RuBisCO
Figure 1. Charged domains [red(-), blue(+)] on RuBisCO allow it to assemble into tightly packed multi-meric complexes, maximizing the number of copies of this inefficient enzyme inside plant cells.
Gene code:	Entrez ID#: 3052726 (L chain)
Structure:	molecular structure
Recent publications:	evolution, regulation by phosphate

Ribulose-1,5-bisphosphate carboxylase/oxygenase, most commonly known by the shorter name RuBisCO, is an enzyme (EC 4.1.1.39) that is used in the Calvin cycle to catalyze the first major step of carbon fixation, a process by which the atoms of atmospheric carbon dioxide are made available to organisms in the form of energy-rich molecules such as sucrose. RuBisCO catalyzes either the carboxylation or oxygenation of ribulose-1,5-bisphosphate (also known as RuBP) with carbon dioxide or oxygen. Image File history File links Download high resolution version (804x625, 248 KB)Crystal Structure Of Activated Rice Rubisco Complexed With 2-Carboxyarabinitol-1,5-Bisphosphate. ... Ribbon diagram of the catalytically perfect enzyme TIM. Factor D enzyme crystal prevents the immune system from inappropriately running out of control. ... EC numbers (Enzyme Commission numbers) are a numerical classification scheme for enzymes, based on the chemical reactions they catalyze. ... Overview of the Calvin cycle and carbon fixation The Calvin cycle (or Calvin-Benson cycle) is a series of biochemical reactions that takes place in the chloroplasts of photosynthetic organisms. ... Carbon fixation is a process found in photosynthesis in autotrophic plants. ... Carbon dioxide is an atmospheric gas comprised of one carbon and two oxygen atoms. ... Sucrose (C12H22O11) is the common chemical name for table sugar. ... A carboxyl or carboxylic group is a functional group consisting of a carbon atom doubly bonded to an oxygen atom and single-bonded to a hydroxyl (-OH) group. ... Oxygenation refers to the amount of oxygen in a medium. ... Categories: Stub | Photosynthesis ... General Name, Symbol, Number oxygen, O, 8 Chemical series nonmetals Group, Period, Block 16, 2, p Appearance colorless Atomic mass 15. ...

RuBisCO is very important because it catalyzes the most commonly used chemical reaction by which inorganic carbon enters the biosphere. RuBisCO is apparently the most abundant protein in leaves, and it may be the most abundant protein on Earth^[1]. Given its important role in the biosphere, there are currently efforts to "improve on nature" and genetically engineer crop plants so as to contain more efficient RuBisCO (see below). Inorganic chemistry is the branch of chemistry concerned with the properties and reactions of inorganic compounds. ... General Name, Symbol, Number carbon, C, 6 Chemical series nonmetals Group, Period, Block 14, 2, p Appearance black (graphite) colorless (diamond) Atomic mass 12. ... The biosphere is that part of a planets outer shell—including air, land, surface rocks and water—within which life occurs, and which biotic processes in turn alter or transform. ... A representation of the 3D structure of myoglobin, showing coloured alpha helices. ... The Nature Conservancy - a charitable organization devoted to preserving natural diversity worldwide English Nature UK government organization devoted to preserving natural diversity in the UK Nature Detectives An online research and education project for under 18s in the UK A Guide to Nature and Wildlife Conservation ‹The template below... An iconic image of genetic engineering; this 1986 autoluminograph of a glowing transgenic tobacco plant bearing the luciferase gene of the firefly strikingly demonstrates the power and potential of genetic manipulation. ...

Structure

In plants, algae, cyanobacteria, and phototropic and chemoautotropic proteobacteria the enzyme usually consists of two protein subunits called the large chain (L, about 55,000 Da) and the small chain (S, about 13,000 Da)^[2]. The enzymatically active substrate (ribulose 1,5-bisphosphate) binding sites are located in the large chains that form dimers as shown in Figure 1 (above, right) in which amino acids from each large chain contribute to the binding sites. A total of four large chain dimers and eight small chains assemble into a larger complex of about 540,000 Da^[3]. In some proteobacteria and dinofagellates, enzymes consisting of only a large subunit have been found ^[4]. AMU redirects here, but may also refer to the Arab Maghreb Union The unified atomic mass unit (u), or dalton (Da), is a small unit of mass used to express atomic masses and molecular masses. ... Ribulose is a sugar or carbohydrate. ...

Magnesium ions (Mg²⁺) are needed for enzymatic activity. Correct positioning of Mg²⁺ in the active site of the enzyme involves addition of an "activating" carbon dioxide molecule (CO₂) to a lysine in the active site (forming a carbamate)^[5]. Formation of the carbamate is favored by an alkaline pH. The pH and the concentration of magnesium ions in the fluid compartment (in plants, the stroma of the chloroplast^[6]) increases in the light. The role of changing pH and magnesium ion levels in the regulation of RuBisCO enzyme activity is discussed below. General Name, Symbol, Number magnesium, Mg, 12 Chemical series alkaline earth metals Group, Period, Block 2, 3, s Appearance silvery white Atomic mass 24. ... The active site of an enzyme is the binding site where catalysis occurs. ... Carbon dioxide is an atmospheric gas comprised of one carbon and two oxygen atoms. ... Lysine is one of the 20 amino acids normally found in proteins. ... The carbamate functional group is formed when a carbon dioxide molecule reacts with the amino terminus of a peptide chain or an amino group of an amino acid, adding a COO− group to it and releasing a cation (H+ ion). ... Concentration is a very common concept used in chemistry and related fields. ... The inside of a chloroplast The inside of a chloroplast Chloroplasts are organelles found in plant cells and eukaryotic algae which conduct photosynthesis. ...

Enzymatic Activity

Figure 2. Overview of the Calvin cycle and carbon fixation

As shown in Figure 2 (left), RuBisCO is one of many enzymes in the Calvin cycle.
Substrates. During carbon fixation, the substrate molecules for RuBisCO are ribulose 1,5-bisphosphate, carbon dioxide (distinct from the "activating" carbon dioxide) and water ^[7]. RuBisCO can also allow a reaction to occur with molecular oxygen (O₂) instead of carbon dioxide (CO₂).
Products. When carbon dioxide is the substrate, the product of the carboxylase reaction is 3-phosphoglycerate. The 3-phosphoglycerate can be used to produce larger molecules such as glucose. When molecular oxygen is the substrate, the products of the oxygenase reaction are phosphoglycolate and 3-phosphoglycerate. Phosphoglycolate initiates a sequence of reactions called photorespiration which involves enzymes located in the mitochondria and peroxisomes. In this process, two molecules of phosphoglycolate are converted to one molecule of carbon dioxide and one molecule of 3-phosphoglycerate, which can reenter the Calvin cycle. Some of the phosphoglycolate entering this pathway can be retained by plants to produce other molecules such as glycine. At air levels of carbon dioxide and oxygen, the ratio of the reactions is about 4 to 1, which results in a net carbon dioxide fixation of only 3.5. Thus the inability of the enzyme to prevent the reaction with oxygen greatly reduces the photosynthetic potential of many plants. Some plants and many algae and photosynthetic bacteria have overcome this limitation by devising means to increase the concentration of carbon dioxide around the enzyme (see C4 carbon fixation, crassulacean acid metabolism). Image File history File links Download high resolution version (856x742, 51 KB)This image was copied from wikipedia:en. ... Image File history File links Download high resolution version (856x742, 51 KB)This image was copied from wikipedia:en. ... Overview of the Calvin cycle and carbon fixation The Calvin cycle (or Calvin-Benson cycle) is a series of biochemical reactions that takes place in the chloroplasts of photosynthetic organisms. ... Categories: Stub | Photosynthesis ... Carbon dioxide is an atmospheric gas comprised of one carbon and two oxygen atoms. ... Water has the chemical formula H2O, meaning that one molecule of water is composed of two hydrogen atoms and one oxygen atom. ... General Name, Symbol, Number oxygen, O, 8 Chemical series nonmetals Group, Period, Block 16, 2, p Appearance colorless Atomic mass 15. ... Glucose (Glc), a simple monosaccharide sugar, is one of the most important carbohydrates and is used as a source of energy in animals and plants. ... Photorespiration is an alternate pathway for Rubisco, the main enzyme of photosynthesis (specifically, the Calvin cycle). ... In cell biology, a mitochondrion is an organelle found in the cells of most eukaryotes. ... Peroxisomes are ubiquitous organelles in eukaryotes. ... Glycine (Gly, G) is a nonpolar amino acid. ... C4 carbon fixation is a metabolic pathway found in some land plants (C4 plants). ... Crassulacean acid metabolism (CAM) is a carbon fixation pathway in some photosynthetic plants. ...

Rate of enzymatic activity. Some enzymes can carry out thousands of chemical reactions each second. RuBisCO is slow, being able to "fix" only a few carbon dioxide molecules each second. Under most conditions and when light is not otherwise limiting photosynthesis, RuBisCO is the primary rate-limiting enzyme of the Calvin cycle.

Regulation of its Enzymatic Activity

RuBisCO is usually only active during the day because ribulose 1,5-bisphosphate is not being produced in the dark due to the regulation of several other enzymes in the Calvin cycle. In addition, the activity of Rubisco is coordinated with that of the other enzymes of the Calvin cycle several ways:

1. Regulation by ions. Upon illumination of the chloroplasts, the pH of the stroma rises from 7.0 to 8.0 because of the proton (hydrogen ion, H⁺) gradient created across the thylakoid membrane^[8]. At the same time, magnesium ions (Mg²⁺) move out of the thylakoids, increasing the concentration of magnesium in the stroma of the chloroplasts. RuBisCO has a high optimal pH (can be >9.0, depending on the magnesium ion concentration) and thus becomes "activated" by the addition of carbon dioxide and magnesioum to the active sites as described above.
2. Regulation by activase. In plants and some algae, another enzyme, RuBisCO activase^[9] is required to allow the rapid formation of the critical carbamate in the active site of RuBisCO^[10]. Activase is required because the ribulose 1,5-bisphosphate substrate binds more strongly to the active sites lacking the carbamate and markedly slows down the "activation" process. In the light, RuBisCO activase promotes the release of the inhibitory ribulose 1,5-bisphosphate from the catalytic sites. Activase is also required in some plants (e.g. tobacco and many beans) because in darkness, RuBisCO is inhibited by a competitive inhibitor synthesized by these plants, a substrate analog 2-Carboxy-D-arabitinol 1-phosphate (CA1P)^[11]. CA1P binds tightly to the active site of carbamylated RuBisCO and inhibits catalytic activity. In the light, RuBisCO activase also promotes the release of CA1P from the catalytic sites. After the CA1P is released from RuBisCO, it is rapidly converted to a non-inhibitory form by a light-activated CA1P-phosphatase. Finally, once every several hundred reactions, the normal reactions with carbon dioxide or oxygen are not completed and other inhibitory substrate analogs are formed in the active site. Once again, RuBisCO activase can promote the release of these analogs from the catalytic sites and maintain the enzyme in a catalytically active form. The properties of activase limit the photosynthetic potential of plants at high temperatures ^[12]. CA1P has also been shown to keep Rubisco in a conformation that is protected from proteolysis^[13].
3. Regulation by ATP/ADP and stromal reduction/oxidation state through the activase. The removal of the inhibitory RuBP, CA1P, and the other inhibitory substrate analogs by activase requires the consumption of ATP. This reaction is inhibited by the presence of ADP and thus activase activity depends on the ratio of these compounds in the chloroplast stroma. Furthermore in most plants, the sensitivity of activase to the ratio of ATP/ADP is modified by the stromal reduction/oxidation state through another small regulatory protein, thioredoxin. In this manner, the activity of activase and the activation state of Rubisco can be modulated in response to light intensity and thus the rate of formation of the ribulose 1,5-bisphosphate substrate^[14].
4. Regulation by phosphate. Inorganic phosphate (P_i) participates in the co-ordinated regulation of photosynthesis. P_i binds to the RuBisCO active site and to another site on the large chain where it can influence transitions between activated and less active conformations of the enzyme. Activation of bacterial RuBisCO might be particularly sensitive to P_i levels^[15].
5. Regulation by carbon dioxide. Since carbon dioxide and oxygen compete at the active site of RuBisCO, carbon fixation by RuBisCO can be enhanced by increasing the carbon dioxide level in the compartment containing RuBisCO (chloroplast stroma). Several times during the evolution of plants, mechanisms have evolved for increasing the level of carbon dioxide in the stroma (see C4 carbon fixation).

The title of this article is shown beginning with a capital letter due to technical restrictions. ... Stroma can refer to: 1) The connective supportive framework of a biological cell, tissue, or organ. ... A thylakoid is a phospholipid bilayer membrane internal to chloroplasts. ... In chemistry, a chemical conformation is the spatial arrangement of atoms in a molecule. ... Proteases (proteinases, peptidases or proteolytic enzymes) are enzymes that break peptide bonds between amino acids of proteins. ... Adenosine triphosphate (ATP) Adenosine triphosphate (ATP) is the nucleotide known in biochemistry as the molecular currency of intracellular energy transfer; that is, ATP is able to store and transport chemical energy within cells. ... ADP may stand for: adenosine diphosphate Aeroports de Paris [1] AOLserver Dynamic Pages, web server extensions designed to return dynamically created documents based on the TCL computer programming language using AOLserver. ... Thioredoxins are small proteins involved in thiol-redox processes. ... In chemistry, a phosphate is a polyatomic ion or radical consisting of one phosphorus atom and four oxygen. ... Figure 1: Diagram of a catalytic reaction, showing the energy needed at each stage of the reaction. ... C4 carbon fixation is a metabolic pathway found in some land plants (C4 plants). ...

Genetic engineering

Since RuBisCO is often rate limiting for photosynthesis in plants, it may be possible to improve on photosynthesis by modifying RuBisCO genes in plants to increase its catalytic activity and/or decrease the rate of the oxygenation actiity. Approaches that have begun to be investigated include expressing RuBisCO genes from one organism in another organism, increasing the level of expression of RuBisCO subunits, expressing RuBisCO small chains from the chloroplast DNA, and altering RuBisCO genes so as to try to increase selectivity for carbon dioxide or otherwise increase the rate of carbon fixation^[16].

References

Figure 3. The protein complex shown in Figure 1 (above) contains two RuBisCO large chains and two RuBisCO small chains. In this figure, each protein chain in the (LS)₂ complex is given its own color for easy identification.

Figure 4. Spacefilling view of the complete RuBisCO structure which shows the arrangement of the large chains (white/grey) and the small chains (blue/orange).

1. ^  The Cell - A Molecular Approach. 2nd ed. by Geoffrey M. Cooper, published by Sinauer Associates, Inc. (2000) Sunderland (MA). Online textbook. The Cooper text suggests that RuBisCO is the most abundant protein on Earth (Chapter 10, The Chloroplast Genome). A recent article by Dhingra et al, suggests that RuBisCO accounts for 30–50% of total soluble protein in chloroplasts (full text article online: Entrez PubMed 15067115).
2. ^  The large chain gene is part of the chloroplast DNA molecule in plants (Entrez GeneID: 3052726). There are typically several related small chain genes in the nucleus of plant cells and the small chains are imported to the stromal compartment of chloroplasts from the cytosol by crossing the outer chloroplast membrane (full text article online: Entrez PubMed 15067115). Arabidopsis thaliana has four RuBisCO small chain genes (see: Entrez PubMed 11401297). The pattern of how large chains and small chains assemble is illustrated in Figure 3 (right).
3. ^  Biochemistry by Jeremy M. Berg, John L. Tymoczko, and Lubert Stryer. Published by W. H. Freeman and Co. (2002) New York. Online textbook. Figure 20 in the Stryer textbook shows a color-coded ribbon diagram of the structural components of eukaryotic RuBisCO. Figure 4 (to right on this page) shows another view of the structure.
4. ^  The structure of RuBisCO from the photosynthetic bacterium Rhodospirillum rubrum has been determined by X-ray crystallography, see: Protein Data Bank 9RUB. A comparison of the structures of eukaryotic and bacterial RuBisCO is shown in the Protein Data Bank feature article on Rubisco.
5. ^  Molecular Cell Biology, 4th edition, by Harvey Lodish, Arnold Berk, S. Lawrence Zipursky, Paul Matsudaira, David Baltimore and James E. Darnell. Published by W. H. Freeman & Co. (2000) New York. Online textbook. Figure 16-48 shows a structural model of the active site, including the involvement of magnesium. The Protein Data Bank feature article on RuBisCO also includes a model of magnesium at the active site.
6. ^  The Lodish textbook describes the localization of RuBisCO to the stromal space of chloroplasts. Figure 17-7 illustrates how RuBisCO small subunits move into the chloroplast stroma and assemble with the large subunits.
7. ^  The chemical reactions catalyzed by RuBisCO are described in the online Biochemistry textbook by Stryer et al.
8. ^  Figure 20.14 in the textbook by Stryer et al. illustrates the light-dependent movement of hydrogen and magnesium ions that are important for Light Regulation of the Calvin Cycle. The movement of protons into thylakoids is driven by light and is fundamental to ATP synthesis in chloroplasts.
9. ^  "Rubisco activase - Rubisco's catalytic chaperone." by A. R. Portis, Jr in Photosynthesis Research (2003), volume 75, pages 11-27. (see: Entrez PubMed 16245090).
10. ^  "Characteristics of photosynthesis in rice plants transformed with an antisense Rubisco activase gene" by S. H. Jin, D. A. Jiang, X. Q. Li and J. W. Sun. Transgenic plants that were genetically engineered to have reduced levels of RuBisCO activase were shown to have reduced photosynthesis (see: Entrez PubMed 15236471).
11. ^ "Incorporation of carbon from photosynthetic products into 2-carboxyarabinitol-1-phosphate and 2-carboxyarabinitol." by P. J. Andralojc, G. W. Dawson, M. A. Parry and A. J. Keys in Biochemical Journal (1994), volume 304, pages 781-6. (full text online: Entrez PubMed 7818481).
12. ^  "Rubisco activase constrains the photosynthetic potential of leaves at high temperature and CO2. by S. J. Crafts-Brandner and M. E. Salvucci in Proceedings of the National Academy of Science USA (2000), volume 97, pages 12937-8. (full text online:Entrez PubMed 11069297).
13. ^ "2'-carboxy-D-arabitinol 1-phosphate protects ribulose 1, 5-bisphosphate carboxylase/oxygenase against proteolytic breakdown" by S. Khan, P. J. Andralojc, P. J. Lea and M. A. Parry in European Journal of Biochemistry (1999), volume 266, pages 840-7. (full text online: Entrez PubMed 10583377).
14. ^  "Light modulation of Rubisco in Arabidopsis requires a capacity for redox regulation of the larger Rubisco activase isoform.." by N. Zhang, R. Kallis, R. G. Ewy, A. R. Portis Jr in Proceedings of the National Academy of Science USA (2002), volume 99, pages 3330-4 (full text online:Entrez PubMed 11854454).
15. ^  "Activation of cyanobacterial RuBP-carboxylase/oxygenase is facilitated by inorganic phosphate via two independent mechanisms." by Yehouda Marcus and Michael Gurevitz in European Journal of Biochemistry (2000), volume 267, pages 5995-6003. (full text online:Entrez PubMed 10998060).
16. ^  "Manipulation of Rubisco: the amount, activity, function and regulation." by M. A. Parry, P. J. Andralojc, R. A. Mitchell, P. J. Madgwick and A. J. Keys in Journal of Experimental Botany (2003) volume 54, page 1321-33. (full text online: Entrez PubMed 12709478)

• Sugawara H, Yamamoto H, Shibata N, Inoue T, Okada S, Miyake C, Yokota A, Kai Y. Crystal structure of carboxylase reaction-oriented ribulose 1, 5-bisphosphate carboxylase/oxygenase from a thermophilic red alga, Galdieria partita. J Biol Chem 1999;274:15655-61. Fulltext. PMID 10336462.

Image File history File links RuBisCOL2S2. ... Image File history File links RuBisCOL2S2. ... Image File history File links Download high resolution version (612x605, 191 KB) Summary Spacefilling structure of RuBisCO created using Rasmol and the 8RUC file from the Protein Data Bank. ... Image File history File links Download high resolution version (612x605, 191 KB) Summary Spacefilling structure of RuBisCO created using Rasmol and the 8RUC file from the Protein Data Bank. ... The Entrez Global Query Cross-Database Search System allows access to databases at the National Center for Biotechnology Information (NCBI) website. ... Chloroplasts contain several important membranes, vital for their function. ... The Entrez Global Query Cross-Database Search System allows access to databases at the National Center for Biotechnology Information (NCBI) website. ... Binomial name Arabidopsis thaliana (L.) Heynh. ... The Entrez Global Query Cross-Database Search System allows access to databases at the National Center for Biotechnology Information (NCBI) website. ... Kingdoms Eukaryotes are organisms with complex cells, in which the genetic material is organized into membrane-bound nuclei. ... Genera Rhodospirillum Azospirillum Magnetospirillum Phaeospirillum Rhodocista Rhodospira Rhodothalassium Rhodovibrio Roseospira Skermanella The Rhodospirillaceae are a family of Proteobacteria. ... X-ray crystallography is a technique in crystallography in which the pattern produced by the diffraction of X-rays through the closely spaced lattice of atoms in a crystal is recorded and then analyzed to reveal the nature of that lattice. ... The Protein Data Bank (PDB) is a repository for 3-D structural data of proteins and nucleic acids. ... The first stage of the photosynthetic system is the light-dependent reaction, which converts solar energy into chemical energy. ... An ATP synthase (EC 3. ... The Entrez Global Query Cross-Database Search System allows access to databases at the National Center for Biotechnology Information (NCBI) website. ... The Entrez Global Query Cross-Database Search System allows access to databases at the National Center for Biotechnology Information (NCBI) website. ... The Entrez Global Query Cross-Database Search System allows access to databases at the National Center for Biotechnology Information (NCBI) website. ... The Entrez Global Query Cross-Database Search System allows access to databases at the National Center for Biotechnology Information (NCBI) website. ... The Entrez Global Query Cross-Database Search System allows access to databases at the National Center for Biotechnology Information (NCBI) website. ... The Entrez Global Query Cross-Database Search System allows access to databases at the National Center for Biotechnology Information (NCBI) website. ... The Entrez Global Query Cross-Database Search System allows access to databases at the National Center for Biotechnology Information (NCBI) website. ... The Entrez Global Query Cross-Database Search System allows access to databases at the National Center for Biotechnology Information (NCBI) website. ...

See also

• Carbon cycle
• Photorespiration
• Pyrenoid

The carbon cycle is the biogeochemical cycle by which carbon is exchanged between the biosphere, geosphere, hydrosphere and atmosphere of the Earth. ... Photorespiration is an alternate pathway for Rubisco, the main enzyme of photosynthesis (specifically, the Calvin cycle). ... In cell biology, pyrenoids are centers of carbon dioxide fixation. ...

External links

• Rubisco: Protein Data Bank entry
• The Plant Kingdoms sloth: Protein spotlight article on the "slothful" enzyme RuBisCO