Difference between revisions of "Part:BBa K1465202"

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Revision as of 12:23, 19 October 2014

Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) from Halothiobacillus neapolitanus

The Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) from Halothiobacillus neapolitanus can bind CO₂ by catalyzing the reaction of ribulose 1,5-bisphosphate to 3-phosphoglycerate. The characterization of this part can be found here BBa_K1465213.

Usage and Biology

The Ribulose 1,5-bisphosphate carboxylase oxygenase (RuBisCO) is the most abundant enzyme in the world. Because of its key role in carbon fixation metabolism, it is found in nearly all autotrophic organisms like plants, but also in cyanobacteria and photosynthetic bacteria in high concentrations (Andersson, 2008). RuBisCO catalyses the fixation of atmospheric carbon dioxide by generating two tricarbohydrates out of one pentacarbohydrate. This reaction is part of the Calvin Cycle. It can be stated that the RuBisCO is responsible for conversion of carbon dioxide in biomass or with other words for incorporation of inorganic carbon dioxide to form organic molecules. To give some numbers, more than 10¹¹ tons of atmospheric carbon dioxide are fixated per year baesd on RuBisCO activity (Field et al., 1998).

Figure 1: Catalyzed reaction by the RuBisCO. Ribulose-1,5-bisphosphate and carbon dioxide are converted to two molecules of 3-phosphoglycerate.

RuBisCO catalyses the rate limiting step in the Calvin cycle. RuBisCO catalyses the fixation of one molecule carbon dioxide to ribulose-1,5-bisphosphate (RuBP), a pentacarbohydrate. The product is unstable and decays directly into two molecules of 3-D-phosphoglycerate (3-PGA)(Andersson, 2008; Parikh et al. 2006). The reaction is shown in Figure 1. 3-PGA is further converted in the Calvin cycle to glycerinaldehyde-3-phosphate. This is an essential intermediate in the central metabolism, as it plays a central role in glycolysis and gluconeogenesis.

Beside the carbon fixation reaction of RuBisCO, the enzyme catalyses numerous side reactions. An alternative substrate to carbon dioxide is atmospheric oxygen. When the oxygenation of RuBP is catalyzed instead of the carboxylation, the product is one molecule of 3-PGA and one molecule of 2-phosphoglycolate. 2-phosphoglycolate has only limited use for the metabolism of the cells and the fixed carbon has to be regenerated by a metabolic pathway called photorespiration, a high energy consuming pathway. In photorespiration, two molecules of 2-phosphoglycolate are split up into one molecule of 3-PGA and one molecule of carbon dioxide. 3-PGA can enter the Calvin cycle, whereas CO₂ is a molecule with a low energy content. Because of the oxygenation side reaction the efficiency of the carbon dioxide fixation rate of RuBisCO is reduced about 20 - 50 % (Andersson, 2008; Mann, 1999).
The carboxylation/ oxygenation of RuBP catalyzed by RuBisCO is a multiple step reaction. In detail, the first step is activation of the RuBisCO by carbamylation of the amino group of a lysine in the active centre. The activated RuBisCO is then stabilized by magnesium ions, a cofactor for enzyme activity. In the carboxylation/ oxygenation of Ribulose-1,5-bisphosphate the first step is enolisation of the substrate and enol-RuBP is build up. The enediolate reacts then in an irreversible reaction with either carbon dioxide or oxygen. This reaction determines the specificity and the rate of carbon dioxide fixation as well as the efficiency. If carbon dioxide is bound to the enediolate, the unstable intermediate is protonated and hydrated to build up two molecules of 3-PGA. If oxygen is bound to the enediolate, the intermediate decomposes directly in 3-phosphoglycerate and 2-phosphoglycolate. (Andersson, 2008; Spreitzer, Salvucci 2002)
The competing reaction between CO₂ and O₂ and the resulting oxygenation side reaction limits the efficiency of RuBisCO. The efficiency is often quantified by a specificity factor. This is the ratio of the catalytic efficiency of carboxylation to oxygenation, described by the maximal velocities of carboxylation and oxygenation, and the Michaelis-Menten constants for carbon dioxide and oxygen. (Andersson, 2008; Jordan, Ogren 1981; Spreitzer, Salvucci 2002) The specificity factors of various RuBisCO enzymes differ significantly depending on the host organism of the RuBisCO. Bacteria have low specificity factors in comparison to higher plants or algae. As there exist an inverse correlation between turnover rate (for carboxylation) and specificity factor, Bacteria have low specificity factors, but high turnover rates. Higher organism are characterized by high specificity factors and low turnover rates. (Andersson, 2008; Jordan, Ogren 1981)
RuBisCO is a multiprotein enzyme, which consists of two types of subunits, the large (L) subunit (50-55 kDa) and the small (S) subunit (12-18 kDa). The most common form of RuBisCO (form I or form IA) consists of eight large subunits, which form dimers, and eight small subunits. Together they form a hexadimeric structure. Form I occurs in most autotrophic bacteria, algae and higher plants. The large subunit is the catalytic one, and the small subunit is not essential for catalysis. The octamer of the large subunit still remains its carboxylation activity. RuBisCO form II or form IB is found in some chemoautotrophic bacteria and in dinoflagellates. This form is characterized by the abscence of the small subunits. (Andersson, 2008; Spreitzer, Salvucci 2002)

'Sequence and Features'