A unique structural domain inMethanococcoides burtoniiribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) acts as a small subunit mimic.
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 archaeonMethanococcoides burtoniicontains a Rubisco isoform that functions to scavenge the ribulose-1,5-bisphosphate (RuBP) by-product of purine/pyrimidine metabolism. The crystal structure ofM. burtoniiRubisco (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 L8S8enzymes. 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 L8S8enzymes between LSus of adjacent L2dimers, 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 L2dimers. MbR assembly is ligand-stimulated, and we show that only 6-carbon molecules with a particular stereochemistry at the C3carbon 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.
From the Department of Cell and Molecular Biology, Uppsala University, S-751 24 Uppsala, Sweden laura.gunn@icm.uu.se.
Laura H
0000-0003-2072-0884
LH
Gunn
From the Department of Cell and Molecular Biology, Uppsala University, S-751 24 Uppsala, Sweden.
Karin
0000-0002-8642-9259
K
Valegård
From the Department of Cell and Molecular Biology, Uppsala University, S-751 24 Uppsala, Sweden.
Inger
0000-0002-2729-0787
I
Andersson
D002244:Carbon / Q000737:chemistry; D020134:Catalytic Domain; D003001:Cloning, Molecular; D018360:Crystallography, X-Ray; D004926:Escherichia coli / Q000378:metabolism; D008024:Ligands; D017019:Methanosarcinaceae / Q000201:enzymology*; D016297:Mutagenesis, Site-Directed; D010429:Pentoses / Q000737:chemistry; D010802:Phylogeny; D000072417:Protein Domains; D017510:Protein Folding; D055503:Protein Multimerization; D012273:Ribulose-Bisphosphate Carboxylase / Q000737:chemistry* / Q000378:metabolism; D012274:Ribulosephosphates / Q000737:chemistry*; D018724:Spinacia oleracea / Q000201:enzymology; D055672:Static Electricity; D013237:Stereoisomerism; D014961:X-Ray Diffraction
D008024:Ligands; D010429:Pentoses; D012274:Ribulosephosphates; C001933:ribulose-1,5 diphosphate; C100182:ribulose; D002244:Carbon; D012273:Ribulose-Bisphosphate Carboxylase
X-ray crystallography; archaea; carbon fixation; metal ion-protein interaction; oligomerization; protein evolution; ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco); structure-function