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© 2006 by The International Union of Biochemistry and Molecular Biology BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION

Printed in U.S.A. Vol. 34, No. 4, pp. 275–277, 2006

Articles

Pentose Phosphate and Calvin Cycles


SIMILARITIES AND THREE-DIMENSIONAL VIEWS*

Received for publication, December 6, 2005, and in revised form, February 8, 2006

Antonio Sillero‡§, Vitali A. Selivanov¶, and Marta Cascante¶


‡From Departamento de Bioquı́mica, Instituto de Investigaciones Biomédicas Alberto Sols, Consejo Superior de
Investigaciones Cientı́ficas-Universidad Autónoma de Madrid, Facultad de Medicina, Universidad Autónoma de
Madrid, Arzobispo Morcillo 4, 28029 Madrid, Spain and the ¶Departamento de Bioquı́mica i Biologia Molecular,
Facultat de Quı́mica and Centre de Recerca en Quı́mica Teòrica at Parc Cientific de Barcelona,
Catalunya, Spain

The main object of this work is to present simplified and three-dimensional views of the pentose phosphate
and Calvin cycles, emphasizing their functional and chemical similarities.
Keywords: Pentose phosphate cycle, Calvin cycle, tri-dimensional representation.

The pentose phosphate and Calvin cycles are usually formed into ribulose-5-phosphate by the action in sequence
illustrated, in textbooks [1– 8] and other publications of three enzymes (numbered as in Fig. 1): glucose-6-phos-
[9 –14], as bi-dimensional diagrams composed of nodes phate dehydrogenase (1), gluconolactonase (2), and 6-fos-
and lines (representing substrates and enzymes) and with fogluconate dehydrogenase (3). During this part, formation
connections with the glycolytic pathway. Both cycles of 1 mol of CO2 and 2 mol each of NADPH and proton takes
share characteristics that make them different from other place per mole of glucose-6-phosphate (Fig. 1; Table I).
classical linear pathways. Some of their substrates: (i) The interchange of carbon atoms between the glycolytic
participate in bi-substrate reactions, (ii) are the center of and the pentose pathways takes place at the level of
small metabolic crossroads as can be metabolized by 2–3 fructose-6-phosphate and/or glyceraldehyde-3-phos-
enzymes, and (iii) are part of cyclic pathways. Thus, the phate. The pentose phosphate cycle is also intercon-
planar representation of both cycles is usually composed nected with other pathways, related mainly to nucleotide
of intercrossing lines that cannot be easily grasped by and lipid metabolism (not represented in Fig. 1). As hap-
students of biochemical courses. Also, the similarity be- pens with the Krebs cycle, the pentose phosphate cycle
tween both cycles is not clearly visualized. As shown be- may have anabolic or catabolic functions depending on
low, these difficulties have been partially solved by a three- the entrance or exit of metabolites. Further metabolism of
dimensional representation of the pentose phosphate (Fig. glucose connected with the pentose phosphate cycle is
1) and the Calvin pathways (Fig. 2). For additional details, carried out by the classical glycolytic/gluconeogenic path-
the student may consult any of the excellent biochemistry ways (Fig. 1).
textbooks presently available.
CALVIN CYCLE (FIG. 2)
PENTOSE PHOSPHATE CYCLE (FIG. 1)
This cycle is part of the photosynthetic CO2 fixation
This cycle is a major cytosolic pathway of carbohydrate carried out in the chloroplasts, vegetable cell organelles.
metabolism in some tissues, an alternative to glycolysis for Chloroplasts are surrounded by a double outer membrane
the oxidation of glucose in all tissues, and essential for the and contain in their interior membrane structures called
synthesis of NADPH (a dinucleotide required mainly, but thylakoids, which are piled up into stakes called grana.
not exclusively, for biosynthetic pathways) and ribose-5- Grana bear chlorophyll and the enzymes responsible for
phosphate (a precursor of purine and pyrimidine nucleo- the light reactions of photosynthesis leading to the syn-
tides). Two stages are usually considered in this cycle: the thesis of ATP and NADPH. The grana are immersed in the
oxidative and non-oxidative phases of the pentose pathway. stroma, the gel-like matrix of the chloroplasts containing
In the oxidative part (Fig. 1), glucose-6-phosphate is trans- prokaryotic DNA, RNA, 70 S ribosomes, and soluble en-
zymes implicated in several biosynthetic processes such
* This work was supported by grants from the Instituto de Salud as fatty acids, isoprenoids, amino acids, nucleotides and
Carlos III (Grant RMN-C03/08) Madrid, Spain (to A. S.); the Span- conversion of CO2 to carbohydrates, etc. This last conver-
ish Ministerio de Ciencia y Tecnologı́a (Grants SAF2002-02785 sion, carried out with the help of ATP and NADPH gener-
and PPQ2003-06602-C04) (to M. C.), and Generalitat de Catalu-
nya (Grant ABM/acs/PIV2002-32) (to V. A. S.). ated in the photosynthetic reactions, is called the Calvin
§ To whom correspondence should be addressed. E-mail: cycle, reductive pentose phosphate pathway, or photo-
antonio.sillero@uam.es synthetic carbon reduction cycle.
This paper is available on line at http://www.bambed.org 275
276 BAMBED, Vol. 34, No. 4, pp. 275–277, 2006

FIG. 1. A three-dimensional view of the pentose phosphate


cycle. The cycle is composed of two parts: oxidative and non-
oxidative. Both parts are enclosed in a dotted line. In the first part,
glucose-6-P (G6P) is irreversible transformed into RL5P. The FIG. 2. A three-dimensional view of the Calvin cycle. Three
non-oxidative part of the cycle is depicted with a gray background phases can be considered in this cycle. First, fixation of CO2,
and is carried out by enzymes catalyzing reversible reactions. The carried out by enzymes 23 and 24 (see the abbreviation footnote,
cubic structure comprises the reaction catalyzed by transaldolase Table I, the legend for Fig. 1 for the abbreviations of substrates,
and transketolase. The interconnections between the glycolysis name of enzymes, and reactions catalyzed). Second, reduction of
and the pentose phosphate pathways take place at the level of 3PG, carried out by enzymes 18 and 17, with formation of GAP or
glucose-6-P, fructose-6-phosphate, and glyceraldehyde-3-P. glyceraldehyde-3-P. Third, regeneration of RL5P; this part is
The abbreviations correspond to the following compounds: G1P, composed by enzymes 16, 15, 14, and 4 –7 (catalyzing similar
glucose-1-P; 2PG, 2-phosphoglycerate; PEP, phosphoenol pyru- reactions as in the pentose phosphate cycle, see Fig. 1) and by
vate; 6PGLone, 6-phosphogluconolactone; 6PGLate, 6-phos- enzymes 23, 24, and 14 –16. These reactions occur in the stroma
phogluconate; R5P, ribose-5-P. K 18 represents the Krebs cycle. part of the chloroplast. GAP can also be transported to the
The numbers in the figure correspond to the following enzymes: cytosol where synthesis of starch (reactions 8 –11), and other
1, glucose-6-P dehydrogenase; 2, gluconolactonase; 3, 6-P-glu- reactions (15–22) can bring GAP to the Krebs cycle or to the
conate dehydrogenase; 4, ribulose-5-P 3-epimerase; 5, ribulose- synthesis of other compounds. In addition to the components of
5-P-isomerase; 6, transketolase; 7, transaldolase; 8, enzymes the pentose phosphate pathway specified in Fig. 1, the following
acting in the interconversion glucose 1-P 7 glycogen; 9, phos- elements participate in the Calvin cycle: (i) two more substrates,
phoglucomutase; 10, glucose-6-phosphatase; 11, hexokinase; sedoheptulose-1,7-bisphosphate (S1,7P) and RL1,5P and (ii) the
12, phosphoglucose isomerase; 13, 6-phosphofructokinase; 14, following enzymes, phosphoribulose kinase (23), Rubisco (24),
fructose-1,6-bisphosphatase; 15, aldolase; 16, triosephosphate transaldolase (25), and sedoheptulose 1,7-bisphosphatase (26).
isomerase; 17, glyceraldehyde-3-P dehydrogenase; 18, phos- The parts in gray emphasize the similarity between the pentose
phoglycerate kinase; 19, phosphoglycerate mutase; 20, enolase; phosphate and the Calvin cycles. The reactions more directly
21, pyruvate kinase; 22, pyruvate dehydrogenase. The reactions involved in the Calvin cycle are enclosed by a dotted line.
catalyzed by these enzymes are specified in Table I. The parts in
gray emphasize the similarity between the pentose phosphate
and the Calvin cycles and ribulose-1,5-bisphosphate carboxylase, or Rubisco
(24) (Fig. 2; Table I). This enzyme constitutes of around
Three phases can be considered in the Calvin cycle (Fig. 50% of the soluble protein in a leaf and is considered the
2): fixation of CO2 into 3-phosphoglycerate (3PG),1 or the most abundant protein on earth. Two moles of 3PG are
carboxylation phase; reduction of 3PG into glyceralde- formed from 1 mol of ribulose-1,5-bisphosphate.
hyde-3-phosphate (GAP), or the reduction phase; and re- The reduction of 3PG to GAP is catalyzed by 3-phos-
synthesis of ribulose-1,5-bisphosphate, or the regenera- phoglycerate kinase (18) and glyceraldehyde-3-phosphate
tive phase. The fixation of CO2 is catalyzed by two dehydrogenase (17). Note that these two reactions are
enzymes acting in sequence: phosphoribulose kinase (23) driven in the direction of synthesis of GAP by the conver-
sion of ATP to ADP and NADPH to NADP⫹. It can be
1
The abbreviations used are: 3PG, 3-phosphoglycerate; GAP, considered that 12 mol of GAP are formed from 6 mol of
glyceraldehyde-3-P; RL5P, ribulose-5-phosphate; RL1,5P, ribu- ribulose-5-P, i.e. a net gain of six carbon atoms, through the
lose-1,5-phosphate; G6P, glucose-6-P; XL5P, xilulose 5-P; E4P, carboxylation and reduction phases of the cycle. These 12
erythrose-4-P; DHAP, dihydroxyacetone-P; F6P, fructose-6-phos- mol of glyceraldehyde-3-P may follow two different meta-
phate; F1,6-P, fructose-1,6-bisphosphate; S1,7P, sedoheptu-
lose-1,7-bisphosphate; S7P, sedoheptulose-7-P; 1,3PG, 1,3-bis- bolic routes: 10 mol toward the regeneration of ribulose
phosphoglycerate; Rubisco, ribulose-bisphosphate carboxylase/ 1,5-phosphate (RL1,5P) and 2 mol toward the synthesis of
oxygenase. starch or other organic compounds. The synthesis of ribu-
277
TABLE I
Enzymes and reactions involved in the pentose phosphate and Calvin cycles
Asterisks indicate ketosugars. The number of the enzymes and the abbreviations correspond to those designed in Figs. 1 and 2. G1P,
glucose 1-P; R5P, ribose 5-P; 2PG, 2-phosphoglycerate; PEP, phosphoenol pyruvate.
Enzyme number
Pentose Phosphate Calvin cycle Enzyme name Reaction catalyzed
(Fig. 1) (Fig. 2)
1 — Glucose 6-phosphate dehydrogenase G6P ⫹ NADP⫹ 3 6-PGLone ⫹ NADPH ⫹ H⫹
2 — Gluconolactonase 6-PGone ⫹ H2O 3 6-PGLnate ⫹ H⫹
3 — 6-P-gluconate DH 6-PGLnate ⫹ NADP⫹ 3 *RL5P ⫹ NADPH ⫹ H⫹ ⫹ CO2
4 4 Ribulose 5-phosphate 3-epimerase *RL5P 7 *XL5P
5 5 Ribulose 5-phosphate isomerase *RL5P 7 R5P
6 6 Transketolase *XL5P ⫹ E4P7 GAP ⫹ *F6P
6 6 Transketolase *XL5P ⫹ R5P 7 GAP ⫹ *S7P
7 7 Transaldolase *S7P ⫹ GAP 7 *F6P ⫹ E4P
8 8 Synthesis, degradation of Glycogen/Starch G1P 7 Glycogen/Starch
9 9 Phosphoglucomutase G1P 7 G6P
10 10 Glucose 6-phosphatase G6P 3 Glucose
11 11 Hexokinase Glucose ⫹ATP 3 G6P ⫹ ADP
12 12 Phosphoglucose isomerase G6P 7*F6P
13 13 6-Phosphofructokinase *F6P ⫹ATP 3 *F1,6P ⫹ADP
14 14 Fructose bisphosphatase *F1,6P 3 *F6P ⫹Pi
15 15 Fructose bisphosphate aldolase *F1,6P ⫹ H2O7*DHAP ⫹ GAP
16 16 Triosephosphate isomerase *DHAP 7 GAP
17 — Glyceraldehyde 3-phosphate dehydrogenase GAP ⫹ NAD⫹ ⫹ Pi 7 1,3PG ⫹ NADH ⫹ H⫹
— 17 Glyceraldehyde 3-phosphate dehydrogenase GAP ⫹ NADP⫹ ⫹ Pi 7 1,3PG ⫹ NADPH ⫹ H⫹
18 18 Phosphoglycerate kinase 1,3PG ⫹ ADP 7 3PG ⫹ ATP
19 19 Phosphoglycerate mutase 3PG 7 2PG
20 20 Enolase 2PG 7 PEP ⫹ H2O
21 21 Pyruvate kinase PEP ⫹ ADP 7 Pyruvate ⫹ ATP
22 22 Pyruvate dehydrogenase complex Pyruvate ⫹ CoA ⫹ NAD⫹ 3 Acetyl-CoA ⫹ NADH ⫹
H⫹ ⫹ CO2
— 23 Phosphoribulose kinase *RL5P ⫹ ATP 3 *RL1,5P ⫹ ADP
— 24 Ribulose-bisphosphatecarboxylase (Rubisco) *RL1,5P ⫹ CO2 ⫹ H2O 3 (2) 3PG ⫹ 2 H⫹
— 25 Transaldolase *DHAP ⫹ E4P 7 *S1,7P
— 26 Sedoheptulose 1,7-bisphosphatase *S1,7P ⫹ H2O 3 *S7P ⫹ Pi

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