Enzyme molecular choreography : studies on soluble inorganic pyrophosphatases

Inorganic pyrophosphatases (PPases, EC 3.6.1.1) hydrolyse pyrophosphate in a reaction that provides the thermodynamic 'push' for many reactions in the cell, including DNA and protein synthesis. Soluble PPases can be classified into two families that differ completely in both sequence and structure. While Family I PPases are found in all kingdoms, family II PPases occur only in certain prokaryotes. The enzyme from baker's yeast (Saccharomyces cerevisiae) is very well characterised both kinetically and structurally, but the exact mechanism has remained elusive. The enzyme uses divalent cations as cofactors; in vivo the metal is magnesium. Two metals are permanently bound to the enzyme, while two come with the substrate. The reaction cycle involves the activation of the nucleophilic oxygen and allows different pathways for product release. In this thesis I have solved the crystal structures of wild type yeast PPase and seven active site variants in the presence of the native cofactor magnesium. These structures explain the effects of the mutations and have allowed me to describe each intermediate along the catalytic pathway with a structure. Although establishing the ʻchoreographyʼ of the heavy atoms is an important step in understanding the mechanism, hydrogen atoms are crucial for the mechanism. The most unambiguous method to determine the positions of these hydrogen atoms is neutron crystallography. In order to determine the neutron structure of yeast PPase I perdeuterated the enzyme and grew large crystals of it. Since the crystals were not stable at ambient temperature, a cooling device was developed to allow neutron data collection. In order to investigate the structural changes during the reaction in real time by time-resolved crystallography a photolysable substrate precursor is needed. I synthesised a candidate molecule and characterised its photolysis kinetics, but unfortunately it is hydrolysed by both yeast and Thermotoga maritima PPases. The mechanism of Family II PPases is subtly different from Family I. The native metal cofactor is manganese instead of magnesium, but the metal activation is more complex because the metal ions that arrive with the substrate are magnesium different from those permanently bound to the enzyme. I determined the crystal structures of wild type Bacillus subtilis PPase with the inhibitor imidodiphosphate and an inactive H98Q variant with the substrate pyrophosphate. These structures revealed a new trimetal site that activates the nucleophile. I also determined that the metal ion sites were partially occupied by manganese and iron using anomalous X- ray scattering.

Regio- and stereoselectivity of oxidative coupling reactions of phenols : Spirodienones as construction units in lignin

Dimeric phenolic compounds lignans and dilignols form in the so-called oxidative coupling reaction of phenols. Enzymes such as peroxidases and lac-cases catalyze the reaction using hydrogen peroxide or oxygen respectively as oxidant generating phenoxy radicals which couple together according to certain rules. In this thesis, the effects of the structures of starting materials mono-lignols and the effects of reaction conditions such as pH and solvent system on this coupling mechanism and on its regio- and stereoselectivity have been studied. After the primary coupling of two phenoxy radicals a very reactive quinone me-thide intermediate is formed. This intermediate reacts quickly with a suitable nucleophile which can be, for example, an intramolecular hydroxyl group or another nucleophile such as water, methanol, or a phenolic compound in the reaction system. This reaction is catalyzed by acids. After the nucleophilic addi-tion to the quinone methide, other hydrolytic reactions, rearrangements, and elimination reactions occur leading finally to stable dimeric structures called lignans or dilignols. Similar reactions occur also in the so-called lignification process when monolignol (or dilignol) reacts with the growing lignin polymer. New kinds of structures have been observed in this thesis. The dimeric com-pounds with so-called spirodienone structure have been observed to form both in the dehydrodimerization of methyl sinapate and in the beta-1-type cross-coupling reaction of two different monolignols. This beta-1-type dilignol with a spirodienone structure was the first synthetized and published dilignol model compound, and at present, it has been observed to exist as a fundamental construction unit in lignins. The enantioselectivity of the oxidative coupling reaction was also studied for obtaining enantiopure lignans and dilignols. A rather good enantioselectivity was obtained in the oxidative coupling reaction of two monolignols with chiral auxiliary substituents using peroxidase/H2O2 as an oxidation system. This observation was published as one of the first enantioselective oxidative coupling reaction of phenols. Pure enantiomers of lignans were also obtained by using chiral cryogenic chromatography as a chiral resolution technique. This technique was shown to be an alternative route to prepare enantiopure lignans or lignin model compounds in a preparative scale.