Substrate specificity and mutational studies of KDO8PS
Degree GrantorUniversity of Canterbury
Degree NameDoctor of Philosophy
The enzyme 3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8PS) catalyses the stereospecific aldol-like condensation between phosphoenolpyruvate (PEP) and the five-carbon sugar D-arabinose 5-phosphate (A5P). This is the first biosynthetic step in the formation of 3-deoxy-D-manno-octulosonate (KDO), an essential lipopolysaccharide component of all Gram-negative bacteria. KDO8PS is evolutionarily related to the shikimate pathway enzyme 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (DAH7PS), which catalyses a similar condensation reaction between PEP and the four-carbon sugar D-erythrose 4-phosphate (E4P), in the first step of the shikimate pathway to aromatic compounds in plants and microorganisms. As well as being a one-carbon shorter substrate, E4P has the opposite C2-OH configuration to A5P. While there are both metal-dependent and metal-independent forms of KDO8PS, in contrast, all DAH7PS are metal-dependent enzymes.
Little is understood about the key sequence features that distinguish KDO8PS and DAH7PS. These features, particularly those that contribute to A5P or E4P binding, are thought to be responsible for the differences in substrate specificity between the two enzymes. This thesis describes the functional and structural studies of KDO8PS mutants to examine the roles of these residues, using the metal-dependent KDO8PS from Acidithiobacillus ferrooxidans and the metal-independent KDO8PS from Neisseria meningitidis.
In Chapter 2 an extensive KDO8PS and DAH7PS sequence analysis is presented. The results, which identify sequence conservation in both enzymes, are discussed in the context of the (β/α)8 TIM-barrel structure. Some of the differences in conservation between the two enzymes were highlighted as being obvious in having a role or contributing to the different substrate selection preferences of the two enzymes, such as an extended β7α7 loop in KDO8PS, and motif differences on the β2α2 and β4α4 loops. A similar analysis was also used to compare metal-dependent and metal-independent KDO8PSs, and it was found the two forms differ in the conservation of only three residues.
Chapter 3 describes the characterisation of A. ferrooxidans KDO8PS (AfeKDO8PS) and investigates aspects of metal dependency in KDO8PS. The enzyme was found to be metal dependent, and like all other KDO8PS enzymes, to possess a tetrameric quaternary structure, and display tight substrate specificity. The β8α8 loop was found to have a critical role in binding and positioning the substrates, and AfeKDO8PS could not be engineered to be a metal-independent enzyme.
The role of the KDO8PS-conserved KANRS motif, present on the β2α2 loop and one of the main contributors to the A5P binding site, is probed in Chapter 4. Individual residues of the motif were mutated to investigate function, and the motif was converted to the equivalent motif found in DAH7PS (KPRS). It was found that the Lys plays a critical role in enzymatic catalysis, and is likely intimately involved in the enzyme mechanism. The Asn residue of the motif in KDO8PS was found to be an important contributor to KDO8PS stereospecificity.
The work described in Chapter 5 investigates the role of the β7α7 loop in KDO8PS. This long active-site loop, which exists in a shorter version in DAH7PS, was found not to be essential for catalysis in KDO8PS, but was necessary for efficient catalysis. The two conserved residues on the loop provide interactions to A5P, but the presence of the extended loop as a whole was found to be most important for catalytic efficiency.
In Chapter 6 a conserved residue on the re face of PEP is investigated. In KDO8PS the residue is conserved as Asp, and in DAH7PS the same residue is conserved as a Glu. Mutational analysis found that in KDO8PS the Asp residue appears to be important for enzyme activity but unimportant for PEP binding. Mutating this Asp in KDO8PS to Glu was accommodated by KDO8PS, but it was found its introduction could potentially be optimised by coupling the change with mutation to other conserved differences.
In KDO8PS, one of the interfaces between adjacent subunits in the tetrameric structure is partially composed of a conserved sequence motif, PAFLxR. In Chapter 7, the roles of the residues in this motif are explored. The Arg of the motif was found to be important for A5P binding. The equivalent (and also conserved) motif in DAH7PS is GARNxQ, and mutation of residues in the KDO8PS motif to the equivalent residues in DAH7PS was tolerated by KDO8PS, but negatively impacted upon the enzyme kinetic parameters. The sequence features investigated in the other chapters were combined with those to the subunit interface to create a DAH7PS-like protein. This extensively engineered protein lost all KDO8PS activity, but nor did it gain DAH7PS activity.
Lastly, in Chapter 8 the results from all chapters are reviewed and ideas are discussed for advancing the research presented in this thesis.