| Structural highlights
6g0l is a 12 chain structure with sequence from African clawed frog and Baker's yeast. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Ligands: | , |
| Gene: | hist1h3g, H3l (African clawed frog), XELAEV_18028549mg (African clawed frog), CHD1, YER164W, SYGP-ORF4 (Baker's yeast) |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
[H2A1_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. [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. [CHD1_YEAST] ATP-dependent chromatin-remodeling factor which functions as substrate recognition component of the transcription regulatory histone acetylation (HAT) complexes SAGA and SLIK. It recognizes H3K4me. SAGA is involved in RNA polymerase II-dependent transcriptional regulation of approximately 10% of yeast genes. At the promoters, SAGA is required for recruitment of the basal transcription machinery. It influences RNA polymerase II transcriptional activity through different activities such as TBP interaction (SPT3, SPT8 and SPT20) and promoter selectivity, interaction with transcription activators (GCN5, ADA2, ADA3 and TRA1), and chromatin modification through histone acetylation (GCN5) and deubiquitination (UBP8). SAGA acetylates nucleosomal histone H3 to some extent (to form H3K9ac, H3K14ac, H3K18ac and H3K23ac). SAGA interacts with DNA via upstream activating sequences (UASs). SLIK is proposed to have partly overlapping functions with SAGA. It preferentially acetylates methylated histone H3, at least after activation at the GAL1-10 locus. Acts in opposition to the FACT complex in regulating polymerase II transcription. Also required for efficient transcription by RNA polymerase I, and more specifically the pol I transcription termination step. Regulates negatively DNA replication. Not only involved in transcription-related chromatin-remodeling, but also required to maintain a specific chromatin configuration across the genome.[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [A0A1L8G0X3_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.[RuleBase:RU000528][SAAS:SAAS00581158]
Publication Abstract from PubMed
ATP-dependent chromatin remodelling proteins represent a diverse family of proteins that share ATPase domains that are adapted to regulate protein-DNA interactions. Here we present structures of the Saccharomyces cerevisiae Chd1 protein engaged with nucleosomes in the presence of the transition state mimic ADP-beryllium fluoride. The path of DNA strands through the ATPase domains indicates the presence of contacts conserved with single strand translocases and additional contacts with both strands that are unique to Snf2 related proteins. The structure provides connectivity between rearrangement of ATPase lobes to a closed, nucleotide bound state and the sensing of linker DNA. Two turns of linker DNA are prised off the surface of the histone octamer as a result of Chd1 binding, and both the histone H3 tail and ubiquitin conjugated to lysine 120 are re-orientated towards the unravelled DNA. This indicates how changes to nucleosome structure can alter the way in which histone epitopes are presented.
Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome.,Sundaramoorthy R, Hughes AL, El-Mkami H, Norman DG, Ferreira H, Owen-Hughes T Elife. 2018 Aug 6;7. pii: 35720. doi: 10.7554/eLife.35720. PMID:30079888[12]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Grant PA, Eberharter A, John S, Cook RG, Turner BM, Workman JL. Expanded lysine acetylation specificity of Gcn5 in native complexes. J Biol Chem. 1999 Feb 26;274(9):5895-900. PMID:10026213
- ↑ Tran HG, Steger DJ, Iyer VR, Johnson AD. The chromo domain protein chd1p from budding yeast is an ATP-dependent chromatin-modifying factor. EMBO J. 2000 May 15;19(10):2323-31. PMID:10811623 doi:http://dx.doi.org/10.1093/emboj/19.10.2323
- ↑ Simic R, Lindstrom DL, Tran HG, Roinick KL, Costa PJ, Johnson AD, Hartzog GA, Arndt KM. Chromatin remodeling protein Chd1 interacts with transcription elongation factors and localizes to transcribed genes. EMBO J. 2003 Apr 15;22(8):1846-56. PMID:12682017 doi:http://dx.doi.org/10.1093/emboj/cdg179
- ↑ 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
- ↑ Pray-Grant MG, Daniel JA, Schieltz D, Yates JR 3rd, Grant PA. Chd1 chromodomain links histone H3 methylation with SAGA- and SLIK-dependent acetylation. Nature. 2005 Jan 27;433(7024):434-8. Epub 2005 Jan 12. PMID:15647753 doi:http://dx.doi.org/nature03242
- ↑ Stockdale C, Flaus A, Ferreira H, Owen-Hughes T. Analysis of nucleosome repositioning by yeast ISWI and Chd1 chromatin remodeling complexes. J Biol Chem. 2006 Jun 16;281(24):16279-88. Epub 2006 Apr 10. PMID:16606615 doi:http://dx.doi.org/10.1074/jbc.M600682200
- ↑ Xella B, Goding C, Agricola E, Di Mauro E, Caserta M. The ISWI and CHD1 chromatin remodelling activities influence ADH2 expression and chromatin organization. Mol Microbiol. 2006 Mar;59(5):1531-41. PMID:16468993 doi:http://dx.doi.org/10.1111/j.1365-2958.2005.05031.x
- ↑ Ferreira H, Flaus A, Owen-Hughes T. Histone modifications influence the action of Snf2 family remodelling enzymes by different mechanisms. J Mol Biol. 2007 Nov 30;374(3):563-79. Epub 2007 Sep 26. PMID:17949749 doi:http://dx.doi.org/10.1016/j.jmb.2007.09.059
- ↑ Biswas D, Dutta-Biswas R, Stillman DJ. Chd1 and yFACT act in opposition in regulating transcription. Mol Cell Biol. 2007 Sep;27(18):6279-87. Epub 2007 Jul 9. PMID:17620414 doi:http://dx.doi.org/10.1128/MCB.00978-07
- ↑ Jones HS, Kawauchi J, Braglia P, Alen CM, Kent NA, Proudfoot NJ. RNA polymerase I in yeast transcribes dynamic nucleosomal rDNA. Nat Struct Mol Biol. 2007 Feb;14(2):123-30. Epub 2007 Jan 28. PMID:17259992 doi:http://dx.doi.org/10.1038/nsmb1199
- ↑ Biswas D, Takahata S, Xin H, Dutta-Biswas R, Yu Y, Formosa T, Stillman DJ. A role for Chd1 and Set2 in negatively regulating DNA replication in Saccharomyces cerevisiae. Genetics. 2008 Feb;178(2):649-59. doi: 10.1534/genetics.107.084202. Epub 2008 Feb, 1. PMID:18245327 doi:http://dx.doi.org/10.1534/genetics.107.084202
- ↑ Sundaramoorthy R, Hughes AL, El-Mkami H, Norman DG, Ferreira H, Owen-Hughes T. Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome. Elife. 2018 Aug 6;7. pii: 35720. doi: 10.7554/eLife.35720. PMID:30079888 doi:http://dx.doi.org/10.7554/eLife.35720
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