A Common Structural Basis for the Inhibition of Ribulose 1,5-Bisphosphate Carboxylase by 4-Carboxyarabinitol 1,5-Bisphosphate and Xylulose 1,5-Bisphosphate

Taylor, Thomas C.; Fothergill, Michael; Andersson, Inger

doi:10.1074/jbc.271.51.32894

Cited by 33 publications

(21 citation statements)

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“…4 A ); 4-CABP is a close mimic of the reaction intermediate 2-carboxy-3-keto- d -arabinitol 1,5-bisphosphate, and XuBP is a misfire product of RuBP that is formed at carbamylated catalytic sites on Rubisco (25). Both XuBP and 4-CABP de-carbamylate the activator lysine in Rubisco during or after binding to the active site in the spinach enzyme (25, 26). Given their stereochemistry, the presence of these sugar compounds at the Rubisco active site precludes the presence of a metal ion (26).…”

Section: Resultsmentioning

confidence: 99%

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

Gunn

Valegård

Andersson

2017

Journal of Biological Chemistry

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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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Section: Resultsmentioning

confidence: 99%

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

Gunn

Valegård

Andersson

2017

Journal of Biological Chemistry

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“…Throughout the paper, the numbering of Rubisco large subunit residues is based on the spinach sequence. Rubisco structural data files for spinach 1RBO [37] and 1RCX [38] were obtained from the RCSB Protein Data Bank [39]. The locations and properties of individual amino acids in the Rubisco structure were analyzed using DeepView – Swiss-PdbViewer v.3.7 [40].…”

Section: Methodsmentioning

confidence: 99%

Widespread positive selection in the photosynthetic Rubisco enzyme

2007

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Background: Rubisco enzyme catalyzes the first step in net photosynthetic CO 2 assimilation and photorespiratory carbon oxidation and is responsible for almost all carbon fixation on Earth. The large subunit of Rubisco is encoded by the chloroplast rbcL gene, which is widely used for reconstruction of plant phylogenies due to its conservative nature. Plant systematicists have mainly used rbcL paying little attention to its function, and the question whether it evolves under Darwinian selection has received little attention. The purpose of our study was to evaluate how common is positive selection in Rubisco among the phototrophs and where in the Rubisco structure does positive selection occur.

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“…Complexes with ligands that bind less tightly, such as the natural substrate RuBP or the product 3-phosphoglycerate, or mimics thereof, have turned out to be more difficult to crystallise. Only in a few cases has it been possible to capture these complexes in the crystal [58,59,72,107,108,110]. To obtain a stable complex with RuBP, Ca 2þ was used instead of Mg 2þ [107], because the former ion does not support turnover to an appreciable extent [77].…”

Section: The Active Sitementioning

confidence: 99%

Structure and function of Rubisco

Andersson¹,

Backlund²

2008

Plant Physiology and Biochemistry

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A Common Structural Basis for the Inhibition of Ribulose 1,5-Bisphosphate Carboxylase by 4-Carboxyarabinitol 1,5-Bisphosphate and Xylulose 1,5-Bisphosphate

Abstract: The first step in the assimilation of atmospheric CO 2 into biomass, carboxylation of D-ribulose 1,5-bisphosphate (RuBP)

Cited by 33 publications

References 28 publications

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

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

Widespread positive selection in the photosynthetic Rubisco enzyme

Structure and function of Rubisco

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