subtelomeric gene repression in Saccharomyces cerevisiae.
 Martin AM, Pouchnik DJ, Walker JL, Wyrick JJ.
 Genetics. 2004 Jul;167(3):1123-32. [PMID: 15280228]
 [5] 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]
 [6] Nano-electrospray tandem mass spectrometric analysis of the acetylation state of histones H3 and H4 in stationary phase in Saccharomyces cerevisiae.
 Ngubo M, Kemp G, Patterton HG.
 BMC Biochem. 2011 Jul 4;12:34. [PMID: 21726436]
 [7] Proteome-wide analysis of lysine acetylation suggests its broad regulatory scope in Saccharomyces cerevisiae.
 Henriksen P, Wagner SA, Weinert BT, Sharma S, Bacinskaja G, Rehman M, Juffer AH, Walther TC, Lisby M, Choudhary C.
 Mol Cell Proteomics. 2012 Nov;11(11):1510-22. [PMID: 22865919]
 [8] Chaperone-mediated acetylation of histones by Rtt109 identified by quantitative proteomics.
 Abshiru N, Ippersiel K, Tang Y, Yuan H, Marmorstein R, Verreault A, Thibault P.
 J Proteomics. 2013 Apr 9;81:80-90. [PMID: 23036725]
 [9] Transcription-linked acetylation by Gcn5p of histones H3 and H4 at specific lysines.
 Kuo MH, Brownell JE, Sobel RE, Ranalli TA, Cook RG, Edmondson DG, Roth SY, Allis CD.
 Nature. 1996 Sep 19;383(6597):269-72. [PMID: 8805705]
 [10] Sas4 and Sas5 are required for the histone acetyltransferase activity of Sas2 in the SAS complex.
 Sutton A, Shia WJ, Band D, Kaufman PD, Osada S, Workman JL, Sternglanz R.
 J Biol Chem. 2003 May 9;278(19):16887-92. [PMID: 12626510]
 [11] Identification and verification of lysine propionylation and butyrylation in yeast core histones using PTMap software.
 Zhang K, Chen Y, Zhang Z, Zhao Y.
 J Proteome Res. 2009 Feb;8(2):900-6. [PMID: 19113941]
 [12] mChIP-KAT-MS, a method to map protein interactions and acetylation sites for lysine acetyltransferases.
 Mitchell L, Huard S, Cotrut M, Pourhanifeh-Lemeri R, Steunou AL, Hamza A, Lambert JP, Zhou H, Ning Z, Basu A, Côté J, Figeys DA, Baetz K.
 Proc Natl Acad Sci U S A. 2013 Apr 23;110(17):E1641-50. [PMID: 23572591]
 [13] Global analysis of phosphorylation and ubiquitylation cross-talk in protein degradation.
 Swaney DL, Beltrao P, Starita L, Guo A, Rush J, Fields S, Krogan NJ, Villén J.
 Nat Methods. 2013 Jul;10(7):676-82. [PMID: 23749301]
 [14] Identification of histone H3 lysine 36 acetylation as a highly conserved histone modification.
 Morris SA, Rao B, Garcia BA, Hake SB, Diaz RL, Shabanowitz J, Hunt DF, Allis CD, Lieb JD, Strahl BD.
 J Biol Chem. 2007 Mar 9;282(10):7632-40. [PMID: 17189264]
 [15] Acetylation in histone H3 globular domain regulates gene expression in yeast.
 Xu F, Zhang K, Grunstein M.
 Cell. 2005 May 6;121(3):375-85. [PMID: 15882620]
 [16] Characterization of lysine 56 of histone H3 as an acetylation site in Saccharomyces cerevisiae.
 Ozdemir A, Spicuglia S, Lasonder E, Vermeulen M, Campsteijn C, Stunnenberg HG, Logie C.
 J Biol Chem. 2005 Jul 15;280(28):25949-52. [PMID: 15888442]
 [17] Chromatin assembly factor 1 interacts with histone H3 methylated at lysine 79 in the processes of epigenetic silencing and DNA repair.
 Zhou H, Madden BJ, Muddiman DC, Zhang Z.
 Biochemistry. 2006 Mar 7;45(9):2852-61. [PMID: 16503640]
 [18] Histone chaperone Asf1 is required for histone H3 lysine 56 acetylation, a modification associated with S phase in mitosis and meiosis.
 Recht J, Tsubota T, Tanny JC, Diaz RL, Berger JM, Zhang X, Garcia BA, Shabanowitz J, Burlingame AL, Hunt DF, Kaufman PD, Allis CD.
 Proc Natl Acad Sci U S A. 2006 May 2;103(18):6988-93. [PMID: 16627621]
 [19] Yeast Rtt109 promotes genome stability by acetylating histone H3 on lysine 56.
 Driscoll R, Hudson A, Jackson SP.
 Science. 2007 Feb 2;315(5812):649-52. [PMID: 17272722]
 [20] Rtt109 acetylates histone H3 lysine 56 and functions in DNA replication.
 Han J, Zhou H, Horazdovsky B, Zhang K, Xu RM, Zhang Z.
 Science. 2007 Feb 2;315(5812):653-5. [PMID: 17272723]
 [21] Chaperone control of the activity and specificity of the histone H3 acetyltransferase Rtt109.
 Fillingham J, Recht J, Silva AC, Suter B, Emili A, Stagljar I, Krogan NJ, Allis CD, Keogh MC, Greenblatt JF.
 Mol Cell Biol. 2008 Jul;28(13):4342-53. [PMID: 18458063]
 [22] Acetylated lysine 56 on histone H3 drives chromatin assembly after repair and signals for the completion of repair.
 Chen CC, Carson JJ, Feser J, Tamburini B, Zabaronick S, Linger J, Tyler JK.
 Cell. 2008 Jul 25;134(2):231-43. [PMID: 18662539]
 [23] Acetylation of histone H3 lysine 56 regulates replication-coupled nucleosome assembly.
 Li Q, Zhou H, Wurtele H, Davies B, Horazdovsky B, Verreault A, Zhang Z.
 Cell. 2008 Jul 25;134(2):244-55. [PMID: 18662540]
 [24] Cell cycle- and chaperone-mediated regulation of H3K56ac incorporation in yeast.
 Kaplan T, Liu CL, Erkmann JA, Holik J, Grunstein M, Kaufman PD, Friedman N, Rando OJ.
 PLoS Genet. 2008 Nov;4(11):e1000270. [PMID: 19023413]
 [25] CBP/p300-mediated acetylation of histone H3 on lysine 56.
 Das C, Lucia MS, Hansen KC, Tyler JK.
 Nature. 2009 May 7;459(7243):113-7. [PMID: 19270680]
 [26] Acetylation of H3 K56 is required for RNA polymerase II transcript elongation through heterochromatin in yeast.
 Värv S, Kristjuhan K, Peil K, Lõoke M, Mahlakõiv T, Paapsi K, Kristjuhan A.
 Mol Cell Biol. 2010 Mar;30(6):1467-77. [PMID: 20065036]
 [27] Regulation of chromatin assembly/disassembly by Rtt109p, a histone H3 Lys56-specific acetyltransferase, in vivo.
 Durairaj G, Chaurasia P, Lahudkar S, Malik S, Shukla A, Bhaumik SR.
 J Biol Chem. 2010 Oct 1;285(40):30472-9. [PMID: 20668333]
 [28] Lysine succinylation and lysine malonylation in histones.
 Xie Z, Dai J, Dai L, Tan M, Cheng Z, Wu Y, Boeke JD, Zhao Y.
 Mol Cell Proteomics. 2012 May;11(5):100-7. [PMID: 22389435] 

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. Component of the UAF (upstream activation factor) complex which interacts with the upstream element of the RNA polymerase I promoter and forms a stable preinitiation complex. Together with SPT15/TBP, UAF seems to stimulate basal transcription to a fully activated level. 

Sequence Annotation

 MOD_RES 5 5 N6,N6,N6-trimethyllysine; alternate.
 MOD_RES 5 5 N6,N6-dimethyllysine; alternate.
 MOD_RES 5 5 N6-methyllysine; alternate.
 MOD_RES 10 10 N6-acetyllysine; alternate.
 MOD_RES 10 10 N6-methyllysine; alternate.
 MOD_RES 11 11 Phosphoserine.
 MOD_RES 15 15 N6,N6-dimethyllysine; alternate.
 MOD_RES 15 15 N6-acetyllysine; alternate.
 MOD_RES 19 19 N6-acetyllysine; alternate.
 MOD_RES 19 19 N6-methyllysine; alternate.
 MOD_RES 24 24 N6-acetyllysine; 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-methyllysine; alternate.
 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 57 57 N6-acetyllysine.
 MOD_RES 65 65 N6-acetyllysine.
 MOD_RES 80 80 N6,N6,N6-trimethyllysine; alternate.
 MOD_RES 80 80 N6,N6-dimethyllysine; alternate.
 MOD_RES 80 80 N6-methyllysine; alternate.  

Keyword

 3D-structure; Acetylation; Chromosome; Complete proteome; Direct protein sequencing; DNA damage; DNA repair; DNA-binding; Methylation; Nucleosome core; Nucleus; Phosphoprotein; Reference proteome. 

Sequence Source

 UniProt (SWISSPROT/TrEMBL); GenBank; EMBL 

Protein Length

 136 AA 

Protein Sequence

Gene Ontology

 GO:0000788; C:nuclear nucleosome; TAS:SGD.
 GO:0031298; C:replication fork protection complex; IDA:SGD.
 GO:0003677; F:DNA binding; TAS:SGD.
 GO:0006333; P:chromatin assembly or disassembly; TAS:SGD.
 GO:0070911; P:global genome nucleotide-excision repair; IMP:SGD.
 GO:0007094; P:mitotic spindle assembly checkpoint; IGI:SGD.
 GO:0006334; P:nucleosome assembly; IEA:InterPro.
 GO:0009303; P:rRNA transcription; IMP:SGD.
 GO:0043935; P:sexual sporulation resulting in formation of a cellular spore; IMP:SGD. 

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.