Department of Biological Sciences, Purdue University
One expects that, in comparing enzymes related by divergent evolution,
catalytic residues will be conserved. This hypothesis can be tested and
refined through the study of the relationships of active-site structures
and sequences within enzyme families. We have been studying two enzyme
families whose members are dependent on a cofactor or metal ion for
catalysis.
Members of the "enolase superfamily" catalyze different reactions, and
in some cases their sequences have diverged enough to almost seem
unrelated. Yet active sites look surprisingly similar; the metal-binding
sites especially are well conserved. Other catalytic residues are found at
conserved positions, but do not have the same identity.
We have recently determined the structure of the
thiamine-pyrophosphate dependent enzyme benzoylformate decarboxylase.
Members of this family include decarboxylases that catalyze the same
reaction on different substrates, yet their active sites contain no
conserved residues beyond those involved in binding cofactor.
These apparently conflicting observations can be rationalized in terms
of (1) the prime importance of metals and cofactors in carrying out the
underlying chemistry (the rest of the enzyme is commentary) and (2) the
importance of similarities and slight differences in the overall chemistry
of the reaction. Structural comparisons of catalytic machinery should mold
the kind of predictions we make about related enzymes from their sequences.
In the case of enzymes that require a cofactor or metal ion, the binding
site may be all that is recognizably conserved in a family of sequences.
Other residues in the active site vary as required by the specific reaction
and substrate.