Reaction mechanism of hOMPD and CaAAD at atomic resolution

by Sören Rindfleisch
Doctoral thesis
Date of Examination:2019-02-07
Date of issue:2019-12-12
Advisor:Prof. Dr. Kai Tittmann
Referee:Prof. Dr. Kai Tittmann
Referee:Prof. Dr. Holger Stark
Referee:Prof. Dr. Ricardo Mata
Referee:Prof. Dr. Simone Techert
Referee:Dr. Fabian Commichau
Referee:Prof. Dr. Ulf Diederichsen
Persistent Address: http://dx.doi.org/10.53846/goediss-7767

 

 

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Abstract

English

Decarboxylation reactions are fundamental processes in the chemistry of the animated world. Thus, the evolution of decarboxylases brought up a stunning array of diverse enzymes utilizing a variety of different mechanisms and/or co-factors to achieve the efficient removal of carboxylates. One outstanding example of a highly proficient decarboxylase is the orotidine 5’-monophosphate decarboxylase (OMPD) which catalyses the penultimate step in the pyrimidine biosynthesis pathway and functions as pure protein catalyst. The decarboxylation of orotic acid in neutral aqueous solution and ambient temperature has a half-life time of approx. 78 million years. However, the decarboxylation of orotidine 5’-monophosphate in the enzyme-substrate complex is achieved with several conversions per second. Based on the remarkable catalytic prowess of OMPD, it was termed “the most proficient enzyme” known. However, the precise reaction mechanism and the specific catalytic contributions are still under debate. One prominent proposal claims the destabilization of the substrate in the active site of the enzyme by the spatial proximity of the negative charge of an asparate of the protein and the carboxylate group of OMP. In order to test the so called “Circe Effect” in OMPD mediated catalysis, different substrate analogues were analysed applying X-ray cryo-crystallography. Additionally, the substitution of the catalytic lysine residue of the alternating charge network with acetyllysine enabled structural investigations of the enzyme-substrate complex. The structural data indicates the protonation of the substrate in the active site pocket and a productive interaction between OMP and the enzyme. Consequently, transition-state stabilization rather than ground-state destabilization accounts for the catalytic prowess of OMPD.
Keywords: Orotidine 5'-monophosphate decarboxylase; Acetoacetate decarboxylase; Catalysis; Decarboxylation; Transition-state stabilization; Ground-state destabilization
 
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