Structures of the LPOR-Chlide Complexes Imply the Basis of Membrane Remodeling and a Photocatalytic Mechanism

Flowering plants rely on the photocatalytic enzyme light-dependent protochlorophyllide oxidoreductase (LPOR) to synthesize chlorophyllide (Chlide), a chlorophyll intermediate, and at the same time to remodel lipid membranes into the cubic phase required for chloroplast development. Yet neither the mechanism of this light-driven catalysis nor the structural basis of its membrane remodeling activity is well understood, largely due to the lack of high-resolution structural information. To address these questions, we analyzed Chlide:LPOR:NADPH oligomeric assemblies by cryo-electron microscopy. Eleven maps were obtained, enabling the reconstruction of nine distinct LPOR oligomer models. Most assemblies adopt helical or stacked-ring forms, whereas one displays a segmented string-of-dimers architecture, representing a previously unobserved structural organization. Strings of LPOR dimers induce distinct periodic deformations of the lipid bilayer that stabilize multiple complex architectures. These architectures are maintained by three different inter-string interfaces occurring in various combinations. The plasticity of these interactions suggest that the filaments are capable of twisting and sliding relative to each other. Our highest-resolution map (2.55 [A]) provided a detailed view of the pigment-binding site, revealing a water channel that connects the central magnesium ion of the pigment to the bulk solvent. Unexpectedly, the propionate group of the pigment protrudes out of the porphyrin plane and arches back toward NADPH, ideally positioned for hydride transfer. These structural insights allowed us to propose a novel reaction mechanism for LPOR photocatalysis. Together, our data highlight the critical role of Chlide:LPOR:NADPH complexes in delaying prolamellar body disassembly and point to their possible regulatory function in mature leaves.