| Structural highlights
6o22 is a 6 chain structure with sequence from African clawed frog and Baker's yeast. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Gene: | VPS75, YNL246W, N0890 (Baker's yeast), RTT109, KIM2, REM50, YLL002W, L1377 (Baker's yeast), ASF1, CIA1, YJL115W, J0755 (Baker's yeast) |
| Activity: | Histone acetyltransferase, with EC number 2.3.1.48 |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
[H32_XENLA] 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. [VPS75_YEAST] Histone chaperone which acts as a cofactor stimulating the histone H3 'Lys-56' acetylation by RTT109. May be involved in vacuolar proteins sorting.[1] [2] [ASF1_YEAST] Histone chaperone that facilitates histone deposition and histone exchange and removal during nucleosome assembly and disassembly. Facilitates histone deposition through both replication-dependent and replication-independent chromatin assembly pathways. Cooperates with chromatin assembly factor 1 (CAF-1) to promote replication-dependent chromatin assembly and with the HIR complex to promote replication-independent chromatin assembly, which may occur during transcription and DNA repair. May be required for the maintenance of a subset of replication elongation factors, including DNA polymerase epsilon, the RFC complex and PCNA, at stalled replication forks. Also required for acetylation of histone H3 on 'Lys-9' and 'Lys-56'.[3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [RT109_YEAST] Required for acetylation of 'Lys-56' of histone H3 (H3K56ac) which occurs in S phase and disappears during G(2)/M phase of the cell cycle and is involved in transcription DNA repair process. H3K56 acetylation weakens of the interaction between the histone core and the surrounding DNA in the nucleosomal particle and drives chromatin disassembly. Involved in regulation of Ty1 transposition.[42] [43] [44] [45] [46] [47] [48] [49] [50] [H4_XENLA] 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.
Publication Abstract from PubMed
Histones, the principal protein components of chromatin, contain long disordered sequences, which are extensively post-translationally modified. Although histone chaperones are known to control both the activity and specificity of histone-modifying enzymes, the mechanisms promoting modification of highly disordered substrates, such as lysine-acetylation within the N-terminal tail of histone H3, are not understood. Here, to understand how histone chaperones Asf1 and Vps75 together promote H3 K9-acetylation, we establish the solution structural model of the acetyltransferase Rtt109 in complex with Asf1 and Vps75 and the histone dimer H3:H4. We show that Vps75 promotes K9-acetylation by engaging the H3 N-terminal tail in fuzzy electrostatic interactions with its disordered C-terminal domain, thereby confining the H3 tail to a wide central cavity faced by the Rtt109 active site. These fuzzy interactions between disordered domains achieve localization of lysine residues in the H3 tail to the catalytic site with minimal loss of entropy, and may represent a common mechanism of enzymatic reactions involving highly disordered substrates.
Histone chaperone exploits intrinsic disorder to switch acetylation specificity.,Danilenko N, Lercher L, Kirkpatrick J, Gabel F, Codutti L, Carlomagno T Nat Commun. 2019 Aug 6;10(1):3435. doi: 10.1038/s41467-019-11410-7. PMID:31387991[51]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
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- ↑ Tsubota T, Berndsen CE, Erkmann JA, Smith CL, Yang L, Freitas MA, Denu JM, Kaufman PD. Histone H3-K56 acetylation is catalyzed by histone chaperone-dependent complexes. Mol Cell. 2007 Mar 9;25(5):703-12. Epub 2007 Feb 22. PMID:17320445 doi:S1097-2765(07)00086-X
- ↑ Le S, Davis C, Konopka JB, Sternglanz R. Two new S-phase-specific genes from Saccharomyces cerevisiae. Yeast. 1997 Sep 15;13(11):1029-42. PMID:9290207 doi:<1029::AID-YEA160>3.0.CO;2-1 http://dx.doi.org/10.1002/(SICI)1097-0061(19970915)13:11<1029::AID-YEA160>3.0.CO;2-1
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- ↑ Sharp JA, Fouts ET, Krawitz DC, Kaufman PD. Yeast histone deposition protein Asf1p requires Hir proteins and PCNA for heterochromatic silencing. Curr Biol. 2001 Apr 3;11(7):463-73. PMID:11412995
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- ↑ Osada S, Sutton A, Muster N, Brown CE, Yates JR 3rd, Sternglanz R, Workman JL. The yeast SAS (something about silencing) protein complex contains a MYST-type putative acetyltransferase and functions with chromatin assembly factor ASF1. Genes Dev. 2001 Dec 1;15(23):3155-68. PMID:11731479 doi:http://dx.doi.org/10.1101/gad.907201
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- ↑ Krawitz DC, Kama T, Kaufman PD. Chromatin assembly factor I mutants defective for PCNA binding require Asf1/Hir proteins for silencing. Mol Cell Biol. 2002 Jan;22(2):614-25. PMID:11756556
- ↑ Chimura T, Kuzuhara T, Horikoshi M. Identification and characterization of CIA/ASF1 as an interactor of bromodomains associated with TFIID. Proc Natl Acad Sci U S A. 2002 Jul 9;99(14):9334-9. Epub 2002 Jul 1. PMID:12093919 doi:http://dx.doi.org/10.1073/pnas.142627899
- ↑ Robinson KM, Schultz MC. Replication-independent assembly of nucleosome arrays in a novel yeast chromatin reconstitution system involves antisilencing factor Asf1p and chromodomain protein Chd1p. Mol Cell Biol. 2003 Nov;23(22):7937-46. PMID:14585955
- ↑ Prado F, Cortes-Ledesma F, Aguilera A. The absence of the yeast chromatin assembly factor Asf1 increases genomic instability and sister chromatid exchange. EMBO Rep. 2004 May;5(5):497-502. Epub 2004 Apr 8. PMID:15071494 doi:http://dx.doi.org/10.1038/sj.embor.7400128
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- ↑ Glowczewski L, Waterborg JH, Berman JG. Yeast chromatin assembly complex 1 protein excludes nonacetylatable forms of histone H4 from chromatin and the nucleus. Mol Cell Biol. 2004 Dec;24(23):10180-92. PMID:15542829 doi:http://dx.doi.org/10.1128/MCB.24.23.10180-10192.2004
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- ↑ Robinson KM, Schultz MC. Gal4-VP16 directs ATP-independent chromatin reorganization in a yeast chromatin assembly system. Biochemistry. 2005 Mar 22;44(11):4551-61. PMID:15766286 doi:http://dx.doi.org/10.1021/bi047523u
- ↑ Green EM, Antczak AJ, Bailey AO, Franco AA, Wu KJ, Yates JR 3rd, Kaufman PD. Replication-independent histone deposition by the HIR complex and Asf1. Curr Biol. 2005 Nov 22;15(22):2044-9. PMID:16303565 doi:http://dx.doi.org/S0960-9822(05)01306-0
- ↑ Harkness TA, Arnason TG, Legrand C, Pisclevich MG, Davies GF, Turner EL. Contribution of CAF-I to anaphase-promoting-complex-mediated mitotic chromatin assembly in Saccharomyces cerevisiae. Eukaryot Cell. 2005 Apr;4(4):673-84. PMID:15821127 doi:http://dx.doi.org/4/4/673
- ↑ Franco AA, Lam WM, Burgers PM, Kaufman PD. Histone deposition protein Asf1 maintains DNA replisome integrity and interacts with replication factor C. Genes Dev. 2005 Jun 1;19(11):1365-75. Epub 2005 May 18. PMID:15901673 doi:http://dx.doi.org/10.1101/gad.1305005
- ↑ Sharp JA, Rizki G, Kaufman PD. Regulation of histone deposition proteins Asf1/Hir1 by multiple DNA damage checkpoint kinases in Saccharomyces cerevisiae. Genetics. 2005 Nov;171(3):885-99. Epub 2005 Jul 14. PMID:16020781 doi:http://dx.doi.org/10.1534/genetics.105.044719
- ↑ Linger J, Tyler JK. The yeast histone chaperone chromatin assembly factor 1 protects against double-strand DNA-damaging agents. Genetics. 2005 Dec;171(4):1513-22. Epub 2005 Sep 2. PMID:16143623 doi:http://dx.doi.org/genetics.105.043000
- ↑ Schermer UJ, Korber P, Horz W. Histones are incorporated in trans during reassembly of the yeast PHO5 promoter. Mol Cell. 2005 Jul 22;19(2):279-85. PMID:16039596 doi:http://dx.doi.org/10.1016/j.molcel.2005.05.028
- ↑ Zabaronick SR, Tyler JK. The histone chaperone anti-silencing function 1 is a global regulator of transcription independent of passage through S phase. Mol Cell Biol. 2005 Jan;25(2):652-60. PMID:15632066 doi:http://dx.doi.org/25/2/652
- ↑ Osada S, Kurita M, Nishikawa J, Nishihara T. Chromatin assembly factor Asf1p-dependent occupancy of the SAS histone acetyltransferase complex at the silent mating-type locus HMLalpha. Nucleic Acids Res. 2005 May 12;33(8):2742-50. Print 2005. PMID:15891116 doi:http://dx.doi.org/33/8/2742
- ↑ Lewis LK, Karthikeyan G, Cassiano J, Resnick MA. Reduction of nucleosome assembly during new DNA synthesis impairs both major pathways of double-strand break repair. Nucleic Acids Res. 2005 Sep 1;33(15):4928-39. Print 2005. PMID:16141196 doi:http://dx.doi.org/33/15/4928
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- ↑ Linger J, Tyler JK. Global replication-independent histone H4 exchange in budding yeast. Eukaryot Cell. 2006 Oct;5(10):1780-7. Epub 2006 Aug 25. PMID:16936140 doi:http://dx.doi.org/10.1128/EC.00202-06
- ↑ Tamburini BA, Carson JJ, Linger JG, Tyler JK. Dominant mutants of the Saccharomyces cerevisiae ASF1 histone chaperone bypass the need for CAF-1 in transcriptional silencing by altering histone and Sir protein recruitment. Genetics. 2006 Jun;173(2):599-610. Epub 2006 Apr 2. PMID:16582440 doi:http://dx.doi.org/10.1534/genetics.105.054783
- ↑ Korber P, Barbaric S, Luckenbach T, Schmid A, Schermer UJ, Blaschke D, Horz W. The histone chaperone Asf1 increases the rate of histone eviction at the yeast PHO5 and PHO8 promoters. J Biol Chem. 2006 Mar 3;281(9):5539-45. Epub 2006 Jan 4. PMID:16407267 doi:http://dx.doi.org/M513340200
- ↑ Schneider J, Bajwa P, Johnson FC, Bhaumik SR, Shilatifard A. Rtt109 is required for proper H3K56 acetylation: a chromatin mark associated with the elongating RNA polymerase II. J Biol Chem. 2006 Dec 8;281(49):37270-4. Epub 2006 Oct 17. PMID:17046836 doi:http://dx.doi.org/10.1074/jbc.C600265200
- ↑ Schwabish MA, Struhl K. Asf1 mediates histone eviction and deposition during elongation by RNA polymerase II. Mol Cell. 2006 May 5;22(3):415-22. PMID:16678113 doi:http://dx.doi.org/S1097-2765(06)00180-8
- ↑ Kats ES, Albuquerque CP, Zhou H, Kolodner RD. Checkpoint functions are required for normal S-phase progression in Saccharomyces cerevisiae RCAF- and CAF-I-defective mutants. Proc Natl Acad Sci U S A. 2006 Mar 7;103(10):3710-5. Epub 2006 Feb 24. PMID:16501045 doi:http://dx.doi.org/0511102103
- ↑ Recht J, Tsubota T, Tanny JC, Diaz RL, Berger JM, Zhang X, Garcia BA, Shabanowitz J, Burlingame AL, Hunt DF, Kaufman PD, Allis CD. Histone chaperone Asf1 is required for histone H3 lysine 56 acetylation, a modification associated with S phase in mitosis and meiosis. Proc Natl Acad Sci U S A. 2006 May 2;103(18):6988-93. Epub 2006 Apr 20. PMID:16627621 doi:http://dx.doi.org/0601676103
- ↑ Adkins MW, Carson JJ, English CM, Ramey CJ, Tyler JK. The histone chaperone anti-silencing function 1 stimulates the acetylation of newly synthesized histone H3 in S-phase. J Biol Chem. 2007 Jan 12;282(2):1334-40. Epub 2006 Nov 15. PMID:17107956 doi:http://dx.doi.org/M608025200
- ↑ Tsubota T, Berndsen CE, Erkmann JA, Smith CL, Yang L, Freitas MA, Denu JM, Kaufman PD. Histone H3-K56 acetylation is catalyzed by histone chaperone-dependent complexes. Mol Cell. 2007 Mar 9;25(5):703-12. Epub 2007 Feb 22. PMID:17320445 doi:S1097-2765(07)00086-X
- ↑ Daganzo SM, Erzberger JP, Lam WM, Skordalakes E, Zhang R, Franco AA, Brill SJ, Adams PD, Berger JM, Kaufman PD. Structure and function of the conserved core of histone deposition protein Asf1. Curr Biol. 2003 Dec 16;13(24):2148-58. PMID:14680630
- ↑ Scholes DT, Banerjee M, Bowen B, Curcio MJ. Multiple regulators of Ty1 transposition in Saccharomyces cerevisiae have conserved roles in genome maintenance. Genetics. 2001 Dec;159(4):1449-65. PMID:11779788
- ↑ Schneider J, Bajwa P, Johnson FC, Bhaumik SR, Shilatifard A. Rtt109 is required for proper H3K56 acetylation: a chromatin mark associated with the elongating RNA polymerase II. J Biol Chem. 2006 Dec 8;281(49):37270-4. Epub 2006 Oct 17. PMID:17046836 doi:http://dx.doi.org/10.1074/jbc.C600265200
- ↑ Han J, Zhou H, Li Z, Xu RM, Zhang Z. The Rtt109-Vps75 histone acetyltransferase complex acetylates non-nucleosomal histone H3. J Biol Chem. 2007 May 11;282(19):14158-64. Epub 2007 Mar 16. PMID:17369253 doi:http://dx.doi.org/10.1074/jbc.M700611200
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- ↑ Tsubota T, Berndsen CE, Erkmann JA, Smith CL, Yang L, Freitas MA, Denu JM, Kaufman PD. Histone H3-K56 acetylation is catalyzed by histone chaperone-dependent complexes. Mol Cell. 2007 Mar 9;25(5):703-12. Epub 2007 Feb 22. PMID:17320445 doi:S1097-2765(07)00086-X
- ↑ Driscoll R, Hudson A, Jackson SP. Yeast Rtt109 promotes genome stability by acetylating histone H3 on lysine 56. Science. 2007 Feb 2;315(5812):649-52. PMID:17272722 doi:http://dx.doi.org/315/5812/649
- ↑ Han J, Zhou H, Horazdovsky B, Zhang K, Xu RM, Zhang Z. Rtt109 acetylates histone H3 lysine 56 and functions in DNA replication. Science. 2007 Feb 2;315(5812):653-5. PMID:17272723 doi:http://dx.doi.org/10.1126/science.1133234
- ↑ Williams SK, Truong D, Tyler JK. Acetylation in the globular core of histone H3 on lysine-56 promotes chromatin disassembly during transcriptional activation. Proc Natl Acad Sci U S A. 2008 Jul 1;105(26):9000-5. doi:, 10.1073/pnas.0800057105. Epub 2008 Jun 24. PMID:18577595 doi:http://dx.doi.org/10.1073/pnas.0800057105
- ↑ Tang Y, Meeth K, Jiang E, Luo C, Marmorstein R. Structure of Vps75 and implications for histone chaperone function. Proc Natl Acad Sci U S A. 2008 Aug 26;105(34):12206-11. Epub 2008 Aug 22. PMID:18723682
- ↑ Danilenko N, Lercher L, Kirkpatrick J, Gabel F, Codutti L, Carlomagno T. Histone chaperone exploits intrinsic disorder to switch acetylation specificity. Nat Commun. 2019 Aug 6;10(1):3435. doi: 10.1038/s41467-019-11410-7. PMID:31387991 doi:http://dx.doi.org/10.1038/s41467-019-11410-7
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