Structure and function of para-hydroxybenzoate hydroxylase

Abstract

Enzymes which utilize molecular oxygen to either hydroxylate or cleave an aromatic ring are known as monooxygenases and dioxygenases, respectively. These enzymes contain a non-protein group such as heme, flavin, pterin or a transition metal ion in their active site, for oxygen activation. In his thesis work, Frank van der Bolt has studied the mode of action of para -hydroxybenzoate hydroxylase (PHBH), a flavoprotein monooxygenase involved in the mineralization of aromatic compounds in soil microorganisms. These organic molecules may originate from environmental pollution but also from natural sources since they are liberated during the biodegradation of lignin, one of the principal components of wood. Thus, understanding the action of flavoprotein monooxygenases is of importance for the so-called process of agrification, including the development of processes that enable the use of agro materials as sources for energy and industrial productions. PHBH has become a model enzyme for oxygen activation since its crystal structure and catalytic mechanism are known in considerable detail. In his PhD study, Frank has addressed the structure-function relationship of PHBH by protein engineering. This research was supported financially by the Dutch Organization for Scientific Research (NWO-CW) and has been carried out within the Dutch Research School Environmental Chemistry and Toxicology (M&T).During his research, Frank has made several interesting observations which have led to a better understanding of the action of flavoprotein monooxygenases. The first finding was that one specific cysteine residue in PHBH is responsible for the mercury poisoning of the enzyme, preventing the aromatic substrate of gaining access to the active site. An important other finding was that PHBH activates the aromatic substrate through an elongated network of hydrogen bonds. This hydrogen bonding network is not only essential for efficient catalysis but is also important for the substrate specificity. By changing one of the tyrosine residues in the active site, Frank managed to abolish the regiospecific binding of the aromatic product 3,4-dihydroxybenzoate (protocatechuate). As a result, this compound is further converted by the PHBH mutant protein to the anti-oxidant 3,4,5-trihydroxybenzoate (gallic acid). Elaborating on the broadening of the substrate specificity, Frank showed that it is possible to modify PHBH by protein engineering into an efficient dehalogenase (a detoxificating enzyme).Until recently it was assumed that prosthetic groups (like flavin) in proteins are rigidly bound. However, Frank and his colleagues showed that the flavin molecule in PHBH is mobile and swings in and out of the active site. This mobility of the flavin provides an entrance for the substrate to enter the active site and an exit for the product to leave. Flavin movement most probably is also important for the reaction with NADPH. The latter compound is an essential helper molecule (coenzyme), which visits the enzyme just for a moment to perform its task.In conclusion, this thesis work shows that PHBH is highly optimized for its function by evolution. This optimization includes all residues involved in substrate binding and dynamic movement of the flavin ring. Flavin motion opens the active site cavity to allow substrate binding and product release. The mobility of the flavin is also required for the efficient reduction of the enzyme by NADPH. Following reduction, the flavin swings back into the active site pocket in order to shield the hydroxylation site from solvent. This closure of the active site stabilizes the flavin-hydroperoxide oxygenation species which becomes optimally oriented to allow efficient substrate attack. Substrate burying is a recurrent property of flavoenzymes with a PHBH fold. In cholesterol oxidase, glucose oxidase and D-amino acid oxidase, the embedding of substrates is achieved by movement of an active site lid. The recently determined crystal structure of phenol hydroxylase from yeast suggests that flavin movement might be a common feature of flavoprotein aromatic hydroxylases