A unique structural domain in Methanococcoides burtonii ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) acts as a small subunit mimic

Abstract

The catalytic inefficiencies of the CO2-fixing enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) often limit plant productivity. Strategies to engineer more efficient plant Rubiscos have been hampered by evolutionary constraints, prompting interest in Rubisco isoforms from non-photosynthetic organisms. The methanogenic archaeon Methanococcoides burtonii contains a Rubisco isoform that functions to scavenge the ribulose-1,5-bisphosphate (RuBP) by-product of purine/pyrimidine metabolism. The crystal structure of M. burtonii Rubisco (MbR) presented here at 2.6 Å resolution is composed of catalytic large subunits (LSu) assembled into pentamers of dimers, (L2)5, and differs from Rubiscos from higher plants where LSus are glued together by small subunits (SSu) into hexadecameric L8S8 enzymes. MbR contains a unique 29-amino acid insertion near the C terminus, which folds as a separate domain in the structure. This domain, which is visualized for the first time in this study, is located in a similar position to SSus in L8S8 enzymes between LSus of adjacent L2 dimers, where negatively charged residues coordinate around a Mg2+ ion in a fashion that suggests this domain may be important for the assembly process. The Rubisco assembly domain is thus an inbuilt SSu mimic that concentrates L2 dimers. MbR assembly is ligand-stimulated, and we show that only 6-carbon molecules with a particular stereochemistry at the C3 carbon can induce oligomerization. Based on MbR structure, subunit arrangement, sequence, phylogenetic distribution, and function, MbR and a subset of Rubiscos from the Methanosarcinales order are proposed to belong to a new Rubisco subgroup, named form IIIB.

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“…It is known that Rubisco, SBPase and OEE1 proteins are related to the photosynthetic process. Rubisco is a vital enzyme associated with carbon fixation (Xu, Gifford & Chow, 1994) and its catalytic inefficiencies often limit plant productivity (Andersson, 2008;Gunn, Valegard & Andersson, 2017). SBPase has been shown to increase photosynthetic capacity and plant yield and it also promotes the growth of plants at the early growth stage (Ogawa et al, 2015).…”

A peptide adhesive molded by magnesium glues Rubisco's subunits together

“…However, Form III enzymes can function as substitutes for endogenous Rubiscos in photosynthetic bacteria (4), meaning that they offer alternative assemblies to explore Rubisco structure and function. Gunn et al (6) take advantage of this opportunity in their investigation of an archaeal Rubisco with an unusual insertion that defines a new self-association pathway and a new subtype of Rubisco sequences.…”

“…Based on sequence homology, the M. burtonii Rubisco had been classified as belonging to Form II, but it contains an unusual 29-residue sequence insertion into the TIM barrel fold of the LSU that deviates from this form. Gunn et al (6) use X-ray crystallography to show that this sequence adopts a helical structure flanked by two irregularly structured but well-ordered peptide segments. The domain, which the authors term the "Rubisco assembly domain" (RAD), forms a knob-like extension to the surface of each LSU.…”

“…(6) return to the classification of the M. burtonii Rubisco: their assessment of its sequence homology suggests it is intermediate between Forms II and III. However, based on both structure and function, Gunn et al(6) choose to group this protein with Form III Rubiscos, defining a new subclass named IIIB.…”

“…However, based on both structure and function, Gunn et al(6) choose to group this protein with Form III Rubiscos, defining a new subclass named IIIB.…”