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Ribulose 1,5-bisphosphate

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Ribulose 1,5-bisphosphate(RuBP) is anorganic substancethat is involved inphotosynthesis,notably as the principalCO2acceptorin plants.[1]: 2 It is a colourless anion, a doublephosphate esterof theketopentose(ketone-containing sugar with fivecarbonatoms) calledribulose.Salts of RuBP can be isolated, but its crucial biological function happens in solution.[2]RuBP occurs not only in plants but in alldomains of life,includingArchaea,Bacteria,andEukarya.[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/s1checkY
    Key: YAHZABJORDUQGO-NQXXGFSBSA-NcheckY
  • O=P(O)(OCC(=O)[C@H](O)[C@H](O)COP(=O)(O)O)O
Properties
C5H12O11P2
Molar mass 310.088g·mol−1
Except where otherwise noted, data are given for materials in theirstandard state(at 25 °C [77 °F], 100 kPa).

History

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RuBP was originally discovered byAndrew Bensonin 1951 while working in the lab ofMelvin Calvinat 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 asribulose diphosphate(RDP or RuDP) but the prefixdi-was changed tobis-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 andcarbon 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-carbonβ-ketoacidintermediate hydrates into another six-carbon intermediate in the form of agem-diol.[9]This intermediate then cleaves into two molecules of3-phosphoglycerate(3-PGA) which is used in a number of metabolic pathways and is converted into glucose.[10][11]

In theCalvin-Benson cycle,RuBP is a product of thephosphorylationofribulose-5-phosphate(produced byglyceraldehyde 3-phosphate) byATP.[11][12]

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

Interactions with rubisco

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RuBP acts as anenzyme inhibitorfor 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 withCO2andMg2+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 calledphotorespiration,a process that is more prevalent at high temperatures.[16][17]During photorespiration RuBP combines withO
2to 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 theenzymatic kineticsof rubisco have been contested.[21]Due to enhanced RuBP carboxylation and decreased rubisco oxygenation stemming from the increased concentration ofCO2in thebundle sheath,rates of photorespiration are decreased inC4plants.[1]: 103 Similarly, photorespiration is limited inCAM photosynthesisdue to kinetic delays in enzyme activation, again stemming from the ratio of carbon dioxide to oxygen.[22]

Measurement

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RuBP can bemeasured isotopicallyvia the conversion of14CO2and RuBP intoglyceraldehyde 3-phosphate.[23]G3P can then be measured using anenzymatic 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. ^abcLeegood, 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.ISBN978-0-7923-6143-5.
  2. ^Nelson, D. L.; Cox, M. M. (2000).Lehninger, Principles of Biochemistry(3rd ed.). New York: Worth Publishing.ISBN1-57259-153-6.
  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.S2CID21975329.
  4. ^abcSharkey, T. D. (2018)."Discovery of the canonical Calvin–Benson cycle"(PDF).Photosynthesis Research.140(2): 235–252.doi:10.1007/s11120-018-0600-2.OSTI1607740.PMID30374727.S2CID53092349.
  5. ^abBenson, 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.ISBN978-1-4020-3324-7.
  7. ^Wildman, S. G. (2002)."Along the trail from Fraction I protein to Rubisco (ribulosebisphosphatecarboxylase-oxygenase) "(PDF).Photosynthesis Research.73(1–3): 243–250.doi:10.1023/A:1020467601966.PMID16245127.S2CID7622999.
  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.PMID11686683.
  10. ^Kaiser, G. E."Light Independent Reactions".Biol 230: Microbiology.The Community College of Baltimore County, Catonsville Campus.Retrieved7 May2021.
  11. ^abHatch, 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.ISBN978-1-63635-041-7.
  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.PMID6417133.
  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.PMID12221984.
  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.PMID9034362.
  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.ISBN978-0-7923-4316-5.
  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. ^abKebeish, R.; Niessen, M.; et al. (2007). "Chloroplastic photorespiratory bypass increases photosynthesis and biomass production inArabidopsis thaliana".Nature Biotechnology.25(5): 593–599.doi:10.1038/nbt1299.PMID17435746.S2CID22879451.
  20. ^abLeegood, 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.JSTOR23694986.
  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.PMID29359811.S2CID3718311.
  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.ISBN978-3-540-72954-9.
  23. ^abLatzko, 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.ISBN9780121818876.ISSN0076-6879.PMID4670193.
  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.PMC396097.PMID16657074.
  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.PMC543382.PMID16661073.
  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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