Triosephosphateisomerase
Encyclopedia
Triose-phosphate isomerase (TPI or TIM), is an enzyme
that catalyzes the reversible interconversion of the triose
phosphate isomer
s dihydroxyacetone phosphate and D-glyceraldehyde 3-phosphate
.
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 insect
s as well as in fungi, plant
s, and bacteria
. However, some bacteria that do not perform glycolysis, like ureaplasma
s, 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 mutation
s that cause this disease, most include the mutation of glutamic acid at position 104 to aspartic acid.
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.
. The changes in free energy for each step, including the transition states, have been calculated, and are displayed in the figure.
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, and the electrophilic
histidine 95 residue donates a proton to form the enediol intermediate. 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.
TPI is diffusion-limited. In terms of thermodynamics, DHAP formation is favored 20:1 over GAP production. 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
. Other inhibitors include 2-phosphoglycolate, a transition state analog, and D-glycerol-1-phosphate, a substrate analog
.
of identical subunit
s, 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 state
s on the reaction pathway.
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. Methylglyoxal is a toxin and, if formed, is removed through the glyoxalase system
.
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 is mutated to a neutral amino acid, TPI loses all function, but mutants with a different positively charged amino acid retain some function.
Enzyme
Enzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates...
that catalyzes the reversible interconversion of the triose
Triose
A triose is a monosaccharide, or simple sugar, containing three carbon atoms. There are only three possible trioses: L-Glyceraldehyde and D-Glyceraldehyde, both aldotrioses because the carbonyl group is at the end of the chain, and dihydroxyacetone, a ketotriose because the carbonyl group is in...
phosphate isomer
Isomer
In chemistry, isomers are compounds with the same molecular formula but different structural formulas. Isomers do not necessarily share similar properties, unless they also have the same functional groups. There are many different classes of isomers, like stereoisomers, enantiomers, geometrical...
s dihydroxyacetone phosphate and D-glyceraldehyde 3-phosphate
Glyceraldehyde 3-phosphate
Glyceraldehyde 3-phosphate, also known as triose phosphate or 3-phosphoglyceraldehyde and abbreviated as G3P, GADP, GAP, TP, GALP or PGAL, is a chemical compound that occurs as an intermediate in several central metabolic pathways of all organisms...
.
Glycolysis
Glycolysis is the metabolic pathway that converts glucose C6H12O6, into pyruvate, CH3COCOO− + H+...
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 insect
Insect
Insects are a class of living creatures within the arthropods that have a chitinous exoskeleton, a three-part body , three pairs of jointed legs, compound eyes, and two antennae...
s as well as in fungi, plant
Plant
Plants are living organisms belonging to the kingdom Plantae. Precise definitions of the kingdom vary, but as the term is used here, plants include familiar organisms such as trees, flowers, herbs, bushes, grasses, vines, ferns, mosses, and green algae. The group is also called green plants or...
s, and bacteria
Bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
. However, some bacteria that do not perform glycolysis, like ureaplasma
Ureaplasma
Ureaplasma is a genus of bacteria belonging to the family Mycoplasmataceae. As the name imples, ureaplasma is urease positive.It includes the species:* Ureaplasma canigenitalium* Ureaplasma cati* Ureaplasma diversum...
s, 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
Hemolytic anemia
Hemolytic anemia is a form of anemia due to hemolysis, the abnormal breakdown of red blood cells , either in the blood vessels or elsewhere in the human body . It has numerous possible causes, ranging from relatively harmless to life-threatening...
. While there are various mutation
Mutation
In molecular biology and genetics, mutations are changes in a genomic sequence: the DNA sequence of a cell's genome or the DNA or RNA sequence of a virus. They can be defined as sudden and spontaneous changes in the cell. Mutations are caused by radiation, viruses, transposons and mutagenic...
s that cause this disease, most include the mutation of glutamic acid at position 104 to aspartic acid.
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
Kinetic perfection
Kinetic perfection, also known as catalytic perfection, refers to enzymes that are diffusion-limited; that is, the reaction they catalyze occurs as quickly as the reactants diffuse to the enzyme...
: It is limited only by the rate the substrate can diffuse into and out of the enzyme's active site.
Mechanism
The mechanism involves the intermediate formation of an "enediol"Enol
Enols are alkenes with a hydroxyl group affixed to one of the carbon atoms composing the double bond. Alkenes with a hydroxyl group on both sides of the double bond are called enediols. Deprotonated anions of enols are called enolates...
. The changes in free energy for each step, including the transition states, have been calculated, and are displayed in the figure.
The structure of TPI facilitates the conversion between dihydroxyacetone phosphate (DHAP) and glyceraldehyde 3-phosphate (GAP). The nucleophilic
Nucleophile
A nucleophile is a species that donates an electron-pair to an electrophile to form a chemical bond in a reaction. All molecules or ions with a free pair of electrons can act as nucleophiles. Because nucleophiles donate electrons, they are by definition Lewis bases.Nucleophilic describes the...
glutamate 165 residue of TPI deprotonates the substrate, and the electrophilic
Electrophile
In general electrophiles are positively charged species that are attracted to an electron rich centre. In chemistry, an electrophile is a reagent attracted to electrons that participates in a chemical reaction by accepting an electron pair in order to bond to a nucleophile...
histidine 95 residue donates a proton to form the enediol intermediate. 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.
TPI is diffusion-limited. In terms of thermodynamics, DHAP formation is favored 20:1 over GAP production. However, in glycolysis, the use of GAP in the subsequent steps of metabolism drives the reaction toward its production.
TPI is inhibited by sulfate
Sulfate
In inorganic chemistry, a sulfate is a salt of sulfuric acid.-Chemical properties:...
, phosphate
Phosphate
A phosphate, an inorganic chemical, is a salt of phosphoric acid. In organic chemistry, a phosphate, or organophosphate, is an ester of phosphoric acid. Organic phosphates are important in biochemistry and biogeochemistry or ecology. Inorganic phosphates are mined to obtain phosphorus for use in...
, and arsenate
Arsenate
The arsenate ion is AsO43−.An arsenate is any compound that contains this ion. Arsenates are salts or esters of arsenic acid.The arsenic atom in arsenate has a valency of 5 and is also known as pentavalent arsenic or As[V]....
ions, which bind to the active site
Active site
In biology the active site is part of an enzyme where substrates bind and undergo a chemical reaction. The majority of enzymes are proteins but RNA enzymes called ribozymes also exist. The active site of an enzyme is usually found in a cleft or pocket that is lined by amino acid residues that...
. Other inhibitors include 2-phosphoglycolate, a transition state analog, and D-glycerol-1-phosphate, a substrate analog
Substrate analog
Transition state analogs , are chemical compounds with a chemical structure that resembles the transition state of a substrate molecule in an enzyme-catalyzed chemical reaction. Transition state analogs usually do not undergo a chemical reaction and can act as enzyme inhibitors by blocking their...
.
Structure
Triose phosphate isomerase is a dimerProtein dimer
In biochemistry, a dimer is a macromolecular complex formed by two, usually non-covalently bound, macromolecules like proteins or nucleic acids...
of identical subunit
Protein subunit
In structural biology, a protein subunit or subunit protein is a single protein molecule that assembles with other protein molecules to form a protein complex: a multimeric or oligomeric protein. Many naturally occurring proteins and enzymes are multimeric...
s, each of which is made up of about 250 amino acid
Amino acid
Amino acids are molecules containing an amine group, a carboxylic acid group and a side-chain that varies between different amino acids. The key elements of an amino acid are carbon, hydrogen, oxygen, and nitrogen...
residues. The three-dimensional structure of a subunit contains eight α-helices
Alpha helix
A common motif in the secondary structure of proteins, the alpha helix is a right-handed coiled or spiral conformation, in which every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier...
on the outside and eight parallel β-strands
Beta sheet
The β sheet is the second form of regular secondary structure in proteins, only somewhat less common than the alpha helix. Beta sheets consist of beta strands connected laterally by at least two or three backbone hydrogen bonds, forming a generally twisted, pleated sheet...
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
TIM barrel
The TIM barrel is a conserved protein fold consisting of eight α-helices and eight parallel β-strands that alternate along the peptide backbone. The structure is named after triosephosphate isomerase, a conserved glycolytic enzyme. TIM barrels are quite common among the conserved protein folds...
, and is by far the most commonly observed protein fold
Protein folding
Protein folding is the process by which a protein structure assumes its functional shape or conformation. It is the physical process by which a polypeptide folds into its characteristic and functional three-dimensional structure from random coil....
. The active site
Active site
In biology the active site is part of an enzyme where substrates bind and undergo a chemical reaction. The majority of enzymes are proteins but RNA enzymes called ribozymes also exist. The active site of an enzyme is usually found in a cleft or pocket that is lined by amino acid residues that...
of this enzyme is in the center of the barrel. A glutamic acid
Glutamic acid
Glutamic acid is one of the 20 proteinogenic amino acids, and its codons are GAA and GAG. It is a non-essential amino acid. The carboxylate anions and salts of glutamic acid are known as glutamates...
residue and a histidine
Histidine
Histidine Histidine, an essential amino acid, has a positively charged imidazole functional group. It is one of the 22 proteinogenic amino acids. Its codons are CAU and CAC. Histidine was first isolated by German physician Albrecht Kossel in 1896. Histidine is an essential amino acid in humans...
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
Hydrogen bond
A hydrogen bond is the attractive interaction of a hydrogen atom with an electronegative atom, such as nitrogen, oxygen or fluorine, that comes from another molecule or chemical group. The hydrogen must be covalently bonded to another electronegative atom to create the bond...
to the phosphate group of the substrate. This action stabilizes the enediol intermediate and the other transition state
Transition state
The transition state of a chemical reaction is a particular configuration along the reaction coordinate. It is defined as the state corresponding to the highest energy along this reaction coordinate. At this point, assuming a perfectly irreversible reaction, colliding reactant molecules will always...
s on the reaction pathway.
In addition to making the reaction kinetically feasible, the TPI loop sequesters the reactive enediol intermediate to prevent decomposition to methylglyoxal
Methylglyoxal
Methylglyoxal, also called pyruvaldehyde or 2-oxopropanal is the aldehyde form of pyruvic acid. It has two carbonyl groups, so it is a dicarbonyl compound. Methylglyoxal is both an aldehyde and a ketone....
and inorganic phosphate. The hydrogen bond between the enzyme and the phosphate group of the substrate makes such decomposition stereoelectronically unfavorable. Methylglyoxal is a toxin and, if formed, is removed through the glyoxalase system
Glyoxalase system
The glyoxalase system is a set of enzymes that carry out the detoxification of methylglyoxal and the other reactive aldehydes that are produced as a normal part of metabolism...
.
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 is mutated to a neutral amino acid, TPI loses all function, but mutants with a different positively charged amino acid retain some function.
See also
- TIM barrelTIM barrelThe TIM barrel is a conserved protein fold consisting of eight α-helices and eight parallel β-strands that alternate along the peptide backbone. The structure is named after triosephosphate isomerase, a conserved glycolytic enzyme. TIM barrels are quite common among the conserved protein folds...
- Triose Phosphate Isomerase deficiency
- TPI1TPI1Triosephosphate isomerase is an enzyme that in humans is encoded by the TPI1 gene.-Further reading:...
- Triosephosphate isomerase in interactive 3D at ProteopediaProteopediaProteopedia is a wiki, 3D encyclopedia of proteins and other molecules..The site contains a page for every entry in the Protein Data Bank , as well as pages that are more descriptive of protein structures in general such as acetylcholinesterase, hemoglobin, and the photosystem II with a Jmol view...
- Triosephosphate isomerase (TIM) family in PROSITEPROSITEPROSITE is a protein database. It consists of entries describing the protein families, domains and functional sites as well as amino acid patterns, signatures, and profiles in them. These are manually curated by a team of the Swiss Institute of Bioinformatics and tightly integrated into Swiss-Prot...