5TDR

Set3 PHD finger in complex with histone H3K4me2

Summary for 5TDR

• Entry DOI: 10.2210/pdb5tdr/pdb
• Related: 5TDW
• Descriptor: SET domain-containing protein 3, Histone H3, ZINC ION, ... (5 entities in total)
• Functional Keywords: transcription, epigenetics, methylation, histone
• Biological source: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast); More
• Total number of polymer chains: 2
• Total formula weight: 9496.43

Authors

Andrews, F.H.,Ali, M.,Kutateladze, T.G. (deposition date: 2016-09-19, release date: 2016-11-02, Last modification date: 2017-06-28)

Primary citation

Gatchalian, J.,Ali, M.,Andrews, F.H.,Zhang, Y.,Barrett, A.S.,Kutateladze, T.G.
Structural Insight into Recognition of Methylated Histone H3K4 by Set3.
J. Mol. Biol., 429:2066-2074, 2017

PubMed Abstract: The plant homeodomain (PHD) finger of Set3 binds methylated lysine 4 of histone H3 in vitro and in vivo; however, precise selectivity of this domain has not been fully characterized. Here, we explore the determinants of methyllysine recognition by the PHD fingers of Set3 and its orthologs. We use X-ray crystallographic and spectroscopic approaches to show that the Set3 PHD finger binds di- and trimethylated states of H3K4 with comparable affinities and employs similar molecular mechanisms to form complexes with either mark. Composition of the methyllysine-binding pocket plays an essential role in determining the selectivity of the PHD fingers. The finding that the histone-binding activity is not conserved in the PHD finger of Set4 suggests different functions for the Set3 and Set4 paralogs.

PubMed: 27697561
DOI: 10.1016/j.jmb.2016.09.020

Experimental method

X-RAY DIFFRACTION (1.42 Å)