Abstract
Phylogenomic analysis of the occurrence and abundance of protein domains in proteomes has recently showed that the α/β architecture is probably the oldest fold design. This holds important implications for the origins of biochemistry. Here we explore structure-function relationships addressing the use of chemical mechanisms by ancestral enzymes. We test the hypothesis that the oldest folds used the most mechanisms. We start by tracing biocatalytic mechanisms operating in metabolic enzymes along a phylogenetic timeline of the first appearance of homologous superfamilies of protein domain structures from CATH. A total of 335 enzyme reactions were retrieved from MACiE and were mapped over fold age. We define a mechanistic step type as one of the 51 mechanistic annotations given in MACiE, and each step of each of the 335 mechanisms was described using one or more of these annotations. We find that the first two folds, the P-loop containing nucleotide triphosphate hydrolase and the NAD(P)-binding Rossmann-like homologous superfamilies, were α/β architectures responsible for introducing 35% (18/51) of the known mechanistic step types. We find that these two oldest structures in the phylogenomic analysis of protein domains introduced many mechanistic step types that were later combinatorially spread in catalytic history. The most common mechanistic step types included fundamental building blocks of enzyme chemistry: “Proton transfer,” “Bimolecular nucleophilic addition,” “Bimolecular nucleophilic substitution,” and “Unimolecular elimination by the conjugate base.” They were associated with the most ancestral fold structure typical of P-loop containing nucleotide triphosphate hydrolases. Over half of the mechanistic step types were introduced in the evolutionary timeline before the appearance of structures specific to diversified organisms, during a period of architectural diversification. The other half unfolded gradually after organismal diversification and during a period that spanned ∼2 billion years of evolutionary history.
Highlights
The three-dimensional (3D) atomic structures of contemporary proteins provide clues about how both structure and function unfolded in the course of billions of years of evolution [1]
In order to test the hypothesis that the most ancestral protein domains use the greatest number of biocatalytic mechanistic step types, we assume that extant protein domain structure is the best historical archive that is available to explore ancient enzyme functions
We use the ages of domain structures, derived from phylogenomic reconstruction and a recent census of CATH domain structure in hundreds of genomes [5], to study how chemical mechanisms developed in protein evolution
Summary
The three-dimensional (3D) atomic structures of contemporary proteins provide clues about how both structure and function unfolded in the course of billions of years of evolution [1]. Two recent studies of this kind showed congruently that the a/b architecture is probably the oldest type of fold design [2,3]. The EC classification provides functional annotations that can be used to link a gene with the chemical reaction catalysed by its gene product. The EC classification does not explore the detailed chemical mechanism of the enzyme reaction. The classification was designed before much information concerning enzyme structures [11] and mechanisms [12,13] was available
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