Triosephosphate isomerase

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triosephosphate isomerase
TriosePhosphateIsomerase Ribbon pastel trans.png
Side view of triose P isomerase monomer, active site at top center
Identifiers
EC no. 5.3.1.1
CAS no. 9023-78-3
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

Triose-phosphate isomerase (TPI or TIM) is an enzyme (EC 5.3.1.1) that catalyzes the reversible interconversion of the triose phosphate isomers dihydroxyacetone phosphate and D-glyceraldehyde 3-phosphate.

Contents

Dihydroxyacetone phosphate triose phosphate isomerase D-glyceraldehyde 3-phosphate
Glycerone-phosphate wpmp.png   D-glyceraldehyde-3-phosphate wpmp.png
Biochem reaction arrow reversible NNNN horiz med.svg
 
  triose phosphate isomerase

Compound C00111 at KEGG Pathway Database.Enzyme 5.3.1.1 at KEGG Pathway Database.Compound C00118 at KEGG Pathway Database.

TPI plays an important role in glycolysis and is essential for efficient energy production. TPI has been found in nearly every organism searched for the enzyme, including animals such as mammals and insects as well as in fungi, plants, and bacteria. However, some bacteria that do not perform glycolysis, like ureaplasmas, lack TPI.

In humans, deficiencies in TPI are associated with a progressive, severe neurological disorder called triose phosphate isomerase deficiency. Triose phosphate isomerase deficiency is characterized by chronic hemolytic anemia. While there are various mutations that cause this disease, most include the replacement of glutamic acid at position 104 with an aspartic acid. [1]

Triose phosphate isomerase is a highly efficient enzyme, performing the reaction billions of times faster than it would occur naturally in solution. The reaction is so efficient that it is said to be catalytically perfect: It is limited only by the rate the substrate can diffuse into and out of the enzyme's active site. [2] [3]

Mechanism

The mechanism involves the intermediate formation of an enediol. The relative free energy of each ground state and transition state has been determined experimentally, and is displayed in the figure. [2]

Triosephosphate Isomerase DeltaG.svg

The structure of TPI facilitates the conversion between dihydroxyacetone phosphate (DHAP) and glyceraldehyde 3-phosphate (GAP). The nucleophilic glutamate 165 residue of TPI deprotonates the substrate, [4] and the electrophilic histidine 95 residue donates a proton to form the enediol intermediate. [5] [6] When deprotonated, the enediolate then collapses and, abstracting a proton from protonated glutamate 165, forms the GAP product. Catalysis of the reverse reaction proceeds analogously, forming the same enediol but with enediolate collapse from the oxygen at C2. [7]

TPI is diffusion-limited. In terms of thermodynamics, DHAP formation is favored 20:1 over GAP production. [8] However, in glycolysis, the use of GAP in the subsequent steps of metabolism drives the reaction toward its production. TPI is inhibited by sulfate, phosphate, and arsenate ions, which bind to the active site. [9] Other inhibitors include 2-phosphoglycolate, a transition state analog, and D-glycerol-1-phosphate, a substrate analog. [10]

Side view of triose phosphate isomerase dimer. TPI1 structure.png
Side view of triose phosphate isomerase dimer.

Structure

Triosephosphate isomerase
Identifiers
SymbolTIM
Pfam PF00121
Pfam clan CL0036
InterPro IPR000652
PROSITE PDOC00155
SCOP2 1tph / SCOPe / SUPFAM

Triose phosphate isomerase is a dimer of identical subunits, each of which is made up of about 250 amino acid residues. The three-dimensional structure of a subunit contains eight α-helices on the outside and eight parallel β-strands on the inside. In the illustration, the ribbon backbone of each subunit is colored in blue to red from N-terminus to C-terminus. This structural motif is called an αβ-barrel, or a TIM-barrel, and is by far the most commonly observed protein fold. The active site of this enzyme is in the center of the barrel. A glutamic acid residue and a histidine are involved in the catalytic mechanism. The sequence around the active site residues is conserved in all known triose phosphate isomerases.

The structure of triose phosphate isomerase contributes to its function. Besides the precisely placed glutamate and histidine residues to form the enediol, a ten- or eleven-amino acid chain of TPI acts as a loop to stabilize the intermediate. The loop, formed by residues 166 to 176, closes and forms a hydrogen bond to the phosphate group of the substrate. This action stabilizes the enediol intermediate and the other transition states on the reaction pathway. [7]

In addition to making the reaction kinetically feasible, the TPI loop sequesters the reactive enediol intermediate to prevent decomposition to methylglyoxal and inorganic phosphate. The hydrogen bond between the enzyme and the phosphate group of the substrate makes such decomposition stereoelectronically unfavorable. [7] Methylglyoxal is a toxin and, if formed, is removed through the glyoxalase system. [11] The loss of a high-energy phosphate bond and the substrate for the rest of glycolysis makes formation of methylglyoxal inefficient.

Studies suggest that a lysine close to the active site (at position 12) is also crucial for enzyme function. The lysine, protonated at physiological pH, may help neutralize the negative charge of the phosphate group. When this lysine residue is replaced with a neutral amino acid, TPI loses all function, but variants with a different positively charged amino acid retain some function. [12]

See also

Related Research Articles

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:

Pyridoxal phosphate Active formof vitamin B6

Pyridoxal phosphate (PLP, pyridoxal 5'-phosphate, P5P), the active form of vitamin B6, is a coenzyme in a variety of enzymatic reactions. The International Union of Biochemistry and Molecular Biology has catalogued more than 140 PLP-dependent activities, corresponding to ~4% of all classified activities. The versatility of PLP arises from its ability to covalently bind the substrate, and then to act as an electrophilic catalyst, thereby stabilizing different types of carbanionic reaction intermediates.

Catalytic triad Set of three coordinated amino acids

A catalytic triad is a set of three coordinated amino acids that can be found in the active site of some enzymes. Catalytic triads are most commonly found in hydrolase and transferase enzymes. An acid-base-nucleophile triad is a common motif for generating a nucleophilic residue for covalent catalysis. The residues form a charge-relay network to polarise and activate the nucleophile, which attacks the substrate, forming a covalent intermediate which is then hydrolysed to release the product and regenerate free enzyme. The nucleophile is most commonly a serine or cysteine amino acid, but occasionally threonine or even selenocysteine. The 3D structure of the enzyme brings together the triad residues in a precise orientation, even though they may be far apart in the sequence.

Transketolase Enzyme involved in metabolic pathways

Transketolase is an enzyme that 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.

Succinyl coenzyme A synthetase

Succinyl coenzyme A synthetase is an enzyme that catalyzes the reversible reaction of succinyl-CoA to succinate. The enzyme facilitates the coupling of this reaction to the formation of a nucleoside triphosphate molecule from an inorganic phosphate molecule and a nucleoside diphosphate molecule. It plays a key role as one of the catalysts involved in the citric acid cycle, a central pathway in cellular metabolism, and it is located within the mitochondrial matrix of a cell.

Phosphoglycerate kinase Enzyme

Phosphoglycerate kinase is an enzyme that catalyzes the reversible transfer of a phosphate group from 1,3-bisphosphoglycerate (1,3-BPG) to ADP producing 3-phosphoglycerate (3-PG) and ATP :

Phosphoglycerate mutase

Phosphoglycerate mutase (PGM) is any enzyme that catalyzes step 8 of glycolysis - the internal transfer of a phosphate group from C-3 to C-2 which results in the conversion of 3-phosphoglycerate (3PG) to 2-phosphoglycerate (2PG) through a 2,3-bisphosphoglycerate intermediate. These enzymes are categorized into the two distinct classes of either cofactor-dependent (dPGM) or cofactor-independent (iPGM). The dPGM enzyme is composed of approximately 250 amino acids and is found in all vertebrates as well as in some invertebrates, fungi, and bacteria. The iPGM class is found in all plants and algae as well as in some invertebrate, fungi, and Gram-positive bacteria. This class of PGM enzyme shares the same superfamily as alkaline phosphatase.

Enzyme catalysis Catalysis of chemical reactions by specialized proteins known as enzymes

Enzyme catalysis is the increase in the rate of a process by a biological molecule, an "enzyme". Most enzymes are proteins, and most such processes are chemical reactions. Within the enzyme, generally catalysis occurs at a localized site, called the active site.

Triosephosphate isomerase deficiency Medical condition

Triosephosphate isomerase deficiency is a rare autosomal recessive metabolic disorder which was initially described in 1965.

Ribose 5-phosphate 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.

Phosphopentose epimerase

Phosphopentose 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.

Fructose-bisphosphate aldolase

Fructose-bisphosphate aldolase, often just aldolase, is an enzyme catalyzing a reversible reaction that splits the aldol, fructose 1,6-bisphosphate, into the triose phosphates dihydroxyacetone phosphate (DHAP) and glyceraldehyde 3-phosphate (G3P). Aldolase can also produce DHAP from other (3S,4R)-ketose 1-phosphates such as fructose 1-phosphate and sedoheptulose 1,7-bisphosphate. Gluconeogenesis and the Calvin cycle, which are anabolic pathways, use the reverse reaction. Glycolysis, a catabolic pathway, uses the forward reaction. Aldolase is divided into two classes by mechanism.

Mannose phosphate isomerase

Mannose-6 phosphate isomerase (MPI), alternately phosphomannose isomerase (PMI) is an enzyme which facilitates the interconversion of fructose 6-phosphate (F6P) and mannose-6-phosphate (M6P). Mannose-6-phosphate isomerase may also enable the synthesis of GDP-mannose in eukaryotic organisms. M6P can be converted to F6P by mannose-6-phosphate isomerase and subsequently utilized in several metabolic pathways including glycolysis and capsular polysaccharide biosynthesis. PMI is monomeric and metallodependent on zinc as a cofactor ligand. PMI is inhibited by erythrose 4-phosphate, mannitol 1-phosphate, and to a lesser extent, the alpha anomer of M6P.

Alanine racemase

In enzymology, an alanine racemase is an enzyme that catalyzes the chemical reaction

Steroid Delta-isomerase

In enzymology, a steroid Δ5-isomerase is an enzyme that catalyzes the chemical reaction

Lactoylglutathione lyase

In enzymology, a lactoylglutathione lyase is an enzyme that catalyzes the isomerization of hemithioacetal adducts, which are formed in a spontaneous reaction between a glutathionyl group and aldehydes such as methylglyoxal.

2-Dehydro-3-deoxy-phosphogluconate aldolase

In enzymology, a 2-dehydro-3-deoxy-phosphogluconate aldolase, commonly known as KDPG aldolase, is an enzyme that catalyzes the chemical reaction

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

TPI1

Triosephosphate isomerase is an enzyme that in humans is encoded by the TPI1 gene.

Jeremy Randall Knowles was a professor of chemistry at Harvard University who served as dean of the Harvard University faculty of arts and sciences (FAS) from 1991 to 2002. He joined Harvard in 1974, received many awards for his research, and remained at Harvard until his death, leaving the faculty for a decade to serve as Dean. Knowles died on 3 April 2008 at his home.

References

  1. Orosz F, Oláh J, Ovádi J (December 2006). "Triosephosphate isomerase deficiency: facts and doubts". IUBMB Life. 58 (12): 703–15. doi: 10.1080/15216540601115960 . PMID   17424909.
  2. 1 2 Albery WJ, Knowles JR (December 1976). "Free-energy profile of the reaction catalyzed by triosephosphate isomerase". Biochemistry. 15 (25): 5627–31. doi:10.1021/bi00670a031. PMID   999838.
  3. Rose IA, Fung WJ, Warms JV (May 1990). "Proton diffusion in the active site of triosephosphate isomerase". Biochemistry. 29 (18): 4312–7. doi:10.1021/bi00470a008. PMID   2161683.
  4. Alber T, Banner DW, Bloomer AC, Petsko GA, Phillips D, Rivers PS, Wilson IA (June 1981). "On the three-dimensional structure and catalytic mechanism of triose phosphate isomerase". Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 293 (1063): 159–71. doi: 10.1098/rstb.1981.0069 . PMID   6115415.
  5. Nickbarg EB, Davenport RC, Petsko GA, Knowles JR (August 1988). "Triosephosphate isomerase: removal of a putatively electrophilic histidine residue results in a subtle change in catalytic mechanism". Biochemistry. 27 (16): 5948–60. doi:10.1021/bi00416a019. PMID   2847777.
  6. Komives EA, Chang LC, Lolis E, Tilton RF, Petsko GA, Knowles JR (March 1991). "Electrophilic catalysis in triosephosphate isomerase: the role of histidine-95". Biochemistry. 30 (12): 3011–9. doi:10.1021/bi00226a005. PMID   2007138.
  7. 1 2 3 Knowles JR (March 1991). "Enzyme catalysis: not different, just better". Nature. 350 (6314): 121–4. doi:10.1038/350121a0. PMID   2005961.
  8. Harris TK, Cole RN, Comer FI, Mildvan AS (November 1998). "Proton transfer in the mechanism of triosephosphate isomerase". Biochemistry. 37 (47): 16828–38. doi:10.1021/bi982089f. PMID   9843453.
  9. Lambeir AM, Opperdoes FR, Wierenga RK (October 1987). "Kinetic properties of triose-phosphate isomerase from Trypanosoma brucei brucei. A comparison with the rabbit muscle and yeast enzymes". European Journal of Biochemistry. 168 (1): 69–74. doi: 10.1111/j.1432-1033.1987.tb13388.x . PMID   3311744.
  10. Lolis E, Petsko GA (July 1990). "Crystallographic analysis of the complex between triosephosphate isomerase and 2-phosphoglycolate at 2.5-A resolution: implications for catalysis". Biochemistry. 29 (28): 6619–25. doi:10.1021/bi00480a010. PMID   2204418.
  11. Creighton DJ, Hamilton DS (March 2001). "Brief history of glyoxalase I and what we have learned about metal ion-dependent, enzyme-catalyzed isomerizations". Archives of Biochemistry and Biophysics. 387 (1): 1–10. doi:10.1006/abbi.2000.2253. PMID   11368170.
  12. Lodi PJ, Chang LC, Knowles JR, Komives EA (March 1994). "Triosephosphate isomerase requires a positively charged active site: the role of lysine-12". Biochemistry. 33 (10): 2809–14. doi:10.1021/bi00176a009. PMID   8130193.