Dynamic Regulation of Histone Lysine Methylation by Demethylases Yang Shi, Johnathan R. Whetstine  Molecular Cell  Volume 25, Issue 1, Pages 1-14 (January 2007) DOI: 10.1016/j.molcel.2006.12.010 Copyright © 2007 Elsevier Inc. Terms and Conditions

Figure 1 Schematic Diagrams of LSD1 Domains, 3D Structures, and Mechanism of Action LSD1 domains are indicated by different colors. AOD stands for amine oxidase domain. The 3D structures are taken from two recent studies (Stavropoulos et al., 2006; Yang et al., 2006). LSD1 alone demethylates H3K4me1/Me2 (Shi et al., 2004). Co-REST interacts with the tower/insert region of LSD1 (upper interaction). This interaction results in nucleosomal demethylation (Lee et al., 2005; Shi et al., 2005; Yang et al., 2006). The human androgen receptor (AR) has also been shown to interact with LSD1 and result in H3K9me1 and Me2 demethylation (Metzger et al., 2005). Molecular Cell 2007 25, 1-14DOI: (10.1016/j.molcel.2006.12.010) Copyright © 2007 Elsevier Inc. Terms and Conditions

Figure 2 Chemical Mechanism for LSD1-Mediated Demethylation The reaction mechanism, adapted from Shi et al. (2004), depicts LSD1 removing a methyl group from a dimethylated lysine residue, but the reaction can proceed until an unmethylated lysine is generated. Molecular Cell 2007 25, 1-14DOI: (10.1016/j.molcel.2006.12.010) Copyright © 2007 Elsevier Inc. Terms and Conditions

Figure 3 Phylogenic Analysis of the 28 Human JmjC-Containing Proteins The JmjC domain for each human member was analyzed with DRAWGRAM (Biology WorkBench 3.2-DRAWGRAM; Felsenstein, 1989), and diagrammatic representations of their associated protein domains are depicted. Some of the JmjC-containing genes have multiple splice variants, but the variant with the JmjC domain or the one with the most domains recorded in Genbank is shown. The corresponding Gene ID is indicated, and protein schematics are shown on the right. Molecular Cell 2007 25, 1-14DOI: (10.1016/j.molcel.2006.12.010) Copyright © 2007 Elsevier Inc. Terms and Conditions

Figure 4 Chemical Mechanism for Demethylation Mediated by the JmjC Proteins This mechanism is based on the biochemical and structure/function data generated for JHDM1 (Tsukada et al., 2006) and the JMJD2 family (Whetstine et al., 2006; Chen et al., 2006a) as well as the proposed chemical reactions for the HIF hydroxylase (Dann and Bruick, 2005) and TauD (Price et al., 2005). The amino acids responsible for coordinating the Fe(II) (red circle) and α-ketoglutarate are depicted in the JMJD2A catalytic core crystal structure taken from Chen et al. (2006a). A schematic of the interaction and coordination of the molecular oxygen, α-ketoglutarate, and substrate is indicated as reaction step 1. An electron is transferred from the Fe(II) to the coordinated molecular oxygen, yielding a superoxide radical and Fe(III). The radical attacks the carbonyl group (C2) in the α-ketoglutarate, which accepts an electron from the iron. Decarboxylation ensues, and succinate and CO2 are produced (step 3). During the split of molecular oxygen, a highly unstable Fe(IV)-oxo intermediate is generated. This oxoferryl group extracts a proton from the methylated lysine, forming an Fe(III) hydroxide that subsequently hydroxylates the radical on the methyl group (step 4), which forms a carbonyl group that will spontaneously demethylate (step 5). The reaction is then able to continue in the presence of molecular oxygen, Fe(II), and α-ketoglutarate. Molecular Cell 2007 25, 1-14DOI: (10.1016/j.molcel.2006.12.010) Copyright © 2007 Elsevier Inc. Terms and Conditions

Figure 5 Site and Methyl Group Specificities of Histone Methyltransferases and Demethylases The histone methyltransferases for various lysine residues are indicated on the left, and the corresponding demethylases are listed on the right. The mammalian counterparts are indicated for most of the known enzymes. The degree of methylation/demethylation is indicated with the arrows. The arrow was determined by analyzing the literature for in vitro activity and/or genetic data from different species. The histone methyltransferases with a gray arrow and a dashed line have not been extensively analyzed for the degree of methylation. The white arrow indicates a lower-affinity methylation substrate or demethylation reaction. Due to size limitations, the primary references were omitted, but information about most of the methyltransferases has been reviewed in Lachner et al. (2003) and Dillon et al. (2005). Molecular Cell 2007 25, 1-14DOI: (10.1016/j.molcel.2006.12.010) Copyright © 2007 Elsevier Inc. Terms and Conditions

Figure 6 Chemical Mechanism for Putative Demethylation Reaction Mediated by the Radical SAM Family of Enzymes (A) The 4Fe-4S center is depicted with SAM from the Radical SAM enzymes. When the substrate binds, the SAM and iron-sulfur center come in close proximity and an electron is transferred from iron to SAM. The S-C-5′ bond is then homolyitcally cleaved, forming the 5′-deoxyadenosyl radical and methionine. (B) A candidate mechanism for Radical SAM demethylation of di- or monomethylated lysines. The 5′-deoxyadenosyl radical abstracts a hydrogen from the methyl residue, resulting in adenosine and a free radical on the methyl group. The carbon-centered radical is stabilized by one pair of electrons on the nitrogen atom. The imine structure forms, and the electron is transferred either to the iron-sulfur center or to another protein. A water molecule is added and gives the carbinolamine, which releases formaldehyde and an unmethylated lysine upon hydrolysis. (C) A candidate mechanism for tridemethylation. The 5′-deoxyadenosyl radical intermediate abstracts a hydrogen atom from the substrate and adds a hydroxyl moiety by using water after electron transfer. This generates a carbonyl group that would undergo spontaneous demethylation. Molecular Cell 2007 25, 1-14DOI: (10.1016/j.molcel.2006.12.010) Copyright © 2007 Elsevier Inc. Terms and Conditions