Wikipedia

Ribulose 1,5-bisphosphate

Ribulose 1,5-bisphosphate (RuBP) is an organic substance that is involved in photosynthesis, notably as the principal CO2 acceptor in plants.[1]: 2  It is a colourless anion, a double phosphate ester of the ketopentose (ketone-containing sugar with five carbon atoms) called ribulose. Salts of RuBP can be isolated, but its crucial biological function happens in solution.[2] RuBP occurs not only in plants but in all domains of life, including Archaea, Bacteria, and Eukarya.[3]

Ribulose 1,5-bisphosphate
Skeletal formula of RuBP
The acid form of the RuBP anion
Ball-and-stick model, based on x-ray diffraction data
Names
IUPAC name
1,5-Di-O-phosphono-D-ribulose
Other names
Ribulose 1,5-diphosphate
Identifiers
3D model (JSmol)
ChEBI
ChemSpider
KEGG
UNII
  • InChI=1S/C5H12O11P2/c6-3(1-15-17(9,10)11)5(8)4(7)2-16-18(12,13)14/h3,5-6,8H,1-2H2,(H2,9,10,11)(H2,12,13,14)/t3-,5-/m1/s1 checkY
    Key: YAHZABJORDUQGO-NQXXGFSBSA-N checkY
  • O=P(O)(OCC(=O)[C@H](O)[C@H](O)COP(=O)(O)O)O
Properties
C5H12O11P2
Molar mass 310.088 g·mol−1
Except where otherwise noted, data are given for materials in their standard state (at 25 °C [77 °F], 100 kPa).
☒N verify (what is checkY☒N ?)

History

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RuBP was originally discovered by Andrew Benson in 1951 while working in the lab of Melvin Calvin at UC Berkeley.[4][5] Calvin, who had been away from the lab at the time of discovery and was not listed as a co-author, controversially removed the full molecule name from the title of the initial paper, identifying it solely as "ribulose".[4][6] At the time, the molecule was known as ribulose diphosphate (RDP or RuDP) but the prefix di- was changed to bis- to emphasize the nonadjacency of the two phosphate groups.[4][5][7]

Role in photosynthesis and the Calvin-Benson Cycle

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See also: Calvin-Benson Cycle

The enzyme ribulose-1,5-bisphosphate carboxylase-oxygenase (rubisco) catalyzes the reaction between RuBP and carbon dioxide. The product is the highly unstable six-carbon intermediate known as 3-keto-2-carboxyarabinitol 1,5-bisphosphate, or 2'-carboxy-3-keto-D-arabinitol 1,5-bisphosphate (CKABP).[8] This six-carbon β-ketoacid intermediate hydrates into another six-carbon intermediate in the form of a gem-diol.[9] This intermediate then cleaves into two molecules of 3-phosphoglycerate (3-PGA) which is used in a number of metabolic pathways and is converted into glucose.[10][11]

In the Calvin-Benson cycle, RuBP is a product of the phosphorylation of ribulose-5-phosphate (produced by glyceraldehyde 3-phosphate) by ATP.[11][12]

 
The Calvin-Benson cycle showing the role of ribulose-1,5-bisphosphate.

Interactions with rubisco

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RuBP acts as an enzyme inhibitor for the enzyme rubisco, which regulates the net activity of carbon fixation.[13][14][15] When RuBP is bound to an active site of rubisco, the ability to activate via carbamylation with CO2 and Mg2 is blocked. The functionality of rubisco activase involves removing RuBP and other inhibitory bonded molecules to re-enable carbamylation on the active site.[1]: 5 

Role in photorespiration

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See also: Photorespiration

Rubisco also catalyzes RuBP with oxygen (O
2) in an interaction called photorespiration, a process that is more prevalent at high temperatures.[16][17] During photorespiration RuBP combines with O
2 to become 3-PGA and phosphoglycolic acid.[18][19][20] Like the Calvin-Benson Cycle, the photorespiratory pathway has been noted for its enzymatic inefficiency[19][20] although this characterization of the enzymatic kinetics of rubisco have been contested.[21] Due to enhanced RuBP carboxylation and decreased rubisco oxygenation stemming from the increased concentration of CO2 in the bundle sheath, rates of photorespiration are decreased in C4 plants.[1]: 103  Similarly, photorespiration is limited in CAM photosynthesis due to kinetic delays in enzyme activation, again stemming from the ratio of carbon dioxide to oxygen.[22]

Measurement

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RuBP can be measured isotopically via the conversion of 14CO2 and RuBP into glyceraldehyde 3-phosphate.[23] G3P can then be measured using an enzymatic optical assay.[23][24][a] Given the abundance of RuBP in biological samples, an added difficulty is distinguishing particular reservoirs of the substrate, such as the RuBP internal to a chloroplast vs external. One approach to resolving this is by subtractive inference, or measuring the total RuBP of a system, removing a reservoir (e.g. by centrifugation), re-measuring the total RuBP, and using the difference to infer the concentration in the given repository.[25]

See also

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References

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  1. ^ a b c Leegood, R. C.; Sharkey, T. D.; von Caemmerer, S., eds. (2000). Photosynthesis: Physiology and Metabolism. Advances in Photosynthesis. Vol. 9. Kluwer Academic Publishers. doi:10.1007/0-306-48137-5. ISBN 978-0-7923-6143-5.
  2. ^ Nelson, D. L.; Cox, M. M. (2000). Lehninger, Principles of Biochemistry (3rd ed.). New York: Worth Publishing. ISBN 1-57259-153-6.
  3. ^ Tabita, F. R. (1999). "Microbial ribulose 1,5-bisphosphate carboxylase/oxygenase: A different perspective". Photosynthesis Research. 60: 1–28. doi:10.1023/A:1006211417981. S2CID 21975329.
  4. ^ a b c Sharkey, T. D. (2018). "Discovery of the canonical Calvin–Benson cycle" (PDF). Photosynthesis Research. 140 (2): 235–252. doi:10.1007/s11120-018-0600-2. OSTI 1607740. PMID 30374727. S2CID 53092349.
  5. ^ a b Benson, A. A. (1951). "Identificiation of Ribulose in C14O2 Photosynthesis Products". Journal of the American Chemical Society. 73 (6): 2971–2972. doi:10.1021/ja01150a545.
  6. ^ Benson, A. A. (2005). "Following the path of carbon in photosynthesis: a personal story". In Govindjee; Beatty, J. T.; Gest, H.; Allen, J. F. (eds.). Discoveries in Photosynthesis. Advances in Photosynthesis and Respiration. Vol. 20. pp. 795–813. doi:10.1007/1-4020-3324-9_71. ISBN 978-1-4020-3324-7.
  7. ^ Wildman, S. G. (2002). "Along the trail from Fraction I protein to Rubisco (ribulose bisphosphate carboxylase-oxygenase)" (PDF). Photosynthesis Research. 73 (1–3): 243–250. doi:10.1023/A:1020467601966. PMID 16245127. S2CID 7622999.
  8. ^ Lorimer, G. H.; Andrews, T. J.; et al. (1986). "2´-carboxy-3-keto-D-arabinitol 1,5-bisphosphate, the six-carbon intermediate of the ribulose bisphosphate carboxylase reaction". Phil. Trans. R. Soc. Lond. B. 313 (1162): 397–407. Bibcode:1986RSPTB.313..397L. doi:10.1098/rstb.1986.0046.
  9. ^ Mauser, H.; King, W. A.; Gready, J. E.; Andrews, T. J. (2001). "CO2 Fixation by Rubisco: Computational Dissection of the Key Steps of Carboxylation, Hydration, and C−C Bond Cleavage". J. Am. Chem. Soc. 123 (44): 10821–10829. doi:10.1021/ja011362p. PMID 11686683.
  10. ^ Kaiser, G. E. "Light Independent Reactions". Biol 230: Microbiology. The Community College of Baltimore County, Catonsville Campus. Retrieved 7 May 2021.
  11. ^ a b Hatch, M. D.; Slack, C. R. (1970). "Photosynthetic CO2-Fixation Pathways". Annual Review of Plant Physiology. 21: 141–162. doi:10.1146/annurev.pp.21.060170.001041.
  12. ^ Bartee, L.; Shriner, W.; Creech, C. (2017). "The Light Independent Reactions (aka the Calvin Cycle)". Principles of Biology. Open Oregon Educational Resources. ISBN 978-1-63635-041-7.
  13. ^ Jordan, D. B.; Chollet, R. (1983). "Inhibition of ribulose bisphosphate carboxylase by substrate ribulose 1,5-bisphosphate". Journal of Biological Chemistry. 258 (22): 13752–13758. doi:10.1016/S0021-9258(17)43982-2. PMID 6417133.
  14. ^ Spreitzer, R. J.; Salvucci, M. E. (2002). "Rubisco: Structure, Regulatory Interactions, and Possibilities for a Better Enzyme". Annual Review of Plant Biology. 53: 449–475. doi:10.1146/annurev.arplant.53.100301.135233. PMID 12221984.
  15. ^ Taylor, Thomas C.; Andersson, Inger (1997). "The structure of the complex between rubisco and its natural substrate ribulose 1,5-bisphosphate". Journal of Molecular Biology. 265 (4): 432–444. doi:10.1006/jmbi.1996.0738. PMID 9034362.
  16. ^ Leegood, R. C.; Edwards, G. E. (2004). "Carbon Metabolism and Photorespiration: Temperature Dependence in Relation to Other Environmental Factors". In Baker, N. R. (ed.). Photosynthesis and the Environment. Advances in Photosynthesis and Respiration. Vol. 5. Kluwer Academic Publishers. pp. 191–221. doi:10.1007/0-306-48135-9_7. ISBN 978-0-7923-4316-5.
  17. ^ Keys, A. J.; Sampaio, E. V. S. B.; et al. (1977). "Effect of Temperature on Photosynthesis and Photorespiration of Wheat Leaves". Journal of Experimental Botany. 28 (3): 525–533. doi:10.1093/jxb/28.3.525.
  18. ^ Sharkey, T. D. (1988). "Estimating the rate of photorespiration in leaves". Physiologia Plantarum. 73 (1): 147–152. doi:10.1111/j.1399-3054.1988.tb09205.x.
  19. ^ a b Kebeish, R.; Niessen, M.; et al. (2007). "Chloroplastic photorespiratory bypass increases photosynthesis and biomass production in Arabidopsis thaliana". Nature Biotechnology. 25 (5): 593–599. doi:10.1038/nbt1299. PMID 17435746. S2CID 22879451.
  20. ^ a b Leegood, R. C.; Lea, P. J.; et al. (1995). "The regulation and control of photorespiration". Journal of Experimental Botany. 46: 1397–1414. doi:10.1093/jxb/46.special_issue.1397. JSTOR 23694986.
  21. ^ Bathellier, C.; Tcherkez, G.; et al. (2018). "Rubisco is not really so bad". Plant, Cell and Environment. 41 (4): 705–716. doi:10.1111/pce.13149. hdl:1885/231026. PMID 29359811. S2CID 3718311.
  22. ^ Niewiadomska, E.; Borland, A. M. (2008). "Crassulacean Acid Metabolism: A Cause or Consequence of Oxidative Stress in Planta?". In Lüttge, U.; Beyschlag, W.; Murata, J. (eds.). Progress in Botany. Vol. 69. pp. 247–266. doi:10.1007/978-3-540-72954-9_10. ISBN 978-3-540-72954-9.
  23. ^ a b Latzko, E.; Gibbs, M. (1972). "Measurement of the intermediates of the photosynthetic carbon reduction cycle, using enzymatic methods". Photosynthesis and Nitrogen Fixation Part B. Methods in Enzymology. Vol. 24. Academic Press. pp. 261–268. doi:10.1016/0076-6879(72)24073-3. ISBN 9780121818876. ISSN 0076-6879. PMID 4670193.
  24. ^ Latzko, E.; Gibbs, M. (1969). "Level of Photosynthetic Intermediates in Isolated Spinach Chloroplasts". Plant Physiology. 44 (3): 396–402. doi:10.1104/pp.44.3.396. PMC 396097. PMID 16657074.
  25. ^ Sicher, R. C.; Bahr, J. T.; Jensen, R. G. (1979). "Measurement of Ribulose 1,5-Bisphosphate from Spinach Chloroplasts". Plant Physiology. 64 (5): 876–879. doi:10.1104/pp.64.5.876. PMC 543382. PMID 16661073.
  1. ^ Note that G3P is a 3-carbon sugar so its abundance should be twice that of the 6-carbon RuBP, after accounting for rates of enzymatic catalysis.
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