5MAC

Crystal structure of decameric Methanococcoides burtonii Rubisco complexed with 2-carboxyarabinitol bisphosphate

Summary for 5MAC

• Entry DOI: 10.2210/pdb5mac/pdb
• Descriptor: Ribulose-1,5-bisphosphate carboxylase-oxygenase type III, 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE, MAGNESIUM ION, ... (5 entities in total)
• Functional Keywords: lyase, archaea, rubisco, decamer
• Biological source: Methanococcoides burtonii
• Total number of polymer chains: 5
• Total formula weight: 266991.75

Authors

Gunn, L.H.,Valegard, K.,Andersson, I. (deposition date: 2016-11-03, release date: 2017-02-08, Last modification date: 2024-01-17)

Primary citation

Gunn, L.H.,Valegard, K.,Andersson, I.
A unique structural domain in Methanococcoides burtonii ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) acts as a small subunit mimic.
J. Biol. Chem., 292:6838-6850, 2017

PubMed Abstract: The catalytic inefficiencies of the CO-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 contains a Rubisco isoform that functions to scavenge the ribulose-1,5-bisphosphate (RuBP) by-product of purine/pyrimidine metabolism. The crystal structure of Rubisco (MbR) presented here at 2.6 Å resolution is composed of catalytic large subunits (LSu) assembled into pentamers of dimers, (L), and differs from Rubiscos from higher plants where LSus are glued together by small subunits (SSu) into hexadecameric LS 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 LS enzymes between LSus of adjacent L dimers, where negatively charged residues coordinate around a Mg 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 L dimers. MbR assembly is ligand-stimulated, and we show that only 6-carbon molecules with a particular stereochemistry at the C 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.

PubMed: 28154188
DOI: 10.1074/jbc.M116.767145

Experimental method

X-RAY DIFFRACTION (2.6 Å)