A zinc‐finger like metal binding site in the nucleosome

Abstract

UV spectroscopy demonstrated that chicken mononucleosomes bind Co(II) and Zn(II) ions at submicromolar concentrations in a tetrahedral mode, at a conserved zinc finger-like site, composed of Cys110 and His113 residues of both H3 molecules. Neither of these metal ions substituted for another, indicating a limited binding reversibility. Molecular modeling indicated that the tetrahedral site is formed by unhindered rotations around Ca-Cb bonds in the side chains of the zinc binding residues. The resulting local rearrangement of the protein structure shields the bound metal ion from the solvent, explaining the observed lack of reversibility of the binding. Consequences of these findings for zinc homeostasis, metal toxicology and nucleosomal regulation are discussed.

The Histone H3-H4 Tetramer is a Copper Reductase Enzyme

“…Reactions carried out in the presence of RNase A, which contains eight redox reactive 144 cysteines capable of forming four disulfide bonds (Klink et al, 2000), at the same concentration 145 as the tetramer did not enhance the rate of copper reduction (Figure 2 -figure supplement 2F). 146 Similarly, 1 µM of DTT directly reduced an equimolar 2 µM of Cu 2+ but did not substantially 147 enhance the rate of cupric ion reduction by TCEP (Figure 2 -figure supplement 2F), emphasizing 148 the unique role of H3C110 in the structural context of the H3-H4 tetramer for enzymatic activity.149The pair of histidine residues at position 113 (H3H113) at the H3-H3' interface have also 150 been proposed to participate in metal coordination (Adamczyk et al, 2007; Saavedra, 1986). This 151 highly conserved residue is present in the canonical histone H3 of all 166 eukaryotes that span the 152 major kingdoms (Macadangdang et al, 2014), as well as in the structurally-equivalent position of 153 most (29 out of 33) archaeal histones spanning the major phyla (Henneman et al, 2018) (Figure 154 157 et al, 2015), had little effect on the rate of reduction with Cu 2+ -Tricine as the substrate (data not 158 shown) but diminished cupric ion reduction in reactions with Cu 2+ -ADA (Figure 2I and Figure 2 159 -figure supplement 2G) or Cu 2+ -NTA as Cu 2+ substrates (Figure 2 -figure supplement 2H and I).160The differing effects of ADA, NTA, and Tricine on copper reduction rates are likely due in part to 161 their differing Cu 2+ coordination ability and/or geometry.…”

“…The region of the nucleosome where the 54 two histone H3 proteins form a dimerization interface contains amino acid residues, including 55 cysteine 110 (H3C110) and histidine 113 (H3H113), that are common in transition metal binding 56 sites, particularly those that coordinate copper ions (Katz et al, 2003). These residues display some 57 ability to coordinate transition metal ions in vitro, but it is unclear whether such interactions are 58 functionally significant (Adamczyk et al, 2007; Bal et al, 1995; Saavedra, 1986). The 59 evolutionary conservation of residues in this region is greater than expected given their 60 contributions to the thermodynamic stability of the nucleosome (Ramachandran et al, 2011), 61 leading to the suggestion that "a novel function" provided by the H3-H3' interface is driving the 62 unexpected conservation (Ramachandran et al, 2011).…”

“…We performed tetramer assembly and subsequent assays in solutions and glassware thoroughly 93 depleted of contaminating metal ions, a critical precaution for in vitro studies (see Methods). 94 We focused first on the role of the pair of cysteine residues at position 110 (H3C110), one 95 from each apposing H3 protein (Adamczyk et al, 2007; Saavedra, 1986), in copper ion binding.…”

Loss of Pluripotency in Human Embryonic Stem Cells Directly Correlates with an Increase in Nuclear Zinc

“…This hypothesis arises partly from reports that RA can induce chromatin remodeling [32], [33] and from the idea that nucleosomes have a potential zinc binding site [34], [35]. Our current methods do not allow us to directly examine the zinc content of heterochromatin versus the euchromatin of a differentiated stem cell, though the development of x-ray fluorescence nanoprobes may soon make this possible.…”

XFM of “Trace Metals” in Cultured Cells: Framing the Picture

“…We have published that mitotic chromosomes exclude zinc [4], suggesting that zinc is excluded from heterochromatin. This result calls into question the postulate of zinc binding to histones in condensed chromatin [5,6]. In the search for a protein that may be both a zinc target and involved in differentiation, we considered metallothionein.…”