Structural studies on the biosynthesis and biological functions of natural products

Natural products are chemical compounds that are synthesized by living organisms and have biological and pharmacological functions. Many natural products or their derivatives have been successfully developed as pharmaceuticals and have thus made great contributions to human health. However, there is still an urgent need for novel and more potent pharmaceuticals, largely due to the rapidly increasing incidence of drug resistance. Natural products and their derivatives continue to be an important source for the development of new drugs. Critical steps in the investigation of natural products include the dissecting of the biosynthesis pathways of these compounds and elucidating the biological processes affected by these compounds. These studies would facilitate the production of potential drugs through biosynthesis or semi-biosynthesis, and provide valuable guidance in engineering these compounds towards improved efficacy. In this dissertation I present such studies on several natural products produced by bacteria and plants. Teicoplanin is a glycopeptide antibiotic produced by Actinoplanes teichomyceticus and has been shown to be potent against many vancomycin-resistant strains. Such improved efficacy is mainly attributed to two special tailoring modifications that are unique for teicoplanin-type glycopeptide antibiotics and are catalyzed by a P450 monooxygenase, Orf6*, and an acyltransferase, Orf11*, respectively. The structural characterization of these two enzymes presented in Chapter 2 provides insight into the substrate specificity of both enzymes. 4-coumarate-CoA and its derivatives represent the key branching point in the phenylpropanoid pathway in plants. They are the precursors to many molecules that are important either pharmaceutically or for plant development. Studies on 4-coumarate:CoA ligase (4CL), the enzyme that synthesizes 4-coumarate-CoA, are thus crucial for plant engineering and drug discovery. In Chapter 3, I present thorough biochemical and structural studies on a tobacco 4CL enzyme, and a successful example of engineering this enzyme. Bis-(3’-5’) cyclic dimeric guanosine monophosphate (c-di-GMP) is a second messenger molecule that plays a vital role in the global regulation in bacteria. By binding to different effectors, it triggers diverse responses that confer adaptability to various environmental conditions. In the last chapter of this dissertation I present the structural characterization of a novel c-di-GMP effector PelD from Pseudomonas aeruginosa that is critical for the formation of pellicles. The PelD structures shown here reveal an unprecedented binding mode for c-di-GMP