Wikipedia:WikiProject Chemicals/Chembox validation/VerifiedDataSandbox and Ribulose 1,5-bisphosphate: Difference between pages

| Verifiedfields = changed

| verifiedrevid = 464382264

| ImageCaption = The acid form of the RuBP anion

| IUPACName = 1,5-Di-''O''-phosphono-<small>D</small>-ribulose

| OtherNames = Ribulose 1,5-diphosphate

|Section1 = {{Chembox Identifiers

| CASNo_Ref = {{cascite|correct|CAS}}

| CASNo = 2002-28-0

| StdInChI_Ref = {{stdinchicite|correct|chemspider}}

| ChemSpiderID = 110238

| KEGG = C01182

| PubChem = 123658

| UNII = BR374X7NAH

| SMILES = O=P(O)(OCC(=O)[C@H](O)[C@H](O)COP(=O)(O)O)O

}}

|Section2 = {{Chembox Properties

'''Ribulose 1,5-bisphosphate''' ('''RuBP''') is an [[organic substance]] that is involved in [[photosynthesis]], notably as the principal [[carbon fixation|{{chem2|CO2}} acceptor]] in plants.<ref name="ppm">{{cite book | title = Photosynthesis: Physiology and Metabolism | editor-last1 = Leegood | editor-first1 = R. C. | editor-last2 = Sharkey | editor-first2 = T. D. | editor-last3 = von Caemmerer | editor-first3 = S. | date = 2000 | publisher = Kluwer Academic Publishers | series = Advances in Photosynthesis | volume = 9 | isbn = 978-0-7923-6143-5 | doi = 10.1007/0-306-48137-5 | url = https://archive.org/details/springer_10.1007-0-306-48137-5/}}</ref>{{rp|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.<ref name="lehninger2000">{{cite book | last1 = Nelson | first1 = D. L. | last2 = Cox | first2 = M. M. | title = Lehninger, Principles of Biochemistry | edition = 3rd | publisher = Worth Publishing | location = New York | date = 2000 | isbn = 1-57259-153-6}}</ref> RuBP occurs not only in plants but in all [[Domain (biology)|domains of life]], including [[Archaea]], [[Bacteria]], and [[Eukarya]].<ref name="tabita1999">{{cite journal | last = Tabita | first = F. R. | title = Microbial ribulose 1,5-bisphosphate carboxylase/oxygenase: A different perspective | journal = Photosynthesis Research | volume = 60 | pages = 1–28 | date = 1999 | doi = 10.1023/A:1006211417981| s2cid = 21975329 }}</ref>

==History==

RuBP was originally discovered by [[Andrew Benson]] in 1951 while working in the lab of [[Melvin Calvin]] at UC Berkeley.<ref name="sharkey2018">{{cite journal | title = Discovery of the canonical Calvin–Benson cycle | last = Sharkey | first = T. D. | date = 2018 | journal = Photosynthesis Research | volume = 140 | issue = 2 | pages = 235–252 | doi = 10.1007/s11120-018-0600-2 | pmid = 30374727 | osti = 1607740 | s2cid = 53092349 | url = https://link.springer.com/content/pdf/10.1007/s11120-018-0600-2.pdf}}</ref><ref name="benson1951">{{cite journal | title = Identificiation of Ribulose in C14O2 Photosynthesis Products | last = Benson | first = A. A. | date = 1951 | journal = Journal of the American Chemical Society | volume = 73 | issue = 6 | pages = 2971–2972 | doi = 10.1021/ja01150a545}}</ref> 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".<ref name="sharkey2018" /><ref name="benson2005">{{cite book | title = Discoveries in Photosynthesis | series = Advances in Photosynthesis and Respiration | volume = 20 | chapter = Following the path of carbon in photosynthesis: a personal story | last = Benson | first = A. A. | editor-last1 = Govindjee | editor-last2 = Beatty | editor-first2 = J. T. | editor-last3 = Gest | editor-first3 = H. | editor-last4 = Allen | editor-first4 = J. F. | date = 2005 | doi = 10.1007/1-4020-3324-9_71 | isbn = 978-1-4020-3324-7 | chapter-url = https://link.springer.com/chapter/10.1007%2F1-4020-3324-9_71 | pages = 795–813}}</ref> At the time, the molecule was known as ''ribulose diphosphate'' (RDP or RuDP) but the prefix [[wikt:di|di-]] was changed to [[wikt:bis|bis-]] to emphasize the nonadjacency of the two phosphate groups.<ref name="sharkey2018" /><ref name="benson1951" /><ref name="wildman2002">{{cite journal | last = Wildman | first = S. G. | title = Along the trail from Fraction I protein to Rubisco (''r''ib''u''lose ''bis''phosphate ''c''arboxylase-''o''xygenase) | journal = Photosynthesis Research | volume = 73 | pages = 243–250 | date = 2002 | issue = 1–3 | doi = 10.1023/A:1020467601966 | pmid = 16245127 | s2cid = 7622999 | url = https://link.springer.com/content/pdf/10.1023/A:1020467601966.pdf}}</ref>

==Role in photosynthesis and the Calvin-Benson Cycle==

{{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).<ref name="lorimer1986">{{cite journal | title = 2´-carboxy-3-keto-D-arabinitol 1,5-bisphosphate, the six-carbon intermediate of the ribulose bisphosphate carboxylase reaction | journal = Phil. Trans. R. Soc. Lond. B | volume = 313 | pages = 397–407 | last1 = Lorimer | first1 = G. H. | last2 = Andrews | first2 = T. J. | display-authors = etal | date = 1986 | issue = 1162 | doi = 10.1098/rstb.1986.0046| bibcode = 1986RSPTB.313..397L }}</ref> This six-carbon [[Keto acid|β-ketoacid]] intermediate hydrates into another six-carbon intermediate in the form of a [[Geminal diol|gem-diol]].<ref name="mauser2001">{{cite journal | title = CO2 Fixation by Rubisco: Computational Dissection of the Key Steps of Carboxylation, Hydration, and C−C Bond Cleavage | last1 = Mauser | first1 = H. | last2 = King | first2 = W. A. | last3 = Gready | first3 = J. E. | last4 = Andrews | first4 = T. J. | journal = J. Am. Chem. Soc. | date = 2001 | volume = 123 | issue = 44 | pages = 10821–10829 | doi = 10.1021/ja011362p| pmid = 11686683 }}</ref> 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.<ref name="kaiser">{{cite web | last = Kaiser | first = G. E. | title = Light Independent Reactions | website = Biol 230: Microbiology | url = http://faculty.ccbcmd.edu/courses/bio141/lecguide/unit7/metabolism/photosyn/lindr.html | access-date = 7 May 2021 | publisher = The Community College of Baltimore County, Catonsville Campus}}</ref><ref name="hatch1970">{{cite journal | title = Photosynthetic CO2-Fixation Pathways | last1 = Hatch | first1 = M. D. | last2 = Slack | first2 = C. R. | date = 1970 | volume = 21 | journal = Annual Review of Plant Physiology | pages = 141–162 | doi = 10.1146/annurev.pp.21.060170.001041}}</ref>

In the [[Calvin-Benson cycle]], RuBP is a product of the [[phosphorylation]] of [[ribulose-5-phosphate]] (produced by [[glyceraldehyde 3-phosphate]]) by [[Adenosine triphosphate|ATP]].<ref name="hatch1970" /><ref name="bartee">{{cite book | chapter = The Light Independent Reactions (aka the Calvin Cycle) | title = Principles of Biology | first1 = L. | last1 = Bartee | first2 = W. | last2 = Shriner | first3 = C. | last3 = Creech | year = 2017 | chapter-url = https://openoregon.pressbooks.pub/mhccmajorsbio/chapter/calvin-cycle/ | isbn = 978-1-63635-041-7 | publisher = Open Oregon Educational Resources | url = https://openoregon.pressbooks.pub/mhccmajorsbio/}}</ref>

[[File:Calvin-cycle4.svg|thumb|left|400px|The Calvin-Benson cycle showing the role of ribulose-1,5-bisphosphate.]]

===Interactions with rubisco===

RuBP acts as an [[enzyme inhibitor]] for the enzyme rubisco, which regulates the net activity of carbon fixation.<ref name="jordan1983">{{cite journal | last1 = Jordan | first1 = D. B. | last2 = Chollet | first2 = R. | title = Inhibition of ribulose bisphosphate carboxylase by substrate ribulose 1,5-bisphosphate | journal = Journal of Biological Chemistry | volume = 258 | issue = 22 | date = 1983 | pages = 13752–13758 | doi = 10.1016/S0021-9258(17)43982-2 | pmid = 6417133| doi-access = free }}</ref><ref name="spreitzer2002">{{cite journal | title = Rubisco: Structure, Regulatory Interactions, and Possibilities for a Better Enzyme | journal = Annual Review of Plant Biology | volume = 53 | pages = 449–475 | doi = 10.1146/annurev.arplant.53.100301.135233 | date = 2002 | last2 = Salvucci | first2 = M. E. | last1 = Spreitzer | first1 = R. J.| pmid = 12221984 }}</ref><ref name="taylor1997">{{cite journal | title = The structure of the complex between rubisco and its natural substrate ribulose 1,5-bisphosphate | first1 = Thomas C. | last1 = Taylor | first2 = Inger | last2 = Andersson | journal = Journal of Molecular Biology | volume = 265 | issue = 4 | date = 1997 | doi = 10.1006/jmbi.1996.0738 | pages = 432–444| pmid = 9034362 }}</ref> When RuBP is bound to an active site of rubisco, the ability to activate via carbamylation with {{chem2|CO2}} and {{chem2|Mg(2+)}} is blocked. The functionality of rubisco activase involves removing RuBP and other inhibitory bonded molecules to re-enable carbamylation on the active site.<ref name="ppm" />{{rp|5}}

==Role in photorespiration==

{{see also|Photorespiration}}

Rubisco also catalyzes RuBP with oxygen ({{chem|O|2}}) in an interaction called [[photorespiration]], a process that is more prevalent at high temperatures.<ref name="baker1996">{{cite book | last1 = Leegood | first1 = R. C. | last2 = Edwards | first2 = G. E. | title = Photosynthesis and the Environment | chapter = Carbon Metabolism and Photorespiration: Temperature Dependence in Relation to Other Environmental Factors | pages = 191–221 | editor-last = Baker | editor-first = N. R. | publisher = Kluwer Academic Publishers | isbn = 978-0-7923-4316-5 | chapter-url = https://link.springer.com/chapter/10.1007/0-306-48135-9_7 | series = Advances in Photosynthesis and Respiration | year = 2004 | volume = 5| doi = 10.1007/0-306-48135-9_7 }}</ref><ref name="keys1977">{{cite journal | title = Effect of Temperature on Photosynthesis and Photorespiration of Wheat Leaves | last1 = Keys | first1 = A. J. | last2 = Sampaio | first2 = E. V. S. B. | display-authors = etal | journal = Journal of Experimental Botany | volume = 28 | issue = 3 | date = 1977 | pages = 525–533 | doi = 10.1093/jxb/28.3.525}}</ref> During photorespiration RuBP combines with {{chem|O|2}} to become 3-PGA and {{chem name|phosphoglycolic acid}}.<ref name="sharkey1988">{{cite journal | title = Estimating the rate of photorespiration in leaves | last = Sharkey | first = T. D. | date = 1988 | journal = Physiologia Plantarum | volume = 73 | issue = 1 | pages = 147–152 | doi = 10.1111/j.1399-3054.1988.tb09205.x}}</ref><ref name="kebeish2007">{{cite journal | title = Chloroplastic photorespiratory bypass increases photosynthesis and biomass production in ''Arabidopsis thaliana''

| last1 = Kebeish | first1 = R. | last2 = Niessen | first2 = M. | display-authors = etal | journal = Nature Biotechnology | volume = 25 | pages = 593–599 | date = 2007 | issue = 5 | doi = 10.1038/nbt1299| pmid = 17435746 | s2cid = 22879451 }}</ref><ref name="leegood1995">{{cite journal | title = The regulation and control of photorespiration | last1 = Leegood | first1 = R. C. | last2 = Lea | first2 = P. J. | display-authors = etal | journal = Journal of Experimental Botany | volume = 46 | date = 1995 | pages = 1397–1414 | jstor = 23694986 | doi = 10.1093/jxb/46.special_issue.1397}}</ref> Like the Calvin-Benson Cycle, the photorespiratory pathway has been noted for its enzymatic inefficiency<ref name="kebeish2007" /><ref name="leegood1995" /> although this characterization of the [[Enzyme kinetics|enzymatic kinetics]] of rubisco have been contested.<ref name="bathellier2018">{{cite journal | title = Rubisco is not really so bad | journal = Plant, Cell and Environment | volume = 41 | issue = 4 | pages = 705–716 | last1 = Bathellier | first1 = C. | last2 = Tcherkez | first2 = G. | year = 2018 | display-authors = etal | doi = 10.1111/pce.13149| pmid = 29359811 | hdl = 1885/231026 | s2cid = 3718311 | hdl-access = free }}</ref> Due to enhanced RuBP carboxylation and decreased rubisco oxygenation stemming from the increased concentration of {{chem2|CO2}} in the [[Vascular bundle#Bundle-sheath cells|bundle sheath]], rates of photorespiration are decreased in [[C4 carbon fixation|{{chem2|C4}} plants]].<ref name="ppm" />{{rp|103}} Similarly, photorespiration is limited in [[Crassulacean acid metabolism|CAM photosynthesis]] due to kinetic delays in enzyme activation, again stemming from the ratio of carbon dioxide to oxygen.<ref name="Niewiadomska2008">{{cite book | last1 = Niewiadomska | first1 = E. | last2 = Borland | first2 = A. M. | chapter = Crassulacean Acid Metabolism: A Cause or Consequence of Oxidative Stress in Planta? | title = Progress in Botany | volume = 69 | year = 2008 | pages = 247–266 | doi = 10.1007/978-3-540-72954-9_10 | isbn = 978-3-540-72954-9 | editor-last1 = Lüttge | editor-first1 = U. | editor-last2 = Beyschlag | editor-first2 = W. | editor-last3 = Murata | editor-first3 = J.}}</ref>

==Measurement==

RuBP can be [[isotope analysis|measured isotopically]] via the conversion of {{chem2|^{14}CO2}} and RuBP into [[glyceraldehyde 3-phosphate]].<ref name="latzko1972">{{cite book | last1 = Latzko | first1 = E. | last2 = Gibbs | first2 = M. | chapter = Measurement of the intermediates of the photosynthetic carbon reduction cycle, using enzymatic methods | title = Photosynthesis and Nitrogen Fixation Part B | series = Methods in Enzymology | volume = 24 | publisher = Academic Press | date = 1972 | pages = 261–268 | issn = 0076-6879 | isbn = 9780121818876 | doi = 10.1016/0076-6879(72)24073-3| pmid = 4670193 }}</ref> G3P can then be measured using an [[Enzyme assay|enzymatic optical assay]].<ref name="latzko1972" /><ref name="latzko1969">{{cite journal | last1 = Latzko | first1 = E. | last2 = Gibbs | first2 = M. | title = Level of Photosynthetic Intermediates in Isolated Spinach Chloroplasts | journal = Plant Physiology | volume = 44 | issue = 3 | pages = 396–402 | pmid = 16657074 | date = 1969 | doi = 10.1104/pp.44.3.396| pmc = 396097 }}</ref>{{efn|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.}} 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.<ref name="sicher1979">{{cite journal | last1 = Sicher | first1 = R. C. | last2 = Bahr | first2 = J. T. | last3 = Jensen | first3 = R. G. | title = Measurement of Ribulose 1,5-Bisphosphate from Spinach Chloroplasts | date = 1979 | journal = Plant Physiology | volume = 64 | issue = 5 | pages = 876–879 | doi = 10.1104/pp.64.5.876 | pmid = 16661073| pmc = 543382 }}</ref>

==See also==

* [[Rubisco]]

* [[Calvin-Benson cycle]]

* [[3-Phosphoglyceric acid]]

* [[Photosynthesis]]

==References==

{{reflist}}

{{notelist}}

[[Category:Photosynthesis]]

[[Category:Organophosphates]]

[[Category:Monosaccharide derivatives]]