The Structural and Functional Uniqueness of the glmS Ribozyme - Progress in Molecular Biology and Translational Science - page 178

glmS self-cleavage is also supported by molar concentrations of monova-
lent metal ions, 30,31 providing additional evidence that inner sphere metal
ion coordination is not essential. With saturating GlcN6P (10 mM) and
monovalent metal ion at 1 M, the glmS ribozyme exhibits greater self-
cleavage activity in the presence of Li þ followed by NH 4 þ and Na þ . Under
these conditions, nominal self-cleavage activity was observed in the presence
of K þ ,Rb þ , and Cs þ . 31 In consideration of the physicochemical properties
of metal ions, correlations of ribozyme activity are apparent with ionic radius
and absolute hardness. Interestingly, Li þ and Mg 2 þ have near identical prop-
erties which provide for maximal performance of the glmS ribozyme (ionic
radius of Li þ 0.72 ˚ ; and absolute hardness of Li þ 0.59 and Mg 2 þ ¼ ¼ ¼

35.12 h and Mg 2 þ 47.59 h ). 31 Otherwise, ribozyme reactivity with metal

ions appears to correlate with absolute hardness to the point that ionic radius
exceed approximately 1.3-1.5 ˚ .
Although other cations can support glmS ribozyme activity, self-cleavage
rates are lower when performed in the presence of monovalent metal ions or
exchange-inert cobalt(III) complexes, suggesting that not all roles of divalent
metal ions can be compensated for by other positively charged ions. These
results suggest that aside from an obvious difference in divalent and mono-
valent metal ion charge density and binding affinity, mediation of ligand
phosphate recognition and coenzyme binding contribute to the glmS
ribozyme's preference for divalent metal ions.
Although metal ions do not directly promote catalysis, 30 it has been
shown that metal ion identity and the varying physicochemical properties
of metal ions (monovalent or divalent) have an impact on glmS ribozyme
self-cleavage. 31 Specifically, metal ion identity influenced the overall
apparent p K a of ribozyme self-cleavage, and metal ion binding largely
reflected phosphate oxygen affinity. 31 These results suggest that metal
ions likely play indirect roles in supporting the mechanism of catalysis.
Further studies focusing on the rapid ligand-binding chemical catalysis
step observed for prefolded glmS RNA were in agreement with other
results indicating a key role for divalent metal ions in coordinating the
phosphate of GlcN6P in the ligand-binding pocket. 6,12-15,17,27,31 In addi-
tion, GlcN did not promote rapid ligand binding and catalysis in the pres-
ence of divalent cations. Therefore, it can be assumed that folding of the
ribozyme is relatively independent of cation identity, but that rapid ini-
tiation of catalysis upon the addition of ligand requires a more precise
metal ion presence in order to properly coordinate the ligand phosphate
functionality. 34

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