Ribulose 5-phosphate

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Ribulose 5-phosphate
Ribulose 5-phosphate.svg
Names
IUPAC name
  • D-Ribulose 5-phosphate
  • 5-O-Phosphono-D-ribulose
Systematic IUPAC name
[(2R,3R)-2,3,5-Trihydroxy-4-oxopentyl] dihydrogen phosphate
Identifiers
3D model (JSmol)
ChEBI
ChemSpider
MeSH ribulose+5-phosphate
PubChem CID
UNII
  • InChI=1S/C5H11O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h4-6,8-9H,1-2H2,(H2,10,11,12)/p-2/t4-,5+/m1/s1 Yes check.svgY
    Key: FNZLKVNUWIIPSJ-UHNVWZDZSA-L Yes check.svgY
  • InChI=1/C5H11O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h4-6,8-9H,1-2H2,(H2,10,11,12)/p-2/t4-,5+/m1/s1
    Key: FNZLKVNUWIIPSJ-DAZPBWGKBO
  • C([C@H]([C@H](C(=O)CO)O)O)OP(=O)(O)O
Properties
C5H11O8P
Molar mass 230.109 g·mol−1
Except where otherwise noted, data are given for materials in their standard state (at 25 °C [77 °F], 100 kPa).
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Ribulose 5-phosphate is one of the end-products of the pentose phosphate pathway. It is also an intermediate in the Calvin cycle.

It is formed by phosphogluconate dehydrogenase in the pentose phosphate pathway. [1] [2] Ribulose 5-phosphate is involved in various metabolic pathways. Ribulose 5-phosphate can be acted upon by phosphopentose isomerase to form Ribose 5-phosphate, which is a precursor for nucleotide and co-factor biosynthesis. [1] Ribulose-5 phosphate can also be acted upon by phosphopentose epimerase to form Xylulose 5-phosphate, which is used in the nonoxidative phase of the pentose phosphate pathway in humans to generate precursor molecules for the synthesis of aromatic amino acids and production of energy. [2]

In plants, Ribulose 5-phosphate produced from the pentose-phosphate pathway is converted into Ribulose-1-5-bisphosphate by the enzyme phosphoribokinase.

See also


Related Research Articles

In biochemistry, isomerases are a general class of enzymes that convert a molecule from one isomer to another. Isomerases facilitate intramolecular rearrangements in which bonds are broken and formed. The general form of such a reaction is as follows:

In organic chemistry, a tetrose is a monosaccharide with 4 carbon atoms. They have either an aldehyde functional group in position 1 (aldotetroses) or a ketone group in position 2 (ketotetroses).

<span class="mw-page-title-main">Calvin cycle</span> Light-independent reactions in photosynthesis

The Calvin cycle, light-independent reactions, bio synthetic phase, dark reactions, or photosynthetic carbon reduction (PCR) cycle of photosynthesis is a series of chemical reactions that convert carbon dioxide and hydrogen-carrier compounds into glucose. The Calvin cycle is present in all photosynthetic eukaryotes and also many photosynthetic bacteria. In plants, these reactions occur in the stroma, the fluid-filled region of a chloroplast outside the thylakoid membranes. These reactions take the products of light-dependent reactions and perform further chemical processes on them. The Calvin cycle uses the chemical energy of ATP and reducing power of NADPH from the light dependent reactions to produce sugars for the plant to use. These substrates are used in a series of reduction-oxidation (redox) reactions to produce sugars in a step-wise process; there is no direct reaction that converts several molecules of CO2 to a sugar. There are three phases to the light-independent reactions, collectively called the Calvin cycle: carboxylation, reduction reactions, and ribulose 1,5-bisphosphate (RuBP) regeneration.

<span class="mw-page-title-main">Pentose phosphate pathway</span> Series of interconnected biochemical reactions

The pentose phosphate pathway is a metabolic pathway parallel to glycolysis. It generates NADPH and pentoses as well as ribose 5-phosphate, a precursor for the synthesis of nucleotides. While the pentose phosphate pathway does involve oxidation of glucose, its primary role is anabolic rather than catabolic. The pathway is especially important in red blood cells (erythrocytes). The reactions of the pathway were elucidated in the early 1950s by Bernard Horecker and co-workers.

<span class="mw-page-title-main">Ribulose</span> Monosaccharide with five carbon atoms and a ketone functional group

Ribulose is a ketopentose — a monosaccharide containing five carbon atoms, and including a ketone functional group. It has chemical formula C5H10O5. Two enantiomers are possible, d-ribulose and l-ribulose. d-Ribulose is the diastereomer of d-xylulose.

<span class="mw-page-title-main">Transketolase</span> Enzyme involved in metabolic pathways

Transketolase is an enzyme that, in humans, is encoded by the TKT gene. It participates in both the pentose phosphate pathway in all organisms and the Calvin cycle of photosynthesis. Transketolase catalyzes two important reactions, which operate in opposite directions in these two pathways. In the first reaction of the non-oxidative pentose phosphate pathway, the cofactor thiamine diphosphate accepts a 2-carbon fragment from a 5-carbon ketose (D-xylulose-5-P), then transfers this fragment to a 5-carbon aldose (D-ribose-5-P) to form a 7-carbon ketose (sedoheptulose-7-P). The abstraction of two carbons from D-xylulose-5-P yields the 3-carbon aldose glyceraldehyde-3-P. In the Calvin cycle, transketolase catalyzes the reverse reaction, the conversion of sedoheptulose-7-P and glyceraldehyde-3-P to pentoses, the aldose D-ribose-5-P and the ketose D-xylulose-5-P.

The L-arabinose operon, also called the ara or araBAD operon, is an operon required for the breakdown of the five-carbon sugar L-arabinose in Escherichia coli. The L-arabinose operon contains three structural genes: araB, araA, araD, which encode for three metabolic enzymes that are required for the metabolism of L-arabinose. AraB (ribulokinase), AraA, and AraD produced by these genes catalyse conversion of L-arabinose to an intermediate of the pentose phosphate pathway, D-xylulose-5-phosphate.

<span class="mw-page-title-main">Ribose 5-phosphate</span> Chemical compound

Ribose 5-phosphate (R5P) is both a product and an intermediate of the pentose phosphate pathway. The last step of the oxidative reactions in the pentose phosphate pathway is the production of ribulose 5-phosphate. Depending on the body's state, ribulose 5-phosphate can reversibly isomerize to ribose 5-phosphate. Ribulose 5-phosphate can alternatively undergo a series of isomerizations as well as transaldolations and transketolations that result in the production of other pentose phosphates as well as fructose 6-phosphate and glyceraldehyde 3-phosphate.

<span class="mw-page-title-main">Xylulose 5-phosphate</span> Chemical compound

D-Xylulose 5-phosphate (D-xylulose-5-P) is an intermediate in the pentose phosphate pathway. It is a ketose sugar formed from ribulose-5-phosphate by ribulose-5-phosphate epimerase. In the non-oxidative branch of the pentose phosphate pathway, xylulose-5-phosphate acts as a donor of two-carbon ketone groups in transketolase reactions.

<span class="mw-page-title-main">Phosphopentose epimerase</span> Class of enzymes

Phosphopentose epimerase encoded in humans by the RPE gene is a metalloprotein that catalyzes the interconversion between D-ribulose 5-phosphate and D-xylulose 5-phosphate.

<span class="mw-page-title-main">6-phosphogluconolactonase</span> Cytosolic enzyme

6-Phosphogluconolactonase (EC 3.1.1.31, 6PGL, PGLS, systematic name 6-phospho-D-glucono-1,5-lactone lactonohydrolase) is a cytosolic enzyme found in all organisms that catalyzes the hydrolysis of 6-phosphogluconolactone to 6-phosphogluconic acid in the oxidative phase of the pentose phosphate pathway:

Glucose-1,6-bisphosphate synthase is a type of enzyme called a phosphotransferase and is involved in mammalian starch and sucrose metabolism. It catalyzes the transfer of a phosphate group from 1,3-bisphosphoglycerate to glucose-1-phosphate, yielding 3-phosphoglycerate and glucose-1,6-bisphosphate.

<span class="mw-page-title-main">Xylose metabolism</span>

D-Xylose is a five-carbon aldose that can be catabolized or metabolized into useful products by a variety of organisms.

<span class="mw-page-title-main">Phosphogluconate dehydrogenase (decarboxylating)</span>

In enzymology, a phosphogluconate dehydrogenase (decarboxylating) (EC 1.1.1.44) is an enzyme that catalyzes the chemical reaction

<span class="mw-page-title-main">L-ribulose-5-phosphate 4-epimerase</span>

In enzymology, a L-ribulose-5-phosphate 4-epimerase is an enzyme that catalyzes the interconversion of ribulose 5-phosphate and xylulose 5-phosphate in the oxidative phase of the Pentose phosphate pathway.

In enzymology, a phosphopentomutase is an enzyme that catalyzes the chemical reaction

<span class="mw-page-title-main">Ribose-5-phosphate isomerase</span>

Ribose-5-phosphate isomerase (Rpi) encoded by the RPIA gene is an enzyme that catalyzes the conversion between ribose-5-phosphate (R5P) and ribulose-5-phosphate (Ru5P). It is a member of a larger class of isomerases which catalyze the interconversion of chemical isomers. It plays a vital role in biochemical metabolism in both the pentose phosphate pathway and the Calvin cycle. The systematic name of this enzyme class is D-ribose-5-phosphate aldose-ketose-isomerase.

<span class="mw-page-title-main">Phosphoribulokinase</span>

Phosphoribulokinase (PRK) (EC 2.7.1.19) is an essential photosynthetic enzyme that catalyzes the ATP-dependent phosphorylation of ribulose 5-phosphate (RuP) into ribulose 1,5-bisphosphate (RuBP), both intermediates in the Calvin Cycle. Its main function is to regenerate RuBP, which is the initial substrate and CO2-acceptor molecule of the Calvin Cycle. PRK belongs to the family of transferase enzymes, specifically those transferring phosphorus-containing groups (phosphotransferases) to an alcohol group acceptor. Along with ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCo), phosphoribulokinase is unique to the Calvin Cycle. Therefore, PRK activity often determines the metabolic rate in organisms for which carbon fixation is key to survival. Much initial work on PRK was done with spinach leaf extracts in the 1950s; subsequent studies of PRK in other photosynthetic prokaryotic and eukaryotic organisms have followed. The possibility that PRK might exist was first recognized by Weissbach et al. in 1954; for example, the group noted that carbon dioxide fixation in crude spinach extracts was enhanced by the addition of ATP. The first purification of PRK was conducted by Hurwitz and colleagues in 1956.

ATP + Mg2+ - D-ribulose 5-phosphate  ADP + D-ribulose 1,5-bisphosphate

In enzymology, a ribose 1,5-bisphosphate phosphokinase is an enzyme that catalyzes the chemical reaction

Ribose-5-phosphate isomerase deficiency (RPID) is a rare human disorder caused by mutations in ribose-5-phosphate isomerase, an enzyme of the pentose phosphate pathway. With only four diagnosed patients over a 27-year period, RPI deficiency is the second rarest disease known as of now, being beaten only by Fields Condition affecting two known individuals, Catherine and Kirstie Fields.

References

  1. 1 2 Edwards, Thomas E.; Abramov, Ariel B.; Smith, Eric R.; Baydo, Ruth O.; Leonard, Jess T.; Leibly, David J.; Thompkins, Kaitlin B.; Clifton, Matthew C.; Gardberg, Anna S.; Staker, Bart L.; Van Voorhis, Wesley C.; Myler, Peter J.; Stewart, Lance J. (2011-10-13). "Structural characterization of a ribose-5-phosphate isomerase B from the pathogenic fungus Coccidioides immitis". BMC Structural Biology. 11: 39. doi: 10.1186/1472-6807-11-39 . ISSN   1472-6807. PMC   3212906 . PMID   21995815.
  2. 1 2 Liang, Wenguang; Ouyang, Songying; Shaw, Neil; Joachimiak, Andrzej; Zhang, Rongguang; Liu, Zhi-Jie (2010-10-05). "Conversion of<scp>d</scp>-ribulose 5-phosphate to<scp>D</scp>-xylulose 5-phosphate: new insights from structural and biochemical studies on human RPE". The FASEB Journal. 25 (2): 497–504. doi: 10.1096/fj.10-171207 . ISSN   0892-6638. PMC   6188353 . PMID   20923965.