6-phosphogluconolactonase

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6-phosphogluconolactonase
6-phosphogluconolactonase complexed with 6-phosphogluconic acid. PDB- 3E7F.png
Crystallized monomer of 6-phosphogluconolactonase from Trypanosoma brucei complexed with 6-phosphogluconic acid [1]
Identifiers
SymbolPGLS
NCBI gene 25796
HGNC 8903
OMIM 604951
RefSeq NM_012088
UniProt O95336
Other data
EC number 3.1.1.31
Locus Chr. 19 p13.2
Search for
Structures Swiss-model
Domains InterPro

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: [2]

Contents

6-phospho-D-glucono-1,5-lactone + H2O = 6-phospho-D-gluconate

The tertiary structure of 6PGL employs an α/β hydrolase fold, with active site residues clustered on the loops of the α-helices. Based on the crystal structure of the enzyme, the mechanism is proposed to be dependent on proton transfer by a histidine residue in the active site. [1] 6PGL selectively catalyzes the hydrolysis of δ-6-phosphogluconolactone, and has no activity on the γ isomer. [3]

Enzyme Mechanism

6PGL hydrolysis of 6-phosphogluconolactone to 6-phosphogluconic acid has been proposed to proceed via proton transfer to the O5 ring oxygen atom, [4] similar to xylose isomerase [5] and ribose-5-phosphate isomerase. [6] The reaction initiates via attack of a hydroxide ion at the C5 ester. A tetrahedral intermediate forms and elimination of the ester linkage follows, aided by donation of a proton from an active site histidine residue. The specific residue that participates in the proton transfer eluded researchers until 2009, as previous structural studies demonstrated two possible conformations of the substrate in the active site, which position the O5 ring oxygen proximal to either an arginine or a histidine residue. [1] Molecular dynamic simulations were employed to discover that the residue that donates a proton is histidine, and that the arginine residues are only involved in electric stabilization of the negatively charged phosphate group. [4] Electric stabilization of the enzyme-substrate complex also occurs between the product carboxylate and backbone amines of surrounding glycine residues. [4]

Proposed mechanism of 6-phosphogluconolactone hydrolysis by 6PGL. 6PGL Mechanism.png
Proposed mechanism of 6-phosphogluconolactone hydrolysis by 6PGL.

Enzyme Structure

6PGL in Homo sapiens exists as a monomer at cytosolic physiological conditions, and is composed of 258 amino acid residues with a total molecular mass of ~30 kDa. [7] The tertiary structure of the enzyme utilizes an α/β hydrolase fold, with both parallel and anti-parallel β-sheets surrounded by eight α-helices and five 310 helices. [1] Stability of the tertiary structure of the protein is reinforced through salt bridges between aspartic acid and arginine residues, and from aromatic side-chain stacking interactions. [1] 6PGL isolated from Trypanosoma brucei was found to bind with a Zn2+ ion in a non-catalytic role, but this has not been observed in other organisms, including Thermotoga maritima and Vibrio cholerae . [1]

Biological Function

6-phosphogluconolactonase catalyzes the conversion of 6-phosphogluconolactone to 6-phosphogluconic acid, both intermediates in the oxidative phase of the pentose phosphate pathway, in which glucose is converted into ribulose 5-phosphate. The oxidative phase of the pentose phosphate pathway releases CO2 and results in the generation of two equivalents of NADPH from NADP+. The final product, ribulose 5-phosphate, is further processed by the organism during the non-oxidative phase of the pentose phosphate pathway to synthesize biomolecules including nucleotides, ATP, and Coenzyme A. [2]

The enzyme that precedes 6PGL in the pentose phosphate pathway, glucose-6-phosphate dehydrogenase, exclusively forms the δ-isomer of 6-phosphogluconolactone. However, if accumulated, this compound can undergo intramolecular rearrangement to isomerize to the more stable γ-form, which is unable to be hydrolyzed by 6PGL and cannot continue to the non-oxidative phase of the pentose phosphate pathway. By quickly hydrolyzing the δ-isomer of 6-phosphogluconolactone, 6PGL prevents its accumulation and subsequent formation of the γ-isomer, which would be wasteful of the glucose resources available to the cell. [3] 6-phosphogluconolactone is also susceptible to attack from intracellular nucleophiles, evidenced by α-N-6-phosphogluconoylation of His-tagged proteins expressed in E. coli, [8] [9] and efficient hydrolysis of 6-phosphogluconolactone by 6PGL prevents lactone accumulation and consequent toxic reactions from occurring between the lactone intermediate and the cell. [3]

Disease Relevance

Malarial parasites Plasmodium berghei and Plasmodium falciparum have been shown to express a bi-functional enzyme that exhibits both glucose-6-phosphate dehydrogenase and 6-phosphogluconolactonase activity, enabling it to catalyze the first two steps of the pentose phosphate pathway. [10] This bifunctional enzyme has been identified as a druggable target for malarial parasites, [11] and high-throughput screening of small molecule inhibitors has resulted in the discovery of novel compounds that can potentially be translated into potent antimalarials. [12] [13]

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">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">Triosephosphate isomerase</span> Enzyme involved in glycolysis

Triose-phosphate isomerase is an enzyme that catalyzes the reversible interconversion of the triose phosphate isomers dihydroxyacetone phosphate and D-glyceraldehyde 3-phosphate.

<span class="mw-page-title-main">Glucose-6-phosphate dehydrogenase</span> Enzyme involved in the production of energy by cells

Glucose-6-phosphate dehydrogenase (G6PD or G6PDH) (EC 1.1.1.49) is a cytosolic enzyme that catalyzes the chemical reaction

<span class="mw-page-title-main">Amino acid synthesis</span> The set of biochemical processes by which amino acids are produced

Amino acid biosynthesis is the set of biochemical processes by which the amino acids are produced. The substrates for these processes are various compounds in the organism's diet or growth media. Not all organisms are able to synthesize all amino acids. For example, humans can synthesize 11 of the 20 standard amino acids. These 11 are called the non-essential amino acids.

<span class="mw-page-title-main">Aldose reductase</span> Enzyme

In enzymology, aldose reductase is an enzyme in humans encoded by the gene AKR1B1. It is an cytosolic NADPH-dependent oxidoreductase that catalyzes the reduction of a variety of aldehydes and carbonyls, including monosaccharides, and primarily known for catalyzing the reduction of glucose to sorbitol, the first step in polyol pathway of glucose metabolism.

<span class="mw-page-title-main">Transaldolase</span> Enzyme family

Transaldolase is an enzyme of the non-oxidative phase of the pentose phosphate pathway. In humans, transaldolase is encoded by the TALDO1 gene.

<span class="mw-page-title-main">6-Phosphogluconic acid</span> Chemical compound

6-Phosphogluconic acid is a phosphorylated sugar acid which appears in the pentose phosphate pathway and the Entner–Doudoroff pathway.

<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">6-Phosphogluconolactone</span> Chemical compound

6-Phosphogluconolactone is an intermediate in the pentose phosphate pathway (PPP).

<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">Sucrose phosphorylase</span> Class of enzymes

Sucrose phosphorylase is an important enzyme in the metabolism of sucrose and regulation of other metabolic intermediates. Sucrose phosphorylase is in the class of hexosyltransferases. More specifically it has been placed in the retaining glycoside hydrolases family although it catalyzes a transglycosidation rather than hydrolysis. Sucrose phosphorylase catalyzes the conversion of sucrose to D-fructose and α-D-glucose-1-phosphate. It has been shown in multiple experiments that the enzyme catalyzes this conversion by a double displacement mechanism.

<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">D-xylulose reductase</span>

In enzymology, a D-xylulose reductase (EC 1.1.1.9) is an enzyme that is classified as an Oxidoreductase (EC 1) specifically acting on the CH-OH group of donors (EC 1.1.1) that uses NAD+ or NADP+ as an acceptor (EC 1.1.1.9). This enzyme participates in pentose and glucuronate interconversions; a set of metabolic pathways that involve converting pentose sugars and glucuronate into other compounds.

<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">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">2-Dehydro-3-deoxy-phosphogluconate aldolase</span> Class of enzymes

The enzyme 2-dehydro-3-deoxy-phosphogluconate aldolase, commonly known as KDPG aldolase, catalyzes the chemical reaction

<span class="mw-page-title-main">Xylose isomerase</span> Class of enzymes

In enzymology, a xylose isomerase is an enzyme that catalyzes the interconversion of D-xylose and D-xylulose. This enzyme belongs to the family of isomerases, specifically those intramolecular oxidoreductases interconverting aldoses and ketoses. The isomerase has now been observed in nearly a hundred species of bacteria. Xylose-isomerases are also commonly called fructose-isomerases due to their ability to interconvert glucose and fructose. The systematic name of this enzyme class is D-xylose aldose-ketose-isomerase. Other names in common use include D-xylose isomerase, D-xylose ketoisomerase, and D-xylose ketol-isomerase.

D-Ribose pyranase is an enzyme that catalyzes the interconversion of β-D-ribopyranose and β-D-ribofuranose. This enzyme is an isomerase that has only been found in bacteria and viruses. It has two known functions of helping transport ribose into cells and producing β-D-ribofuranose, which can later be used to make ribose 5-phosphate for the pentose phosphate pathway (PPP). D-Ribose pyranase does not have a defined crystal structure but there are two different proposed structures. The active site of D-ribose pyranase is high in histidine residues along with a few other key binding sites.

References

  1. 1 2 3 4 5 6 Delarue M, Duclert-Savatier N, Miclet E, Haouz A, Giganti D, Ouazzani J, Lopez P, Nilges M, Stoven V (February 2007). "Three dimensional structure and implications for the catalytic mechanism of 6-phosphogluconolactonase from Trypanosoma brucei". Journal of Molecular Biology. 366 (3): 868–81. doi:10.1016/j.jmb.2006.11.063. PMID   17196981.
  2. 1 2 Berg J, Tymoczko J, Stryer L (2012). Biochemistry (Seventh ed.). New York, NY: W.H. Freeman and Company. pp. 600–601. ISBN   9781429229364.
  3. 1 2 3 Miclet E, Stoven V, Michels PA, Opperdoes FR, Lallemand JY, Duffieux F (September 2001). "NMR spectroscopic analysis of the first two steps of the pentose-phosphate pathway elucidates the role of 6-phosphogluconolactonase". The Journal of Biological Chemistry. 276 (37): 34840–6. doi: 10.1074/jbc.M105174200 . PMID   11457850.
  4. 1 2 3 Duclert-Savatier N, Poggi L, Miclet E, Lopes P, Ouazzani J, Chevalier N, Nilges M, Delarue M, Stoven V (May 2009). "Insights into the enzymatic mechanism of 6-phosphogluconolactonase from Trypanosoma brucei using structural data and molecular dynamics simulation". Journal of Molecular Biology. 388 (5): 1009–21. doi:10.1016/j.jmb.2009.03.063. PMID   19345229.
  5. ↑ Whitlow M, Howard AJ, Finzel BC, Poulos TL, Winborne E, Gilliland GL (1991-03-01). "A metal-mediated hydride shift mechanism for xylose isomerase based on the 1.6 A Streptomyces rubiginosus structures with xylitol and D-xylose". Proteins. 9 (3): 153–73. doi:10.1002/prot.340090302. PMID   2006134. S2CID   39905317.
  6. ↑ Zhang RG, Andersson CE, Savchenko A, Skarina T, Evdokimova E, Beasley S, Arrowsmith CH, Edwards AM, Joachimiak A, Mowbray SL (January 2003). "Structure of Escherichia coli ribose-5-phosphate isomerase: a ubiquitous enzyme of the pentose phosphate pathway and the Calvin cycle". Structure. 11 (1): 31–42. doi:10.1016/S0969-2126(02)00933-4. PMC   2792023 . PMID   12517338.
  7. ↑ Collard F, Collet JF, Gerin I, Veiga-da-Cunha M, Van Schaftingen E (October 1999). "Identification of the cDNA encoding human 6-phosphogluconolactonase, the enzyme catalyzing the second step of the pentose phosphate pathway(1)". FEBS Letters. 459 (2): 223–6. doi: 10.1016/S0014-5793(99)01247-8 . PMID   10518023. S2CID   29302175.
  8. ↑ Geoghegan KF, Dixon HB, Rosner PJ, Hoth LR, Lanzetti AJ, Borzilleri KA, Marr ES, Pezzullo LH, Martin LB, LeMotte PK, McColl AS, Kamath AV, Stroh JG (February 1999). "Spontaneous α-N-6-phosphogluconoylation of a "His tag" in Escherichia coli: the cause of extra mass of 258 or 178 Da in fusion proteins". Analytical Biochemistry. 267 (1): 169–84. doi:10.1006/abio.1998.2990. PMID   9918669.
  9. ↑ Kim KM, Yi EC, Baker D, Zhang KY (May 2001). "Post-translational modification of the N-terminal His tag interferes with the crystallization of the wild-type and mutant SH3 domains from chicken src tyrosine kinase". Acta Crystallographica Section D. 57 (Pt 5): 759–62. doi: 10.1107/s0907444901002918 . PMID   11320329.
  10. ↑ Clarke JL, Scopes DA, Sodeinde O, Mason PJ (April 2001). "Glucose-6-phosphate dehydrogenase-6-phosphogluconolactonase. A novel bifunctional enzyme in malaria parasites". European Journal of Biochemistry. 268 (7): 2013–9. doi: 10.1046/j.1432-1327.2001.02078.x . PMID   11277923.
  11. ↑ Allen SM, Lim EE, Jortzik E, Preuss J, Chua HH, MacRae JI, Rahlfs S, Haeussler K, Downton MT, McConville MJ, Becker K, Ralph SA (October 2015). "Plasmodium falciparum glucose-6-phosphate dehydrogenase 6-phosphogluconolactonase is a potential drug target". The FEBS Journal. 282 (19): 3808–23. doi: 10.1111/febs.13380 . PMID   26198663. S2CID   46398163.
  12. ↑ Preuss J, Hedrick M, Sergienko E, Pinkerton A, Mangravita-Novo A, Smith L, Marx C, Fischer E, Jortzik E, Rahlfs S, Becker K, Bode L (July 2012). "High-throughput screening for small-molecule inhibitors of Plasmodium falciparum glucose-6-phosphate dehydrogenase 6-phosphogluconolactonase". Journal of Biomolecular Screening. 17 (6): 738–51. doi: 10.1177/1087057112442382 . PMC   8765527 . PMID   22496096.
  13. ↑ Preuss J, Maloney P, Peddibhotla S, Hedrick MP, Hershberger P, Gosalia P, Milewski M, Li YL, Sugarman E, Hood B, Suyama E, Nguyen K, Vasile S, Sergienko E, Mangravita-Novo A, Vicchiarelli M, McAnally D, Smith LH, Roth GP, Diwan J, Chung TD, Jortzik E, Rahlfs S, Becker K, Pinkerton AB, Bode L (August 2012). "Discovery of a Plasmodium falciparum' glucose-6-phosphate dehydrogenase 6-phosphogluconolactonase inhibitor (R,Z)-N-((1-ethylpyrrolidin-2-yl)methyl)-2-(2-fluorobenzylidene)-3-oxo-3,4-dihydro-2H-benzo[b][1,4]thiazine-6-carboxamide (ML276) that reduces parasite growth in vitro". Journal of Medicinal Chemistry. 55 (16): 7262–72. doi:10.1021/jm300833h. PMC   3530835 . PMID   22813531.
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