Conspectus
Natural metalloenzymes are often the most proficient
catalysts
in terms of their activity, selectivity, and ability to operate at
mild conditions. However, metalloenzymes are occasionally surprising
in their selection of catalytic metals, and in their responses to
metal substitution. Indeed, from the isolated standpoint of producing
the best catalyst, a chemist designing from first-principles would
likely choose a different metal. For example, some enzymes employ
a redox active metal where a simple Lewis acid is needed. Such are
several hydrolases. In other cases, substitution of a non-native metal
leads to radical improvements in reactivity. For example, histone
deacetylase 8 naturally operates with Zn2+ in the active
site but becomes much more active with Fe2+. For β-lactamases,
the replacement of the native Zn2+ with Ni2+ was suggested to lead to higher activity as predicted computationally.
There are also intriguing cases, such as Fe2+- and Mn2+-dependent ribonucleotide reductases and W4+-
and Mo4+-dependent DMSO reductases, where organisms manage
to circumvent the scarcity of one metal (e.g., Fe2+) by
creating protein structures that utilize another metal (e.g., Mn2+) for the catalysis of the same reaction. Naturally, even
though both metal forms are active, one of the metals is preferred
in every-day life, and the other metal variant remains dormant until
an emergency strikes in the cell. These examples lead to certain questions.
When are catalytic metals selected purely for electronic or structural
reasons, implying that enzymatic catalysis is optimized to its maximum?
When are metal selections a manifestation of competing evolutionary
pressures, where choices are dictated not just by catalytic efficiency
but also by other factors in the cell? In other words, how can enzymes
be improved as catalysts merely through the use of common biological
building blocks available to cells? Addressing these questions is
highly relevant to the enzyme design community, where the goal is
to prepare maximally efficient quasi-natural enzymes for the catalysis
of reactions that interest humankind.
Due to competing evolutionary
pressures, many natural enzymes may
not have evolved to be ideal catalysts and can be improved for the
isolated purpose of catalysis in vitro when the competing
factors are removed.
The goal of this Account is not to cover
all the possible stories
but rather to highlight how variable enzymatic catalysis can be. We
want to bring up possible factors affecting the evolution of enzyme
structure, and the large- and intermediate-scale structural and electronic
effects that metals can induce in the protein, and most importantly,
the opportunities for optimization of these enzymes for catalysis in vitro.