Crystal structures of cyanobacterial light-dependent protochlorophyllide oxidoreductase

Dong, Chen-Song; Zhang, Wei-Lun; Wang, Qiao; Li, Yushuai; Wang, Xiao; Zhang, Min; Liu, Lin

doi:10.1073/pnas.1920244117

Cited by 30 publications

(64 citation statements)

References 61 publications

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“…However, in the absence of crystal structures, the authors presented a model of the structural change involving rigidification of a C‐terminal extension of the protein. A recent crystal structure of POR suggests that the lid regions formed an interface between two POR monomers, although it is not clear if this was an artefact of the crystallisation process [27]. The studies described here support the idea that Pchlide binding leads to a more rigid protein.…”

Section: Discussionsupporting

confidence: 60%

“…We have shown that two lid regions located in the distal region of the active site are important for oligomerisation and photocatalysis. These lid regions are inherently flexible and adopt multiple conformations in the absence of substrate [26,27]. This mobility in the apo-enzyme likely disfavours interaction with lid regions of other POR monomers.…”

Section: Discussionmentioning

confidence: 99%

“…Although several residues important to photocatalysis are known [23][24][25], a structural basis for POR photocatalysis has emerged only recently. Crystal structures of cyanobacterial POR as the apo-enzyme and a NADPH-bound complex are known [26,27]. A crystal structure of the ternary complex is not yet available, which has been attributed to the oligomerisation of POR when Pchlide is bound.…”

Section: Introductionmentioning

confidence: 99%

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Dual role of the active site ‘lid’ regions of protochlorophyllide oxidoreductase in photocatalysis and plant development

et al. 2020

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Protochlorophyllide oxidoreductase (POR) catalyses reduction of protochlorophyllide (Pchlide) to chlorophyllide, a light-dependent reaction of chlorophyll biosynthesis. POR is also important in plant development as it is the main constituent of prolamellar bodies in etioplast membranes. Prolamellar bodies are highly organised, paracrystalline structures comprising aggregated oligomeric structures of POR-Pchlide-NADPH complexes. How these oligomeric structures are formed and the role of Pchlide in oligomerisation remains unclear. POR crystal structures highlight two peptide regions that form a 'lid' to the active site, and undergo conformational change on binding Pchlide. Here, we show that Pchlide binding triggers formation of large oligomers of POR using size exclusion chromatography. A POR 'octamer' has been isolated and its structure investigated by cryoelectron microscopy at 7.7Å resolution. This structure shows that oligomer formation is most likely driven by the interaction of amino acid residues in the highly conserved lid regions. Computational modelling indicates that Pchlide binding stabilises exposure of hydrophobic surfaces formed by the lid regions, which supports POR dimerisation and ultimately oligomer formation. Studies with variant PORs demonstrate that lid residues are involved in substrate binding and photocatalysis. These highly conserved lid regions therefore have a dual function. The lid residues position Pchlide optimally to enable photocatalysis. Following Pchlide binding, they also enable POR oligomerisationa process that is reversed through subsequent photocatalysis in the early stages of chloroplast development.

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Section: Discussionsupporting

confidence: 60%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Dual role of the active site ‘lid’ regions of protochlorophyllide oxidoreductase in photocatalysis and plant development

et al. 2020

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“…To understand the effect of Pchlide and MGDG binding on LPOR, we compared our structure to the Pchlide-free, NADPH-bound cyanobacterial LPORs 6,14 (Fig. 3d, Fig.…”

Section: Pchlide Induces Atporb Conformational Changes That Promote Imentioning

confidence: 99%

Photocatalytic plant LPOR forms helical lattices that shape membranes for chlorophyll synthesis

Nguyen

Melo

Kruk

et al. 2020

Preprint

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Chlorophyll (Chl) biosynthesis, crucial to life on Earth, is tightly regulated because its precursors are phototoxic. In flowering plants, the enzyme Light-dependent Protochlorophyllide OxidoReductase (LPOR) captures photons to catalyze the penultimate reaction: the reduction of a double-bond within protochlorophyllide (Pchlide) to generate chlorophyllide (Chlide). In darkness, LPOR oligomerizes to facilitate photon energy transfer and catalysis. However, the complete 3D structure of LPOR, the higher-order architecture of LPOR oligomers, and the implications of these self-assembled states for catalysis, including how LPOR positions Pchlide and the cofactor NADPH, remain unknown. Here we report the atomic structure of LPOR assemblies by electron cryo-microscopy (cryoEM). LPOR polymerizes with its substrates into helical filaments around constricted lipid bilayer tubes. Portions of LPOR and Pchlide insert into the outer membrane leaflet, targeting the product, Chlide, to the membrane for the final reaction site of chlorophyll biosynthesis. In addition to its crucial photocatalytic role, we show that in darkness LPOR filaments directly shape membranes into high-curvature tubules with the spectral properties of the prolammelar body, whose light-triggered disassembly provides lipids for thylakoid assembly. Our structure of the catalytic site, moreover, challenges previously proposed reaction mechanisms. Together, our results reveal a new and unexpected synergy between photosynthetic membrane biogenesis and chlorophyll synthesis in plants orchestrated by LPOR.

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“…The catalytic YxxxK and the NADPH-bounding G-rich (GxxxGxG) motifs are conservative (Wilks and Timko, 1995 ; Schoefs and Franck, 2003 ; Gabruk and Mysliwa-Kurdziel, 2020 ). LPOR crystal structure remained unknown for a long time; the structures of two cyanobacterial LPOR enzymes have been published only recently (Zhang et al, 2019 ; Dong et al, 2020 ). In general, both structures are compatible with the homology models, however, due to slightly different protocols there were some differences between these two works.…”

Section: Lpor—an Enzyme Operating In Lipid Environmentmentioning

confidence: 99%

The Role of Membranes and Lipid-Protein Interactions in the Mg-Branch of Tetrapyrrole Biosynthesis

Solymosi

Myśliwa-Kurdziel

2021

Front. Plant Sci.

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Chlorophyll (Chl) is essential for photosynthesis and needs to be produced throughout the whole plant life, especially under changing light intensity and stress conditions which may result in the destruction and elimination of these pigments. All steps of the Mg-branch of tetrapyrrole biosynthesis leading to Chl formation are carried out by enzymes associated with plastid membranes. Still the significance of these protein-membrane and protein-lipid interactions in Chl synthesis and chloroplast differentiation are not very well-understood. In this review, we provide an overview on Chl biosynthesis in angiosperms with emphasis on its association with membranes and lipids. Moreover, the last steps of the pathway including the reduction of protochlorophyllide (Pchlide) to chlorophyllide (Chlide), the biosynthesis of the isoprenoid phytyl moiety and the esterification of Chlide are also summarized. The unique biochemical and photophysical properties of the light-dependent NADPH:protochlorophyllide oxidoreductase (LPOR) enzyme catalyzing Pchlide photoreduction and located to peculiar tubuloreticular prolamellar body (PLB) membranes of light-deprived tissues of angiosperms and to envelope membranes, as well as to thylakoids (especially grana margins) are also reviewed. Data about the factors influencing tubuloreticular membrane formation within cells, the spectroscopic properties and the in vitro reconstitution of the native LPOR enzyme complexes are also critically discussed.

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Crystal structures of cyanobacterial light-dependent protochlorophyllide oxidoreductase

Cited by 30 publications

References 61 publications

Dual role of the active site ‘lid’ regions of protochlorophyllide oxidoreductase in photocatalysis and plant development

Dual role of the active site ‘lid’ regions of protochlorophyllide oxidoreductase in photocatalysis and plant development

Photocatalytic plant LPOR forms helical lattices that shape membranes for chlorophyll synthesis

The Role of Membranes and Lipid-Protein Interactions in the Mg-Branch of Tetrapyrrole Biosynthesis

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