Molecular and structural basis of drift in the functions of closely-related homologous enzyme domains: implications for function annotation based on homology searches and structural genomics

Abstract

Using a large database of protein domain families of known 3-D structure we present an analysis on the relationships among sequences, structures and functions of closely-related enzymes performed at the level of catalytic domains. Only in 38% of the pairs of homologous catalytic domains characterized by over about 60% of sequence identity the functions are almost completely identical. Nearly 43% of the pairs differ in their substrate specificity. Hence the most common variation of enzyme function among the closely-related homologues is the differences in the substrate specificity. For homologous pairs characterized by a sequence identity of 30-60%, if the structural difference metric is less than about 30, the functions are highly conserved. For clearly homologous protein domain pairs, usually sharing less than 40% sequence identity, we observe that often the chemical groups involved in the functions, and the cofactors differ. We also report of extremely unusual cases of closely-related homologues belonging to entirely different classes of enzymes. Such drastic shifts in the gross functions of homologues seem to be achieved by retooling of catalytic residues or by altering the stability of the intermediates in the biochemical reactions. Our work provides guidelines on the functional annotation based on homology searches and in structural genomics initiatives.