Enzyme activation and catalysis: characterisation of the vibrational modes of substrate and product in protochlorophyllide oxidoreductase

Ternary Complex Formation and Photoactivation of a Photoenzyme Results in Altered Protein Dynamics

The interplay between protein dynamics and catalysis remains a fundamental question in enzymology. We here investigate the ns-timescale dynamics of a light-dependent NADPH:protochlorophyllide oxidoreductase (LPOR), a photoenzyme crucial for chlorophyll synthesis. LPORs catalyze the light-triggered trans addition of a hydride and a proton across the C17═C18 double bond of the chlorophyll precursor protochlorophyllide (Pchlide). Because of the lack of an LPOR structure, the global structural and dynamic consequences of LPOR/Pchlide/NADPH ternary complex formation remain elusive. Moreover, photoactivation of LPORs by low-light preillumination is controversially discussed as unequivocal proof for this phenomenon is lacking. By employing quasielastic neutron spectroscopy (QENS), we show that the formation of the ternary holoprotein complex as well as photoactivation lead to progressive rigidification of the protein. These findings are supported by thermostability measurements, which reveal different melting behavior and thermostabilities for the apo- and holoprotein ternary complexes. Molecular dynamics simulations in good agreement with the experimental QENS results suggest that the increased flexibility observed for the apoprotein stems from structural fluctuations of the NADPH and Pchlide substrate binding sites of the enzyme. On the basis of our results, in conjunction with activity and stability measurements, we provide independent proof for LPOR photoactivation, defined as a process that modifies the protein structure and dynamics, resulting in an increased substrate turnover. Our findings advance the structural and dynamic understanding of LPORs and provide a first link between protein dynamics and catalysis for this enzyme class.

Theoretical Model of the Protochlorophyllide Oxidoreductase from a Hierarchy of Protocols

The enzyme protochlorophyllide oxidoreductase (LPOR) catalyzes the light-driven reduction of protochlorophyllide (Pchlide), a crucial step in chlorophyll biosynthesis. Molecular understanding of the photocatalytic mechanism of LPOR is essential for harnessing light energy to mediate enzymatic reactions. The absence of X-ray crystal structure has promoted the development of LPOR homology models that lack a catalytically competent active site and could not explain the variously reported spectroscopic evidence, including time-resolved optical spectroscopy data. We have refined previous structural models to account for the catalytic active site and the characteristic experimental spectral features of Pchlide binding, including the 26 cm^-1 red shift of the C₁₃₍₁₎ carbonyl stretch vibration in the mid-infrared (IR) and the 12 nm red shift of the Q _x electronic band. A hierarchy of theoretical methods, including homology modeling, molecular dynamics simulations, hybrid quantum mechanics [(TD-)DFT]/molecular mechanics [AMBER] calculations, and computational vibrational and electronic spectroscopies, have been combined in an iterative protocol to reproduce experimental evidence and to predict ultrafast transient IR spectroscopic fingerprints associated with the catalytic process. The successful application to the LPOR enzyme indicates that the presented hierarchical protocol provides a general workflow to protein structure refinement.

MGDG, PG and SQDG regulate the activity of light-dependent protochlorophyllide oxidoreductase

Light-dependent protochlorophyllide oxidoreductase (POR) is a plant enzyme involved in the chlorophyll biosynthesis pathway. POR reduces one of the double bonds of the protochlorophyllide (Pchlide) using NADPH and light. In the present study, we found out that phosphatidylglycerol and sulfoquinovosyl diacylglycerol are allosteric regulators of the nucleotide binding, which increase the affinity towards NADPH a 100-fold. Moreover, we showed for the first time that NADH can, like NADPH, form active complexes with Pchlide and POR, however, at much higher concentrations. Additionally, monogalactosyldiacylglycerol (MGDG) was shown to be the main factor responsible for the red shift of the fluorescence emission maximum of Pchlide:POR:NADPH complexes. Importantly, the emission maximum at 654 nm was obtained only for the reaction mixtures supplemented with MGDG and at least one of the negatively charged plant lipids. Moreover, the site-directed mutagenesis allowed us to identify amino acid residues that may be responsible for lipid binding and Pchlide coordination. Our experiments allowed us to identify six different Pchlide:POR complexes that differ in the fluorescence emission maxima of the pigment. The results presented here reveal the contribution of thylakoid lipids in the regulation of the chlorophyll biosynthesis pathway; however, the molecular mechanisms of this process are to be clarified.

Light-Dependent Protochlorophyllide Oxidoreductase: Phylogeny, Regulation, and Catalytic Properties

This Current Topic focuses on light-dependent protochlorophyllide oxidoreductase (POR, EC 1.3.1.33). POR catalyzes the penultimate reaction of chlorophyll biosynthesis, i.e., the light-triggered reduction of protochlorophyllide to chlorophyllide. In this reaction, the chlorin ring of the chlorophyll molecule is formed, which is crucial for photosynthesis. POR is one of very few enzymes that are driven by light; however, it is unique in the need for its substrate to absorb photons to induce the conformational changes in the enzyme, which are required for its catalytic activation. Moreover, the enzyme is also involved in the negative feedback of the chlorophyll biosynthesis pathway and controls chlorophyll content via its light-dependent activity. Even though it has been almost 70 years since the first isolation of active POR complexes, our knowledge of them has markedly advanced in recent years. In this review, we summarize the current state of knowledge of POR, including the phylogenetic roots of POR, the mechanisms of the regulation of POR genes expression, the regulation of POR activity, the import of POR into plastids, the role of POR in PLB formation, and the molecular mechanism of protochlorophyllide reduction by POR. To the best of our knowledge, no previous review has compiled such a broad set of recent findings about POR.