Cytochrome P450 biodiversity and biotechnology

Point Mutations at a Key Site Alter the Cytochrome P450 OleP Structural Dynamics

Substrate binding to the cytochrome P450 OleP is coupled to a large open-to-closed transition that remodels the active site, minimizing its exposure to the external solvent. When the aglycone substrate binds, a small empty cavity is formed between the I and G helices, the BC loop, and the substrate itself, where solvent molecules accumulate mediating substrate-enzyme interactions. Herein, we analyzed the role of this cavity in substrate binding to OleP by producing three mutants (E89Y, G92W, and S240Y) to decrease its volume. The crystal structures of the OleP mutants in the closed state bound to the aglycone 6DEB showed that G92W and S240Y occupied the cavity, providing additional contact points with the substrate. Conversely, mutation E89Y induces a flipped-out conformation of this amino acid side chain, that points towards the bulk, increasing the empty volume. Equilibrium titrations and molecular dynamic simulations indicate that the presence of a bulky residue within the cavity impacts the binding properties of the enzyme, perturbing the conformational space explored by the complexes. Our data highlight the relevance of this region in OleP substrate binding and suggest that it represents a key substrate-protein contact site to consider in the perspective of redirecting its activity towards alternative compounds.

Dissecting the Cytochrome P450 OleP Substrate Specificity: Evidence for a Preferential Substrate

The cytochrome P450 OleP catalyzes the epoxidation of aliphatic carbons on both the aglycone 8.8a-deoxyoleandolide (DEO) and the monoglycosylated L-olivosyl-8.8a-deoxyoleandolide (L-O-DEO) intermediates of oleandomycin biosynthesis. We investigated the substrate versatility of the enzyme. X-ray and equilibrium binding data show that the aglycone DEO loosely fits the OleP active site, triggering the closure that prepares it for catalysis only on a minor population of enzyme. The open-to-closed state transition allows solvent molecules to accumulate in a cavity that forms upon closure, mediating protein–substrate interactions. In silico docking of the monoglycosylated L-O-DEO in the closed OleP–DEO structure shows that the L-olivosyl moiety can be hosted in the same cavity, replacing solvent molecules and directly contacting structural elements involved in the transition. X-ray structures of aglycone-bound OleP in the presence of L-rhamnose confirm the cavity as a potential site for sugar binding. All considered, we propose L-O-DEO as the optimal substrate of OleP, the L-olivosyl moiety possibly representing the molecular wedge that triggers a more efficient structural response upon substrate binding, favoring and stabilizing the enzyme closure before catalysis. OleP substrate versatility is supported by structural solvent molecules that compensate for the absence of a glycosyl unit when the aglycone is bound.

Novel traits of Trichoderma predicted through the analysis of its secretome

Mycotrophic species of Trichoderma are among the most common fungi isolated from free soil, dead wood and as parasites on sporocarps of other fungi (mycoparasites). In addition, they undergo various other biotrophic associations ranging from rhizosphere colonization and endophytism up to facultative pathogenesis on such animals as roundworms and humans. Together with occurrence on a variety of less common substrata (marine invertebrates, artificial materials, indoor habitats), these lifestyles illustrate a wealthy opportunistic potential of the fungus. One tropical species, Trichoderma reesei, has become a prominent producer of cellulases and hemicellulases, whereas several other species are applied in agriculture for the biological control of phytopathogenic fungi. The sequencing of the complete genomes of the three species (T. reesei, T. virens, and T. atroviride) has led to a deepened understanding of Trichoderma lifestyle and its molecular physiology. In this review, we present the in silico predicted secretome of Trichoderma, and – in addition to the unique features of carbohydrate active enzymes – demonstrate the importance of such protein families as proteases, oxidative enzymes, and small cysteine-rich proteins, all of that received little attention in Trichoderma genetics so far. We also discuss the link between Trichoderma secretome and biology of the fungus.

Engineering and assaying of cytochrome P450 biocatalysts

Cytochrome P450s constitute a highly fascinating superfamily of enzymes which catalyze a broad range of reactions. They are essential for drug metabolism and promise industrial applications in biotechnology and biosensing. The constant search for cytochrome P450 enzymes with enhanced catalytic performances has generated a large body of research. This review will concentrate on two key aspects related to the identification and improvement of cytochrome P450 biocatalysts, namely the engineering and assaying of these enzymes. To this end, recent advances in cytochrome P450 development are reported and commonly used screening methods are surveyed.