. 2016 Jul 5;113(29):E4180–E4189. doi: 10.1073/pnas.1605862113

Table S1.

Biochemical properties of H3K9 methyltransferases

Enzyme	k_cat (min⁻¹)	K_M (µM)	c (µM)	K_D, _K9me3 (µM)^*	k_m (min⁻¹)^†	α	k_−m (min⁻¹)
hSuv39h1	0.1–0.2^‡	0.3–0.9^‡	0.08^§	20^¶	0.1–0.2	0.004^#	0.0001^\|\|
hSuv39h2	13^**	13–33^**	0.02^§	ND	<4–7	ND	0.0001^\|\|
yClr4	0.02^††	15^††	ND	0.6–1.5^††^,^‡‡	0.01	ND	0.006–0.04^§§

The catalytic rate constant k_cat, Michaelis constant K_M, free intracellular concentration c, dissociation constant for H3K9me3 binding K_D, _K9me3, resulting effective reaction rate k_m, and scale parameter α are listed for different H3K9 methyltransferases. The values of k_cat and K_M for hSuv39h2 refer to its isolated catalytic domain, with the full-length protein being less active. Reverse rates k_−m for H3K9 methylation are also indicated. ND, not determined.

The low micromolar K_D values for binding to H3K9me3 compare with the low nanomolar K_D values for binding of TetR, GAL4, and Cas9 to their target sites (67–69).

^{^†}

The effective modification rate was calculated according to Eq. S2 using the indicated values for k_cat and K_M, as well as the local concentration c₀ ∼ 11–14 µM of the adjacent nucleosome for the respective nucleosome repeat length (40). The modification rates listed here refer to a single enzyme. They should increase (roughly linearly with the number of recruited enzymes) if multimeric DNA-binding proteins are used for recruitment and/or if nucleation sites contain multiple binding sites, provided that only a relatively small fraction of intramolecular collisions is productive and that nucleation sites are relatively small.

^{^‡}

Measured value was taken from ref. 62.

^{^§}

Measured value was taken from ref. 32.

^{^¶}

Measured value was taken from ref. 63.

^{^#}

This value was calculated according to Eq. S4 using the indicated values for c and K_D,K9me3, as well as K_D,1 = 0.2 nM for the TetR-tetO interaction (68) and β = 1.

^{^||}

The decay half-time of 5 d for H3K9me2 in mammalian cells translates into a loss rate of 0.0001 min⁻¹ (19). Small demethylation rates below the detection limit of 0.072 min⁻¹ were also reported for H3K9me3 (66).

^**

Measured value was taken from ref. 64.

^{^††}

Measured value was taken from ref. 35.

^{^‡‡}

Measured value was taken from ref. 65.

^{^§§}

The decay half-time of 2 h measured for an ectopic H3K9me2 domain in WT fission yeast translates into a loss rate of 0.006 min⁻¹ (15). In the absence of Clr4, this rate might increase to ∼0.04 min⁻¹ (Fig. S4B).