Structural modeling of histone methyltransferase complex Set1C from Saccharomyces cerevisiae using constraint-based docking
- PMID: 21046623
- DOI: 10.1002/pmic.201000283
Structural modeling of histone methyltransferase complex Set1C from Saccharomyces cerevisiae using constraint-based docking
Abstract
Set1C is a histone methyltransferase playing an important role in yeast gene regulation. Modeling the structure of this eight-subunit protein complex is an important open problem to further elucidate its functional mechanism. Recently, there has been progress in modeling of larger complexes using constraints to restrict the combinatorial explosion in binary docking of subunits. Here, we model the subunits of Set1C and develop a constraint-based docking approach, which uses high-quality protein interaction as well as functional data to guide and constrain the combinatorial assembly procedure. We obtained 22 final models. The core complex consisting of the subunits Set1, Bre2, Sdc1 and Swd2 is conformationally conserved in over half of the models, thus, giving high confidence. We characterize these high-confidence and the lower confidence interfaces and discuss implications for the function of Set1C.
Similar articles
-
A conserved interaction between the SDI domain of Bre2 and the Dpy-30 domain of Sdc1 is required for histone methylation and gene expression.J Biol Chem. 2010 Jan 1;285(1):595-607. doi: 10.1074/jbc.M109.042697. Epub 2009 Nov 6. J Biol Chem. 2010. PMID: 19897479 Free PMC article.
-
The Saccharomyces cerevisiae Set1 complex includes an Ash2 homologue and methylates histone 3 lysine 4.EMBO J. 2001 Dec 17;20(24):7137-48. doi: 10.1093/emboj/20.24.7137. EMBO J. 2001. PMID: 11742990 Free PMC article.
-
Structural characterization of Set1 RNA recognition motifs and their role in histone H3 lysine 4 methylation.J Mol Biol. 2006 Jun 23;359(5):1170-81. doi: 10.1016/j.jmb.2006.04.050. Epub 2006 May 9. J Mol Biol. 2006. PMID: 16787775
-
Cross-talking histones: implications for the regulation of gene expression and DNA repair.Biochem Cell Biol. 2005 Aug;83(4):460-7. doi: 10.1139/o05-116. Biochem Cell Biol. 2005. PMID: 16094449 Review.
-
Histone-modifying enzymes: encrypting an enigmatic epigenetic code.Curr Opin Struct Biol. 2006 Dec;16(6):753-60. doi: 10.1016/j.sbi.2006.10.002. Epub 2006 Oct 27. Curr Opin Struct Biol. 2006. PMID: 17070031 Review.
Cited by
-
Arabidopsis S2Lb links AtCOMPASS-like and SDG2 activity in H3K4me3 independently from histone H2B monoubiquitination.Genome Biol. 2019 May 21;20(1):100. doi: 10.1186/s13059-019-1705-4. Genome Biol. 2019. PMID: 31113491 Free PMC article.
-
Modeling protein assemblies in the proteome.Mol Cell Proteomics. 2014 Mar;13(3):887-96. doi: 10.1074/mcp.M113.031294. Epub 2014 Jan 20. Mol Cell Proteomics. 2014. PMID: 24445405 Free PMC article.
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Molecular Biology Databases
Miscellaneous