Summary: Ribulose bisphosphate carboxylase large chain, catalytic domain
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RuBisCO Edit Wikipedia article
|Ribulose-1,5-bisphosphate carboxylase oxygenase|
Figure 1. Space-filling view of RuBisCO showing the arrangement of the large chain dimers (white/grey) and the small chains (blue and orange).
|PDB structures||RCSB PDB PDBe PDBsum|
|Gene Ontology||AmiGO / EGO|
Ribulose-1,5-bisphosphate carboxylase/oxygenase, commonly known by the abbreviations RuBisCO or RuBPCase, is an enzyme involved in the first major step of carbon fixation, a process by which atmospheric carbon dioxide is converted by plants and other photosynthetic organisms to energy-rich molecules such as glucose. In chemical terms, it catalyzes the carboxylation of ribulose-1,5-bisphosphate (also known as RuBP). It is probably the most abundant enzyme on Earth.
- 1 RuBisCO vs alternative carbon fixation pathways
- 2 Structure
- 3 Enzymatic activity
- 4 Regulation of its enzymatic activity
- 5 Genetic engineering
- 6 Phylogenetic studies
- 7 History of the term RuBisCO
- 8 See also
- 9 References
- 10 Bibliography
- 11 External links
RuBisCO vs alternative carbon fixation pathways
RuBisCO is important biologically because it catalyzes the primary chemical reaction by which inorganic carbon enters the biosphere. While many autotrophic bacteria and archaea fix carbon via the reductive acetyl CoA pathway, the 3-hydroxypropionate cycle, or the reverse Krebs cycle, these pathways are relatively smaller contributors to global carbon fixation than that catalyzed by RuBisCO. Phosphoenolpyruvate carboxylase, unlike RuBisCO, only temporarily fixes carbon. Reflecting its importance, RuBisCO is the most abundant protein in leaves, accounting for 50% of soluble leaf protein in C3 plants (20–30% of total leaf nitrogen) and 30% of soluble leaf protein in C4 plants (5–9% of total leaf nitrogen). Given its important role in the biosphere, the genetic engineering of RuBisCO in crops is of continuing interest (see below).
In plants, algae, cyanobacteria, and phototrophic and chemoautotrophic proteobacteria, the enzyme usually consists of two types of protein subunit, called the large chain (L, about 55,000 Da) and the small chain (S, about 13,000 Da). The large-chain gene (rbcL) is encoded by the chloroplast DNA in plants. 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. 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 eight large-chains (= 4 dimers) and eight small chains assemble into a larger complex of about 540,000 Da. In some proteobacteria and dinoflagellates, enzymes consisting of only large subunits have been found.
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). 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) increases in the light. The role of changing pH and magnesium ion levels in the regulation of RuBisCO enzyme activity is discussed below.
As shown in Figure 2 (left), RuBisCO is one of many enzymes in the Calvin cycle.
During carbon fixation, the substrate molecules for RuBisCO are ribulose-1,5-bisphosphate and carbon dioxide (distinct from the "activating" carbon dioxide). RuBisCO also catalyses a reaction between ribulose-1,5-bisphosphate and molecular oxygen (O
2) instead of carbon dioxide (CO2).
When carbon dioxide is the substrate, the product of the carboxylase reaction is a highly unstable six-carbon phosphorylated intermediate known as 3-keto-2-carboxyarabinitol-1,5-bisphosphate, which decays virtually instantaneously into two molecules of glycerate-3-phosphate. The extremely unstable molecule created by the initial carboxylation was unknown until 1988, when it was isolated. The 3-phosphoglycerate can be used to produce larger molecules such as glucose. Also, Rubisco side activities can lead to useless or inhibitory by-products; one such product is xylulose-1,5-bisphosphate, which inhibits Rubisco activity. When molecular oxygen is the substrate, the products of the oxygenase reaction are phosphoglycolate and 3-phosphoglycerate. Phosphoglycolate is recycled through a sequence of reactions called photorespiration, which involves enzymes and cytochromes located in the mitochondria and peroxisomes (this is a case of metabolite repair). 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 ambient 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 capacity of many plants. Some plants, many algae, and photosynthetic bacteria have overcome this limitation by devising means to increase the concentration of carbon dioxide around the enzyme, including C4 carbon fixation, crassulacean acid metabolism, and the use of pyrenoid.
Rate of enzymatic activity
Some enzymes can carry out thousands of chemical reactions each second. However, RuBisCO is slow, being able to fix only 3-10 carbon dioxide molecules each second per molecule of enzyme. The reaction catalyzed by RuBisCO is, thus, the primary rate-limiting factor of the Calvin cycle during the day. Nevertheless, under most conditions, and when light is not otherwise limiting photosynthesis, the speed of RuBisCO responds positively to increasing carbon dioxide concentration. However, our descriptive knowledge will become more usable when we can translate them into quantitative models that can enable us to calculate the outcome of the reaction under a given condition. Since RubisCO reacts with RuBP (ribulose 1,5 bisphosphate) first to produces enediol and next with CO2 that after some intermediate changes produces PGA (3-phosphoglycerate), a biochemical model is developed  to represent the effects of these steps quantitatively. Since carboxylation or fixation of CO2 is possible only after the synthesis of enediol, thus it is suggested that the role of RubisCO is to produce enediol that is carboxylase and oxygenase (EnCO). Accordingly, RubisCO is called enolase-phosphglycerase (EPGase) since it is neither carboxylase nor oxygenase.
Regulation of its enzymatic activity
RuBisCO is usually only active during the day as ribulose 1,5-bisphosphate is not regenerated in the dark. This is 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 in several ways.
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. 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 magnesium to the active sites as described above.
Regulation by RuBisCO activase
In plants and some algae, another enzyme, RuBisCO activase, is required to allow the rapid formation of the critical carbamate in the active site of RuBisCO. RuBisCO activase is required because the ribulose 1,5-bisphosphate (RuBP) 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, or — in some views — storage RuBP from the catalytic sites. Activase is also required in some plants (e.g., tobacco and many beans) because, in darkness, RuBisCO is inhibited (or protected from hydrolysis) by a competitive inhibitor synthesized by these plants, a substrate analog 2-Carboxy-D-arabitinol 1-phosphate (CA1P). 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. CA1P has also been shown to keep RuBisCO in a conformation that is protected from proteolysis. At high temperatures, RuBisCO activase aggregates and can no longer activate RuBisCO. This contributes to the decreased carboxylating capacity observed during heat stress.
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 (redox) 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.
Regulation by phosphate
In cyanobacteria, inorganic phosphate (Pi) participates in the co-ordinated regulation of photosynthesis. Pi 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 Pi levels, which can act in the same way as RuBisCO activase in higher plants.
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 use of oxygen as a substrate appears to be a puzzling process, since it seems to throw away captured energy. However, it may be a mechanism for preventing overload during periods of high light flux. This weakness in the enzyme is the cause of photorespiration, such that healthy leaves in bright light may have zero net carbon fixation when the ratio of O
2 to CO2 reaches a threshold at which oxygen is fixed instead of carbon. This phenomenon is primarily temperature-dependent. High temperature decreases the concentration of CO2 dissolved in the moisture in the leaf tissues. This phenomenon is also related to water stress. Since plant leaves are evaporatively cooled, limited water causes high leaf temperatures. C4 plants use the enzyme PEP carboxylase initially, which has a higher affinity for CO2. The process first makes a 4-carbon intermediate compound, which is shuttled into a site of C3 photosynthesis then de-carboxylated, releasing CO2 to boost the concentration of CO2, hence the name C4 plants.
Crassulacean acid metabolism (CAM) plants keep their stomata (on the underside of the leaf) closed during the day, which conserves water but prevents the light-independent reactions (a.k.a. the Calvin Cycle) from taking place, since these reactions require CO2 to pass by gas exchange through these openings. Evaporation through the upper side of a leaf is prevented by a layer of wax.
Since RuBisCO is often rate-limiting for photosynthesis in plants, it may be possible to improve photosynthetic efficiency by modifying RuBisCO genes in plants to increase catalytic activity and/or decrease oxygenation rates. This could improve biosequestration of CO2 and be an important climate change strategy. Approaches under investigation include transferring 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 to increase specificity for carbon dioxide or otherwise increase the rate of carbon fixation.
One avenue is to introduce RuBisCO variants with naturally high specificity values such as the ones from the red alga Galdieria partita into plants. This may improve the photosynthetic efficiency of crop plants, although possible negative impacts have yet to be studied. Advances in this area include the replacement of the tobacco enzyme with that of the purple photosynthetic bacterium Rhodospirillum rubrum. In 2014, two transplastomic tobacco lines with functional Rubisco from the cyanobacterium Synechococcus elongatus PCC7942 (Se7942) were created by replacing the Rubisco with the large and small subunit genes of the Se7942 enzyme, in combination with either the corresponding Se7942 assembly chaperone, RbcX, or an internal carboxysomal protein, CcmM35. Both mutants had increased CO2 fixation rates when measured as carbon molecules per RuBisCO. However, the mutant plants grew more slowly than wild-type.
A recent theory explores the trade-off between the relative specificity (i.e., ability to favour CO2 fixation over O
2 incorporation, which leads to the energy-wasteful process of photorespiration) and the rate at which product is formed. The authors conclude that RuBisCO may actually have evolved to reach a point of 'near-perfection' in many plants (with widely varying substrate availabilities and environmental conditions), reaching a compromise between specificity and reaction rate.
Since photosynthesis is the single most effective natural regulator of carbon dioxide in the Earth's atmosphere, a biochemical model of RuBisCO reaction is used as the core module of climate change models. Thus, a correct model of this reaction is essential to the basic understanding of the relations and interactions of environmental models. A new theory and model of the biochemical reaction of photosynthesis and the draw-backs of today's most widely used model of photosynthesis is discussed in volume 29 of Advances in Photosynthesis and Respiration.
History of the term RuBisCO
The term "RuBisCO" was coined humorously in 1979, by David Eisenberg at a seminar honouring the retirement of the early, prominent RuBisCO researcher, Sam Wildman, and also alluded to the snack food trade name "Nabisco" in reference to Wildman's attempts to create an edible protein supplement from tobacco leaves.
- Cooper, Geoffrey M. (2000). "10.The Chloroplast Genome". The Cell: A Molecular Approach (2nd ed.). Washington, D.C: ASM Press. ISBN 0-87893-106-6.
, one of the subunits of ribulose bisphosphate carboxylase (rubisco) is encoded by chloroplast DNA. Rubisco is the critical enzyme that catalyzes the addition of CO2 to ribulose-1,5-bisphosphate during the Calvin cycle (see Figure 2.39). It is also thought to be the single most abundant protein on Earth, so it is noteworthy that one of its subunits is encoded by the chloroplast genome.
(given that plants make up greater than 99% of the biomass on Earth.)
Dhingra A, Portis AR, Daniell H (April 2004). "Enhanced translation of a chloroplast-expressed RbcS gene restores small subunit levels and photosynthesis in nuclear RbcS antisense plants". Proc. Natl. Acad. Sci. U.S.A. 101 (16): 6315–20. Bibcode:2004PNAS..101.6315D. doi:10.1073/pnas.0400981101. PMC 395966. PMID 15067115.
(Rubisco) is the most prevalent enzyme on this planet, accounting for 30–50% of total soluble protein in the chloroplast;
- Feller U, Anders I, Mae T (2008). "Rubiscolytics: fate of Rubisco after its enzymatic function in a cell is terminated". J. Exp. Bot. 59 (7): 1615–24. doi:10.1093/jxb/erm242. PMID 17975207.
- Curmi PM, Cascio D, Sweet RM, Eisenberg D, Schreuder H (August 1992). "Crystal structure of the unactivated form of ribulose-1,5-bisphosphate carboxylase/oxygenase from tobacco refined at 2.0-A resolution". J. Biol. Chem. 267 (24): 16980–9. PMID 1512238.
- (Entrez GeneID: )
- Dhingra A, Portis AR, Daniell H (April 2004). "Enhanced translation of a chloroplast-expressed RbcS gene restores small subunit levels and photosynthesis in nuclear RbcS antisense plants". Proc. Natl. Acad. Sci. U.S.A. 101 (16): 6315–20. Bibcode:2004PNAS..101.6315D. doi:10.1073/pnas.0400981101. PMC 395966. PMID 15067115.
- Arabidopsis thaliana has four RuBisCO small chain genes. The pattern of how large chains and small chains assemble is illustrated in Figure 3 (right).
Yoon M, Putterill JJ, Ross GS, Laing WA (April 2001). "Determination of the relative expression levels of rubisco small subunit genes in Arabidopsis by rapid amplification of cDNA ends". Anal. Biochem. 291 (2): 237–44. doi:10.1006/abio.2001.5042. PMID 11401297.
- Stryer, Lubert; Berg, Jeremy Mark; Tymoczko, John L. (2002). "20. The Calvin Cycle and the Pentose Phosphate Pathway". Biochemistry (5th ed.). San Francisco: W.H. Freeman. ISBN 0-7167-3051-0.
Figure 20.3. Structure of Rubisco. (Color-coded ribbon diagram)
Figure 1 (on this page, near top) shows another view of the structure.
- The structure of RuBisCO from the photosynthetic bacterium Rhodospirillum rubrum has been determined by X-ray crystallography, see: . A comparison of the structures of eukaryotic and bacterial RuBisCO is shown in the Protein Data Bank feature article on Rubisco.
- 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.
- 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.
- The chemical reactions catalyzed by RuBisCO are described in the online Biochemistry textbook by Stryer et al.
- Pearce, F. Grant (2006-11-01). "Catalytic by-product formation and ligand binding by ribulose bisphosphate carboxylases from different phylogenies". The Biochemical Journal 399 (3): 525–534. doi:10.1042/BJ20060430. ISSN 1470-8728. PMC 1615894. PMID 16822231.
- Ellis J.R. (2010). "Tackling unintelligent design". Nature 463 (7278): 164–5. Bibcode:2010Natur.463..164E. doi:10.1038/463164a. PMID 20075906.
- Farazdaghi H. (2011). "The single-process biochemical reaction of Rubisco: A unified theory and model with the effects of irradiance, CO2 and rate-limiting step on the kinetics of C3 and C4 photosynthesis from gas exchange". BioSystems 103 (2): 265–284. doi:10.1016/j.biosystems.2010.11.004.
- 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.
- Portis AR (2003). "Rubisco activase — Rubisco's catalytic chaperone". Photosyn. Res. 75 (1): 11–27. doi:10.1023/A:1022458108678. PMID 16245090.
- Jin SH, Jiang DA, Li XQ, Sun JW (August 2004). "Characteristics of photosynthesis in rice plants transformed with an antisense Rubisco activase gene". J. Zhejiang Univ. Sci. 5 (8): 897–9. doi:10.1631/jzus.2004.0897. PMID 15236471.
- Andralojc PJ, Dawson GW, Parry MA, Keys AJ (December 1994). "Incorporation of carbon from photosynthetic products into 2-carboxyarabinitol-1-phosphate and 2-carboxyarabinitol". Biochem. J. 304 (3): 781–6. PMC 1137402. PMID 7818481.
- Crafts-Brandner SJ, Salvucci ME (November 2000). "Rubisco activase constrains the photosynthetic potential of leaves at high temperature and CO2". Proc. Natl. Acad. Sci. U.S.A. 97 (24): 13430–5. Bibcode:2000PNAS...9713430C. doi:10.1073/pnas.230451497. PMC 27241. PMID 11069297.
- Khan S, Andralojc PJ, Lea PJ, Parry MA (December 1999). "2'-carboxy-D-arabitinol 1-phosphate protects ribulose 1, 5-bisphosphate carboxylase/oxygenase against proteolytic breakdown". Eur. J. Biochem. 266 (3): 840–7. doi:10.1046/j.1432-1327.1999.00913.x. PMID 10583377.
- Salvucci ME, Osteryoung KW, Crafts-Brandner SJ, Vierling E (November 2001). "Exceptional sensitivity of Rubisco activase to thermal denaturation in vitro and in vivo". Plant Physiol. 127 (3): 1053–64. doi:10.1104/pp.010357. PMC 129275. PMID 11706186.
- Zhang N, Kallis RP, Ewy RG, Portis AR (March 2002). "Light modulation of Rubisco in Arabidopsis requires a capacity for redox regulation of the larger Rubisco activase isoform". Proc. Natl. Acad. Sci. U.S.A. 99 (5): 3330–4. Bibcode:2002PNAS...99.3330Z. doi:10.1073/pnas.042529999. PMC 122518. PMID 11854454.
- Marcus Y, Gurevitz M (October 2000). "Activation of cyanobacterial RuBP-carboxylase/oxygenase is facilitated by inorganic phosphate via two independent mechanisms". Eur. J. Biochem. 267 (19): 5995–6003. doi:10.1046/j.1432-1327.2000.01674.x. PMID 10998060.
- Spreitzer RJ, Salvucci ME (2002). "Rubisco: structure, regulatory interactions, and possibilities for a better enzyme". Annu Rev Plant Biol 53: 449–75. doi:10.1146/annurev.arplant.53.100301.135233. PMID 12221984.
- Parry MA, Andralojc PJ, Mitchell RA, Madgwick PJ, Keys AJ (May 2003). "Manipulation of Rubisco: the amount, activity, function and regulation". J. Exp. Bot. 54 (386): 1321–33. doi:10.1093/jxb/erg141. PMID 12709478.
- Whitney SM, Andrews TJ (December 2001). "Plastome-encoded bacterial ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) supports photosynthesis and growth in tobacco". Proc. Natl. Acad. Sci. U.S.A. 98 (25): 14738–43. Bibcode:2001PNAS...9814738W. doi:10.1073/pnas.261417298. PMC 64751. PMID 11724961.
- John Andrews T, Whitney SM (June 2003). "Manipulating ribulose bisphosphate carboxylase/oxygenase in the chloroplasts of higher plants". Arch. Biochem. Biophys. 414 (2): 159–69. doi:10.1016/S0003-9861(03)00100-0. PMID 12781767.
- Lin, M. T.; Occhialini, A.; Andralojc, P. J.; Parry, M. A. J.; Hanson, M. R. (2014). "A faster Rubisco with potential to increase photosynthesis in crops". Nature 513 (7519): 547. doi:10.1038/nature13776. PMID 25231869.
- Tcherkez GG, Farquhar GD, Andrews TJ (May 2006). "Despite slow catalysis and confused substrate specificity, all ribulose bisphosphate carboxylases may be nearly perfectly optimized". Proc. Natl. Acad. Sci. U.S.A. 103 (19): 7246–51. Bibcode:2006PNAS..103.7246T. doi:10.1073/pnas.0600605103. PMC 1464328. PMID 16641091. Archived from the original on April 6, 2015.
- Farazdaghi, Hadi (2009). "Modeling the Kinetics of Activation and Reaction of Rubisco from Gas Exchange (12)". In Laisk A; Nedbal L; Govindjee. Photosynthesis in silico: Understanding Complexity from Molecules to Ecosystems. Advances in Photosynthesis and Respiration 29. Berlin: Springer. ISBN 1-4020-9236-9.
- Chase et al 1993.
- Wildman SG (2002). "Along the trail from Fraction I protein to Rubisco (ribulose bisphosphate carboxylase-oxygenase)". Photosyn. Res. 73 (1-3): 243–50. doi:10.1023/A:1020467601966. PMID 16245127.
Portis AR, Parry MA (October 2007). "Discoveries in Rubisco (Ribulose 1,5-bisphosphate carboxylase/oxygenase): a historical perspective". Photosyn. Res. 94 (1): 121–43. doi:10.1007/s11120-007-9225-6. PMID 17665149.
- Chase, Mark W.; Soltis, Douglas E.; Olmstead, Richard G.; Morgan, David; Les, Donald H.; Mishler, Brent D.; Duvall, Melvin R.; Price, Robert A.; Hills, Harold G.; Qiu, Yin-Long; Kron, Kathleen A.; Rettig, Jeffrey H.; Conti, Elena; Palmer, Jeffrey D.; Manhart, James R.; Sytsma, Kenneth J.; Michaels, Helen J.; Kress, W. John; Karol, Kenneth G.; Clark, W. Dennis; Hedren, Mikael; Gaut, Brandon S.; Jansen, Robert K.; Kim, Ki-Joong; Wimpee, Charles F.; Smith, James F.; Furnier, Glenn R.; Strauss, Steven H.; Xiang, Qui-Yun; Plunkett, Gregory M.; Soltis, Pamela S.; Swensen, Susan M.; Williams, Stephen E.; Gadek, Paul A.; Quinn, Christopher J.; Eguiarte, Luis E.; Golenberg, Edward; Learn, Gerald H.; Graham, Sean W.; Barrett, Spencer C. H.; Dayanandan, Selvadurai; Albert, Victor A. (1993). "Phylogenetics of Seed Plants: An Analysis of Nucleotide Sequences from the Plastid Gene rbcL". Annals of the Missouri Botanical Garden 80 (3): 528. doi:10.2307/2399846.
- Sugawara H, Yamamoto H, Shibata N, et al. (May 1999). "Crystal structure of carboxylase reaction-oriented ribulose 1, 5-bisphosphate carboxylase/oxygenase from a thermophilic red alga, Galdieria partita". J. Biol. Chem. 274 (22): 15655–61. doi:10.1074/jbc.274.22.15655. PMID 10336462.
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- Ashida H, Danchin A, Yokota A (2005). "Was photosynthetic RuBisCO recruited by acquisitive evolution from RuBisCO-like proteins involved in sulfur metabolism?". Res. Microbiol. 156 (5-6): 611–8. doi:10.1016/j.resmic.2005.01.014. PMID 15950120.
- Marcus Y, Altman-Gueta H, Finkler A, Gurevitz M (June 2005). "Mutagenesis at two distinct phosphate-binding sites unravels their differential roles in regulation of Rubisco activation and catalysis". J. Bacteriol. 187 (12): 4222–8. doi:10.1128/JB.187.12.4222-4228.2005. PMC 1151729. PMID 15937184.
This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.
Ribulose bisphosphate carboxylase large chain, catalytic domain Provide feedback
The C-terminal domain of RuBisCO large chain is the catalytic domain adopting a TIM barrel fold.
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR000685
Ribulose bisphosphate carboxylase (RuBisCO) [PUBMED:6351728, PUBMED:12221984] catalyses the initial step in Calvin's reductive pentose phosphate cycle in plants as well as purple and green bacteria. It consists of a large catalytic unit and a small subunit of undetermined function. In plants, the large subunit is coded by the chloroplastic genome while the small subunit is encoded in the nuclear genome. Molecular activation of RuBisCO by CO2 involves the formation of a carbamate with the epsilon-amino group of a conserved lysine residue. This carbamate is stabilised by a magnesium ion. One of the ligands of the magnesium ion is an aspartic acid residue close to the active site lysine [PUBMED:1969412].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||magnesium ion binding (GO:0000287)|
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- the Pfam graphic itself.
Note that you can see the family page for a particular domain by clicking on the graphic. You can also choose to see all sequences which have a given architecture by clicking on the Show link in each row.
Finally, because some families can be found in a very large number of architectures, we load only the first fifty architectures by default. If you want to see more architectures, click the button at the bottom of the page to load the next set.
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We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
There are various ways to view or download the sequence alignments that we store. We provide several sequence viewers and a plain-text Stockholm-format file for download.
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the UniProtKB sequence database using the family HMM
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
- a Java applet developed at the University of Dundee. You will need Java installed before running jalview
- an HTML page showing the whole alignment.Please note: full Pfam alignments can be very large. These HTML views are extremely large and often cause problems for browsers. Please use either jalview or the Pfam viewer if you have trouble viewing the HTML version
- an HTML-based representation of the alignment, coloured according to the posterior-probability (PP) values from the HMM. As for the standard HTML view, heatmap alignments can also be very large and slow to render.
You can download (or view in your browser) a text representation of a Pfam alignment in various formats:
You can also change the order in which sequences are listed in the alignment, change how insertions are represented, alter the characters that are used to represent gaps in sequences and, finally, choose whether to download the alignment or to view it in your browser directly.
You may find that large alignments cause problems for the viewers and the reformatting tool, so we also provide all alignments in Stockholm format. You can download either the plain text alignment, or a gzipped version of it.
We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...
If you find these logos useful in your own work, please consider citing the following article:
This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.
Note: You can also download the data file for the tree.
Curation and family details
This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.
|Author:||Sonnhammer ELL, Griffiths-Jones SR|
|Number in seed:||21|
|Number in full:||840|
|Average length of the domain:||252.50 aa|
|Average identity of full alignment:||36 %|
|Average coverage of the sequence by the domain:||65.56 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||18|
|Download:||download the raw HMM for this family|
Weight segments by...
Change the size of the sunburst
selected sequences to HMM
a FASTA-format file
- 0 sequences
- 0 species
This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the More....
This chart is a modified "sunburst" visualisation of the species tree for this family. It shows each node in the tree as a separate arc, arranged radially with the superkingdoms at the centre and the species arrayed around the outermost ring.
How the sunburst is generated
The tree is built by considering the taxonomic lineage of each sequence that has a match to this family. For each node in the resulting tree, we draw an arc in the sunburst. The radius of the arc, its distance from the root node at the centre of the sunburst, shows the taxonomic level ("superkingdom", "kingdom", etc). The length of the arc represents either the number of sequences represented at a given level, or the number of species that are found beneath the node in the tree. The weighting scheme can be changed using the sunburst controls.
In order to reduce the complexity of the representation, we reduce the number of taxonomic levels that we show. We consider only the following eight major taxonomic levels:
Colouring and labels
Segments of the tree are coloured approximately according to their superkingdom. For example, archeal branches are coloured with shades of orange, eukaryotes in shades of purple, etc. The colour assignments are shown under the sunburst controls. Where space allows, the name of the taxonomic level will be written on the arc itself.
As you move your mouse across the sunburst, the current node will be highlighted. In the top section of the controls panel we show a summary of the lineage of the currently highlighed node. If you pause over an arc, a tooltip will be shown, giving the name of the taxonomic level in the title and a summary of the number of sequences and species below that node in the tree.
Anomalies in the taxonomy tree
There are some situations that the sunburst tree cannot easily handle and for which we have work-arounds in place.
Missing taxonomic levels
Some species in the taxonomic tree may not have one or more of the main eight levels that we display. For example, Bos taurus is not assigned an order in the NCBI taxonomic tree. In such cases we mark the omitted level with, for example, "No order", in both the tooltip and the lineage summary.
Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
So that these nodes are not simply omitted from the sunburst tree, we group them together in a separate branch (or segment of the sunburst tree). Since we cannot determine the lineage for these unmapped species, we show all levels between the superkingdom and the species as "uncategorised".
Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
Too many species/sequences
For large species trees, you may see blank regions in the outer layers of the sunburst. These occur when there are large numbers of arcs to be drawn in a small space. If an arc is less than approximately one pixel wide, it will not be drawn and the space will be left blank. You may still be able to get some information about the species in that region by moving your mouse across the area, but since each arc will be very small, it will be difficult to accurately locate a particular species.
The tree shows the occurrence of this domain across different species. More...
We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.
Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.
If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.
For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.
We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.
We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.
You can use the tree controls to manipulate how the interactive tree is displayed:
- show/hide the summary boxes
- highlight species that are represented in the seed alignment
- expand/collapse the tree or expand it to a given depth
- select a sub-tree or a set of species within the tree and view them graphically or as an alignment
- save a plain text representation of the tree
Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.
There are 7 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the RuBisCO_large domain has been found. There are 368 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
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