Phosphopentose epimerase

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ribulose-phosphate 3-epimerase
3inp.jpg
D-ribulose-5-phosphate 3-epimerase dodekamer, Francisella tularensis
Identifiers
EC no. 5.1.3.1
CAS no. 9024-20-8
Databases
IntEnz IntEnz view
BRENDA BRENDA entry
ExPASy NiceZyme view
KEGG KEGG entry
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum
Gene Ontology AmiGO / QuickGO
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PMC articles
PubMed articles
NCBI proteins
Ribulose-phosphate 3 epimerase family
Identifiers
SymbolRibul_P_3_epim
Pfam PF00834
InterPro IPR000056
PROSITE PDOC00833
SCOP2 1rpx / SCOPe / SUPFAM
Available protein structures:
Pfam   structures / ECOD  
PDB RCSB PDB; PDBe; PDBj
PDBsum structure summary
PDB 1tqj B:6-208 1rpx A:58-260 1h1z A:8-208 1h1y B:8-208 1tqx A:7-208

Phosphopentose epimerase (also known as ribulose-phosphate 3-epimerase and ribulose 5-phosphate 3-epimerase, EC 5.1.3.1) encoded by the RPE gene is a metalloprotein that catalyzes the interconversion between D-ribulose 5-phosphate and D-xylulose 5-phosphate. [1]

Contents

D-ribulose 5-phosphate D-xylulose 5-phosphate

This reversible conversion is required for carbon fixation in plants – through the Calvin cycle – and for the nonoxidative phase of the pentose phosphate pathway. [2] [3] This enzyme has also been implicated in additional pentose and glucuronate interconversions.

In Cupriavidus metallidurans two copies of the gene coding for PPE are known, [4] one is chromosomally encoded P40117 , the other one is on a plasmid Q04539 . PPE has been found in a wide range of bacteria, archaebacteria, fungi and plants. All the proteins have from 209 to 241 amino acid residues. The enzyme has a TIM barrel structure.

Nomenclature

The systematic name of this enzyme class is D-ribulose-5-phosphate 3-epimerase. Other names in common use include

This enzyme participates in 3 metabolic pathways: pentose phosphate pathway, pentose and glucuronate interconversions, and carbon fixation.

The human protein containing this domain is the RPE (gene).

Family

Phosphopentose epimerase belongs to two protein families of increasing hierarchy. This enzyme belongs to the isomerase family, specifically those racemases and epimerases which act on carbohydrates and their derivatives. [1] In addition, the Structural Classification of Proteins database has defined the “ribulose phosphate binding” superfamily for which this epimerase is a member. [1] Other proteins included in this superfamily are 5‘-monophosphate decarboxylase (OMPDC), and 3-keto-l-gulonate 6-phosphate decarboxylase (KGPDC).

Structure

As of late 2007, 4 structures have been solved for this class of enzymes, with PDB accession codes 1H1Y, 1H1Z, 1RPX, and 1TQJ.

Overall

Crystallographic studies have helped elucidate the apoenzyme structure of phosphopentose epimerase. Results of these studies have shown that this enzyme exists as a homodimer in solution. [5] [6] Furthermore, Phosphopentose epimerase folds into a (β/α)8 triosephosphate isomerase (TIM) barrel that includes loops. [2] The core barrel is composed of 8 parallel strands that make up the central beta sheet, with helices located in between consecutive strands. The loops in this structure have been known to regulate substrate specificities. Specifically, the loop that connects helix α6 with strand β6 caps the active site upon binding of the substrate. [2]

As previously mentioned, Phosphopentose epimerase is a metalloenzyme. It requires a cofactor for functionality and binds one divalent metal cation per subunit. [7] This enzyme has been shown to use Zn2+ predominantly for catalysis, along with Co2+ and Mn2+. [2] However, human phosphopentose epimerase – which is encoded by the RPE gene - differs in that it binds Fe2+ predominantly in catalysis. Fe2+ is octahedrally coordinated and stabilizes the 2,3-enediolate reaction intermediate observed in the figure. [2]

Active site

The β6/α6 loop region interacts with the substrate and regulates access to the active site. Phe147, Gly148, and Ala149 of this region cap the active site once binding has occurred. In addition, the Fe2+ ion is coordinated to His35, His70, Asp37, Asp175, and oxygens O2 and O3 of the substrate. [2] The binding of substrate atoms to the iron cation helps stabilize the complex during catalysis. Mutagenesis studies have also indicated that two aspartic acids are located within the active site and help mediate catalysis through a 1,1-proton transfer reaction. [1] The aspartic acids are the acid/base catalysts. Lastly, once the ligand is attached to the active site, a series of methionines (Met39, Met72, and Met141) restrict further movement through constriction. [8]

Mechanism

This is a mechanism by which phosphopentose epimerase converts ribulose 5-phosphate to xylulose 5-phosphate. The intermediate in 2,3-trans-enediolate. Phosphoenolase Epimerase Mechanism.png
This is a mechanism by which phosphopentose epimerase converts ribulose 5-phosphate to xylulose 5-phosphate. The intermediate in 2,3-trans-enediolate.

Phosphopentose utilizes an acid/base type of catalytic mechanism. The reaction proceeds in such a way that trans-2,3-enediol phosphate is the intermediate. [9] [10] The two aspartic acids mentioned above act as proton donors and acceptors. Asp37 and Asp175 are both hydrogen bonded to the iron cation in the active site. [2] When Asp37 is deprotonated, it attacks a proton on the third carbon of D-ribulose 5-phosphate, which forms the intermediate. [11] In a concerted step, as Asp37 grabs a proton, the carbonyl bond on the substrate grabs a second proton from Asp175 to form a hydroxyl group. The iron complex helps stabilize any additional charges. It is C3 of D-ribulose 5-phosphate which undergoes this epimerization, forming D-xylulose 5-phosphate. [8] The mechanism is clearly demonstrated in the figure.

Function

Calvin cycle

Electron microscopy experiments in plants have shown that phosphopentose epimerase localizes to the thylakoid membrane of chloroplasts. [12] This epimerase participates in the third phase of the Calvin cycle, which involves the regeneration of ribulose 1,5-bisphosphate. RuBP is the acceptor of the carbon dioxide (CO2) in the first step of the pathway, which suggests that phosphopentose epimerase regulates flux through the Calvin cycle. Without the regeneration of ribulose 1,5-bisphosphate, the cycle will be unable to continue. Therefore, xylulose 5-phosphate is reversibly converted into ribulose 5-phosphate by this epimerase. Subsequently, phosphoribulose kinase converts ribulose 5-phosphate into ribulose 1,5-bisphosphate. [11]

Pentose phosphate pathway

The reactions of the pentose phosphate pathway (PPP) take place in the cytoplasm. Phosphopentose epimerase specifically affects the nonoxidative portion of the pathway, which involves the production of various sugars and precursors. [2] This enzyme converts ribulose 5-phosphate into the appropriate epimer for the transketolase reaction, xylulose 5-phosphate. [11] Therefore, the reaction that occurs in the pentose phosphate pathway is exactly the reverse of the reaction which occurs in the Calvin cycle. The mechanism remains the same and involves the formation of an enediolate intermediate.

Due to its involvement in this pathway, phosphopentose epimerase is an important enzyme for the cellular response to oxidative stress. [2] The generation of NADPH by the pentose phosphate pathway helps protect cells against reactive oxygen species. NADPH is able to reduce glutathione, which detoxifies the body by producing water from hydrogen peroxide (H2O2). [2] Therefore, not only does phosphopentose epimerase alter flux through the PPP, but it also prevents buildup of peroxides.

Evolution

The structures of many phosphopentose epimerase analogs have been discovered through crystallographic studies. [13] [14] Due to its role in the Calvin cycle and the pentose phosphate pathway, the overall structure is conserved. When the sequences of evolutionarily-distant organisms were compared, greater than 50% similarity was observed. [15] However, amino acids positioned at the dimer interface – which are involved in many intermolecular interactions – are not necessarily conserved. It is important to note that the members of the “ribulose phosphate binding” superfamily resulted from divergent evolution from a (β/α)8 - barrel ancestor. [1]

Drug targeting and malaria

The protozoan organism Plasmodium falciparum is a major causative agent of malaria. Phosphopentose epimerase has been implicated in the shikimate pathway, an essential pathway for the propagation of malaria. [16] As the enzyme converts ribulose 5-phosphate into xylulose 5-phosphate, the latter is further metabolized into erythrose 4-phosphate. The shikimate pathway then converts erythrose 4-phosphate into chorismate. [16] It is phosphopentose epimerase which allows Plasmodium falciparum to use erythorse 4-phosphate as a substrate. Due to this enzyme’s involvement in the shikimate pathway, phosphopentose epimerase is a potential drug target for developing antimalarials.

See also

Related Research Articles

<span class="mw-page-title-main">RuBisCO</span> Key enzyme of the photosynthesis involved in carbon fixation

Ribulose-1,5-bisphosphate carboxylase/oxygenase, commonly known by the abbreviations RuBisCo, rubisco, RuBPCase, or RuBPco, is an enzyme involved in light-independent part of photosynthesis, including the carbon fixation by which atmospheric carbon dioxide is converted by plants and other photosynthetic organisms to energy-rich molecules such as glucose. It emerged approximately four billion years ago in primordial metabolism prior to the presence of oxygen on earth. It is probably the most abundant enzyme on Earth. In chemical terms, it catalyzes the carboxylation of ribulose-1,5-bisphosphate.

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:

A tetrose is a monosaccharide with 4 carbon atoms. They have either an aldehyde functional group in position 1 (aldotetroses) or a ketone functional 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 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> Metabolic process

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).

<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.

<span class="mw-page-title-main">6-Phosphogluconate dehydrogenase</span> Class of enzymes

6-Phosphogluconate dehydrogenase (6PGD) is an enzyme in the pentose phosphate pathway. It forms ribulose 5-phosphate from 6-phosphogluconate:

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

Ribulose 5-phosphate is one of the end-products of the pentose phosphate pathway. It is also an intermediate in the Calvin cycle.

<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">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:

<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

In enzymology, a L-ribulose-5-phosphate 3-epimerase 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.

<span class="mw-page-title-main">Phosphoribosylanthranilate isomerase</span> Enzyme involved in tryptophan synthesis

In enzymology, a phosphoribosylanthranilate isomerase (PRAI) is an enzyme that catalyzes the third step of the synthesis of the amino acid tryptophan.

<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">Pyridoxine 5'-phosphate synthase</span> Class of enzymes

In enzymology, a pyridoxine 5'-phosphate synthase (EC 2.6.99.2) is an enzyme that catalyzes the chemical reaction

<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
<span class="mw-page-title-main">RPE (gene)</span> Protein-coding gene in the species Homo sapiens

Ribulose-phosphate 3-epimerase is an enzyme that in humans is encoded by the RPE gene.

References

  1. 1 2 3 4 5 Akana J, Fedorov AA, Fedorov E, Novak WR, Babbitt PC, Almo SC, Gerlt JA (Feb 2006). "D-Ribulose 5-phosphate 3-epimerase: functional and structural relationships to members of the ribulose-phosphate binding (beta/alpha)8-barrel superfamily". Biochemistry. 45 (8): 2493–503. doi:10.1021/bi052474m. PMID   16489742.
  2. 1 2 3 4 5 6 7 8 9 10 Liang W, Ouyang S, Shaw N, Joachimiak A, Zhang R, Liu ZJ (Feb 2011). "Conversion of D-ribulose 5-phosphate to D-xylulose 5-phosphate: new insights from structural and biochemical studies on human RPE". FASEB Journal. 25 (2): 497–504. doi:10.1096/fj.10-171207. PMC   6188353 . PMID   20923965.
  3. ↑ Mendz, George; Stuart Hazell (1991). "Evidence for a pentose phosphate pathway in Helicobacter pylori". FEMS Microbiology Letters. 84 (3): 331–336. doi: 10.1111/j.1574-6968.1991.tb04619.x .
  4. ↑ Kusian B, Yoo JG, Bednarski R, Bowien B (Nov 1992). "The Calvin cycle enzyme pentose-5-phosphate 3-epimerase is encoded within the cfx operons of the chemoautotroph Alcaligenes eutrophus". Journal of Bacteriology. 174 (22): 7337–44. doi:10.1128/jb.174.22.7337-7344.1992. PMC   207429 . PMID   1429456.
  5. ↑ Chen YR, Hartman FC, Lu TY, Larimer FW (Sep 1998). "D-Ribulose-5-phosphate 3-epimerase: cloning and heterologous expression of the spinach gene, and purification and characterization of the recombinant enzyme". Plant Physiology. 118 (1): 199–207. doi:10.1104/pp.118.1.199. PMC   34857 . PMID   9733539.
  6. ↑ Karmali A, Drake AF, Spencer N (Jun 1983). "Purification, properties and assay of D-ribulose 5-phosphate 3-epimerase from human erythrocytes". The Biochemical Journal. 211 (3): 617–23. doi:10.1042/bj2110617. PMC   1154406 . PMID   6882362.
  7. ↑ "Ribulose-phosphate 3-epimerase". UniProt. Retrieved 6 March 2013.
  8. 1 2 Jelakovic S, Kopriva S, Süss KH, Schulz GE (Feb 2003). "Structure and catalytic mechanism of the cytosolic D-ribulose-5-phosphate 3-epimerase from rice". Journal of Molecular Biology. 326 (1): 127–35. doi:10.1016/S0022-2836(02)01374-8. PMID   12547196.
  9. ↑ Das, Debajoyti (1978). Biochemistry. Academic Publishers. pp. 454–460.
  10. ↑ Davis L, Lee N, Glaser L (Sep 1972). "On the mechanism of the pentose phosphate epimerases". The Journal of Biological Chemistry. 247 (18): 5862–6. doi: 10.1016/S0021-9258(19)44837-0 . PMID   4560420.
  11. 1 2 3 Berg, Jeremy (2006). Biochemistry. WH Freeman and Company. pp. 570–580. ISBN   978-0-7167-8724-2.
  12. ↑ Chen YR, Larimer FW, Serpersu EH, Hartman FC (Jan 1999). "Identification of a catalytic aspartyl residue of D-ribulose 5-phosphate 3-epimerase by site-directed mutagenesis". The Journal of Biological Chemistry. 274 (4): 2132–6. doi: 10.1074/jbc.274.4.2132 . PMID   9890975.
  13. ↑ Nowitzki U, Wyrich R, Westhoff P, Henze K, Schnarrenberger C, Martin W (Dec 1995). "Cloning of the amphibolic Calvin cycle/OPPP enzyme D-ribulose-5-phosphate 3-epimerase (EC 5.1.3.1) from spinach chloroplasts: functional and evolutionary aspects". Plant Molecular Biology. 29 (6): 1279–91. doi:10.1007/bf00020468. PMID   8616224. S2CID   4215318.
  14. ↑ Wise EL, Akana J, Gerlt JA, Rayment I (Sep 2004). "Structure of D-ribulose 5-phosphate 3-epimerase from Synechocystis to 1.6 A resolution". Acta Crystallographica Section D. 60 (Pt 9): 1687–90. doi:10.1107/S0907444904015896. PMID   15333955.
  15. ↑ Teige M, Kopriva S, Bauwe H, Süss KH (Dec 1995). "Chloroplast pentose-5-phosphate 3-epimerase from potato: cloning, cDNA sequence, and tissue-specific enzyme accumulation". FEBS Letters. 377 (3): 349–52. doi: 10.1016/0014-5793(95)01373-3 . PMID   8549753. S2CID   34359563.
  16. 1 2 Caruthers J, Bosch J, Buckner F, Van Voorhis W, Myler P, Worthey E, Mehlin C, Boni E, DeTitta G, Luft J, Lauricella A, Kalyuzhniy O, Anderson L, Zucker F, Soltis M, Hol WG (Feb 2006). "Structure of a ribulose 5-phosphate 3-epimerase from Plasmodium falciparum". Proteins. 62 (2): 338–42. doi:10.1002/prot.20764. PMID   16304640. S2CID   9256275.
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