3KMT

Crystal structure of vSET/SAH/H3 ternary complex

Summary for 3KMT

• Entry DOI: 10.2210/pdb3kmt/pdb
• Related: 3KMA 3KMJ
• Descriptor: A612L protein, Histone H3, S-ADENOSYL-L-HOMOCYSTEINE, ... (4 entities in total)
• Functional Keywords: set domain, ternary complex, viral protein
• Biological source: Paramecium bursaria Chlorella virus 1 (PBCV-1); More
• Cellular location: Nucleus: P68431
• Total number of polymer chains: 6
• Total formula weight: 44420.92

Authors

Wei, H.,Zhou, M.M. (deposition date: 2009-11-11, release date: 2010-11-10, Last modification date: 2023-09-06)

Primary citation

Wei, H.,Zhou, M.M.
Dimerization of a viral SET protein endows its function.
Proc.Natl.Acad.Sci.USA, 107:18433-18438, 2010

PubMed Abstract: Histone modifications are regarded as the most indispensible phenomena in epigenetics. Of these modifications, lysine methylation is of the greatest complexity and importance as site- and state-specific lysine methylation exerts a plethora of effects on chromatin structure and gene transcription. Notably, paramecium bursaria chlorella viruses encode a conserved SET domain methyltransferase, termed vSET, that functions to suppress host transcription by methylating histone H3 at lysine 27 (H3K27), a mark for eukaryotic gene silencing. Unlike mammalian lysine methyltransferases (KMTs), vSET functions only as a dimer, but the underlying mechanism has remained elusive. In this study, we demonstrate that dimeric vSET operates with negative cooperativity between the two active sites and engages in H3K27 methylation one site at a time. New atomic structures of vSET in the free form and a ternary complex with S-adenosyl homocysteine and a histone H3 peptide and biochemical analyses reveal the molecular origin for the negative cooperativity and explain the substrate specificity of H3K27 methyltransferases. Our study suggests a "walking" mechanism, by which vSET acts all by itself to globally methylate host H3K27, which is accomplished by the mammalian EZH2 KMT only in the context of the Polycomb repressive complex.

PubMed: 20937900
DOI: 10.1073/pnas.1009911107

Experimental method

X-RAY DIFFRACTION (1.78 Å)