Unravelling the Evolution of Allosteric Regulation in 3-Deoxy-D-arabino-heptulosonate 7-phosphate Synthase
Degree GrantorUniversity of Canterbury
Degree NameDoctor of Philosophy
The enzyme 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAH7PS) catalyses the first reaction in the shikimate pathway, leading to the biosynthesis of aromatic compounds including the aromatic amino acids. The catalytic activity of DAH7PS is regulated through feedback inhibition and is the major control point for the pathway. DAH7PSs are divided into two families, type I and type II, based on molecular weight and amino acid sequence. Type I DAH7PSs can be further divided based on sequence similarity. All DAH7PS enzymes with their crystal structures solved share a basic (β/α)₈-barrel fold in which the key catalytic components are housed. Furthermore, all structurally characterised DAH7PSs, except Pyrococcus furiosus DAH7PS (PfuDAH7PS) and Aeropyrum pernix DAH7PS, have recruited extra structural motifs that are implicated in allosteric regulation. However, there are significant differences in the additional structural elements.
This thesis investigates the hypothesis that the diverse regulation strategies for controlling DAH7PS activity have evolved by domain recruitment, whereby regulatory domains have been added to the catalytic barrel.
Chapter 2 describes the functional characterisation of the type Iβ Thermotoga maritima DAH7PS (TmaDAH7PS), and the exploration of its response to inhibitors. The catalytic activity of TmaDAH7PS was found to be substantially inhibited by tyrosine (Tyr) and to a lesser extent, phenylalanine (Phe). The putative regulatory domain previously identified as a ferredoxin-like domain was recognised as an aspartate kinase-chorismate-mutase-tyrA (prephenate dehydrogenase) or ACT domain.
Chapter 3 describes the characterisation of TmaDAH7PS with the N-terminal domain removed. The truncated enzyme was found to be more catalytically active than wild-type TmaDAH7PS and insensitive to inhibition by the aromatic amino acids, Tyr, Phe and tryptophan. Apart from the truncation of the ACT domain, the crystal structure of truncTmaDAH7PS showed no major changes to the monomer structure when compared to wild-type TmaDAH7PS. However, truncTmaDAH7PS crystallises as a dimer, unlike wild-type TmaDAH7PS.
In Chapter 4, the solution of the crystal structure of TmaDAH7PS with Tyr bound is presented. Tyr binding was shown to induce a significant conformational change, and Tyr is observed to bind at the interface between the ACT domains from two diagonally located monomers of the tetramer. The major reorganisation of the regulatory domain with respect to the barrel observed in the crystal structure, was confirmed by small angle X-ray scattering. The closed conformation adopted by the protein on Tyr binding physically gates the neighbouring barrel and blocks substrate entry into the active site.
Chapter 5 explores the interactions between TmaDAH7PS and the allosteric inhibitor, Tyr. The residues His29 and Ser31, which form hydrogen bonds with the hydroxyl moiety of the Tyr ligand, were examined for their impact on the sensitivity and selectivity of the enzyme for the inhibitors Tyr and Phe. The hydroxyl side chain of Ser31 was found to be important for both the preferential inhibition by Tyr over Phe and the inhibitory mechanism. His29 (the hydrogen-bonding partner of Ser31) appears to play a secondary role in determining ligand selectivity and the relative positioning of these two residues is crucial to the inhibition of the enzyme.
Chapter 6 evaluates the transferability of allosteric control of catalytic activity. The ACT domain of TmaDAH7PS was fused onto the barrel of the unregulated PfuDAH7PS. This chimeric enzyme was found to be catalytically active, inhibited by Tyr (although less sensitive) and preliminary crystallographic results show inhibition occurs via the same conformational change observed for wild-type TmaDAH7PS.