Quantum mechanical and molecular mechanical studies on a model for the dihydroxyacetone phosphate-glyceraldehyde phosphate isomerization catalyzed by triose phosphate isomerase (TIM)

1984 ◽  
Vol 106 (12) ◽  
pp. 3623-3632 ◽  
Author(s):  
Giuliano Alagona ◽  
Peter Desmeules ◽  
Caterina Ghio ◽  
Peter A. Kollman
Keyword(s):  
Triose Phosphate Isomerase ◽  
Quantum Mechanical ◽  
Dihydroxyacetone Phosphate ◽  
Triose Phosphate ◽  
Mechanical Studies

On the three-dimensional structure and catalytic mechanism of triose phosphate isomerase

1981 ◽  
Vol 293 (1063) ◽  
pp. 159-171 ◽  
Keyword(s):  
Catalytic Mechanism ◽  
Polypeptide Chain ◽  
Three Dimensional ◽  
Triose Phosphate Isomerase ◽  
Dimensional Structure ◽  
Dihydroxyacetone Phosphate ◽  
Triose Phosphate ◽  
Independent Determination ◽  
Chicken Muscle

Triose phosphate isomerase is a dimeric enzyme of molecular mass 56000 which catalyses the interconversion of dihydroxyacetone phosphate (DHAP) and D-glyceraldehyde-3-phosphate. The crystal structure of the enzyme from chicken muscle has been determined at a resolution of 2.5 A, and an independent determination of the structure of the yeast enzyme has just been completed at 3 A resolution. The conformation of the polypeptide chain is essentially identical in the two structures, and consists of an inner cylinder of eight strands of parallel |3-pleated sheet, with mostly helical segments connecting each strand. The active site is a pocket containing glutamic acid 165, which is believed to act as a base in the reaction. Crystallographic studies of the binding of DHAP to both the chicken and the yeast enzymes reveal a common mode of binding and suggest a mechanism for catalysis involving polarization of the substrate carbonyl group.

scholarly journals Enzyme-substrate and enzyme-inhibitor complexes of triose phosphate isomerase studied by 31P nuclear magnetic resonance

1979 ◽  
Vol 179 (3) ◽  
pp. 607-621 ◽  
Author(s):  
I D Campbell ◽  
R B Jones ◽  
P A Kiener ◽  
S G Waley
Keyword(s):  
Enzyme Inhibitor ◽  
Ph Dependence ◽  
Triose Phosphate Isomerase ◽  
Dihydroxyacetone Phosphate ◽  
Ligand Complex ◽  
Triose Phosphate ◽  
Kinetic Information ◽  
Transition State Analogue ◽  
Chicken Muscle ◽  
Proton Uptake

The complex formed between the enzyme triose phosphate isomerase (EC 5.3.1.1.), from rabbit and chicken muscle, and its substrate dihydroxyacetone phosphate was studied by 31P n.m.r. Two other enzyme-ligant complexes examined were those formed by glycerol 3-phosphate (a substrate analogue) and by 2-phosphoglycollate (potential transition-state analogue). Separate resonances were observed in the 31P n.m.r. spectrum for free and bound 2-phosphoglycollate, and this sets an upper limit to the rate constant for dissociation of the enzyme-inhibitor complex; the linewidth of the resonance assigned to the bound inhibitor provided further kinetic information. The position of this resonance did not vary with pH but remained close to that of the fully ionized form of the free 2-phosphoglycollate. It is the fully ionized form of this ligand that binds to the enzyme. The proton uptake that accompanies binding shows protonation of a group on the enzyme. On the basis of chemical and crystallographic information [Hartman (1971) Biochemistry 10, 146–154; Miller & Waley (1971) Biochem. J. 123, 163–170; De la Mare, Coulson, Knowles, Priddle & Offord 1972) Biochem. J. 129, 321–331; Phillips, Rivers, Sternberg, Thornton & Wilson (1977) Biochem. Soc. Trans. 5, 642–647] this group is believed to be glutamate-165. On the other hand, the position of the resonance of D-glycerol 3 phosphate (sn-glycerol 1-phosphate) in the enzyme-ligand complex changes with pH, and both monoanion and dianon of the ligand bind, although dianion binds better. The substrate, dihydroxyacetone phosphate, behaves essentially like glycerol 3-phosphate. The experiments with dihydroxy-acetone phosphate and triose phosphate isomerase have to be carried out at 1 degree C because at 37 degrees C there is conversion into methyl glyoxal and orthophosphate. The mechanismof the enzymic reaction and the reasons for rate-enhancement are considered, and aspects of the pH-dependence are discussed in an Appendix.

scholarly journals Specificity and kinetics of triose phosphate isomerase from chicken muscle

1972 ◽  
Vol 129 (2) ◽  
pp. 301-310 ◽  
Author(s):  
Sylvia J. Putman ◽  
A. F. W. Coulson ◽  
I. R. T. Farley ◽  
B. Riddleston ◽  
J. R. Knowles
Keyword(s):  
Triose Phosphate Isomerase ◽  
Proton Exchange ◽  
The Other ◽  
Chicken Breast ◽  
Dihydroxyacetone Phosphate ◽  
Exchange Reactions ◽  
Hydrogen Atoms ◽  
Triose Phosphate ◽  
Chicken Muscle ◽  
Kinetics Of

The isolation of crystalline triose phosphate isomerase from chicken breast muscle is described. The values of kcat. and Km for the reaction in each direction were determined from experiments over wide substrate-concentration ranges, and the reactions were shown to obey simple Michaelis–Menten kinetics. With d-glyceraldehyde 3-phosphate as substrate, kcat. is 2.56×105min-1and Km is 0.47mm; with dihydroxyacetone phosphate as substrate, kcat. is 2.59×104min-1and Km is 0.97mm. The enzyme-catalysed exchange of the methyl hydrogen atoms of the ‘virtual substrate’ monohydroxyacetone phosphate with solvent2H2O or3H2O was shown. This exchange is about 104-fold slower than the corresponding exchange of the C-3 hydrogen of dihydroxyacetone phosphate. The other deoxy substrate, 3-hydroxypropionaldehyde phosphate, was synthesized, but is too unstable in aqueous solution for analogous proton-exchange reactions to be studied.

scholarly journals The existence of an electrophilic component in the reaction catalysed by triose phosphate isomerase

1974 ◽  
Vol 141 (2) ◽  
pp. 589-592 ◽  
Author(s):  
Martin R. Webb ◽  
Jeremy R. Knowles
Keyword(s):  
Carbonyl Group ◽  
Triose Phosphate Isomerase ◽  
Dihydroxyacetone Phosphate ◽  
Free Solution ◽  
Triose Phosphate ◽  
Order Of Magnitude

In the presence of triose phosphate isomerase, the substrate dihydroxyacetone phosphate is reduced stereoselectively by NaBH4. The reduction of enzyme-bound substrate is almost completely or completely stereoselective and occurs about one order of magnitude faster than that in free solution. This acceleration implies a polarization of the carbonyl group when dihydroxyacetone phosphate is bound.

scholarly journals Loss of Peroxisomal Hydroxypyruvate Reductase Inhibits Triose Phosphate Isomerase but Stimulates Cyclic Photosynthetic Electron Flow and the Glc-6P-Phosphate Shunt

2018 ◽  
Author(s):  
Jiying Li ◽  
Sarathi M. Weraduwage ◽  
Alyssa L. Preiser ◽  
Sean E. Weise ◽  
Deserah D. Strand ◽  
...  
Keyword(s):  
Photosystem I ◽  
Electron Flow ◽  
Competitive Inhibitor ◽  
Triose Phosphate Isomerase ◽  
Cyclic Electron Flow ◽  
Dihydroxyacetone Phosphate ◽  
Triose Phosphate ◽  
Hydroxypyruvate Reductase ◽  
Photosynthetic Electron Flow ◽  
Mutant Lines

AbstractThe oxygenation of ribulose 1,5-bisphosphate by Rubisco is the first step in photorespiration and reduces the efficiency of photosynthesis in C3 plants. Our recent data indicates that mutants in photorespiration have increased rates of photosynthetic cyclic electron flow around photosystem I. We investigated mutant lines lacking peroxisomal hydroxypyruvate reductase to determine if there are connections between 2-PG accumulation and cyclic electron flow. We found that 2-PG is a competitive inhibitor of triose phosphate isomerase (TPI), an enzyme in the Calvin-Benson cycle that converts glyceraldehyde 3-phosphate to dihydroxyacetone phosphate. This block in metabolism could be overcome if glyceraldehyde 3-phosphate is exported to the cytosol where the cytosolic triose phosphate isomerase could convert it to dihydroxyacetone phosphate. We found evidence that carbon is reimported as Glc-6P-phosphate forming a cytosolic bypass around the block of stromal TPI. However, this also stimulates a Glc-6P-phosphate shunt, which consumes ATP, which can be compensated by higher rates of cyclic electron flow.Once Sentence SummaryTriose phosphate isomerase is inhibited in plants lacking hydroxypyruvate reductase 1 and this is overcome by exporting triose phosphate to the cytosol and importing Glc-6P, which stimulates a Glc-6P-phosphate shunt and cyclic electron flow.

scholarly journals Dihydroxyacetone phosphate. Its structure and reactivity with α-glycerophosphate dehydrogenase, aldolase and triose phosphate isomerase and some possible metabolic implications

1971 ◽  
Vol 122 (3) ◽  
pp. 285-297 ◽  
Author(s):  
S. J. Reynolds ◽  
D. W. Yates ◽  
C. I. Pogson
Keyword(s):  
Aqueous Solution ◽  
Rate Constants ◽  
Reactive Species ◽  
Triose Phosphate Isomerase ◽  
Dihydroxyacetone Phosphate ◽  
Temperature Dependent ◽  
Keto Form ◽  
Triose Phosphate ◽  
Glycerophosphate Dehydrogenase ◽  
Neutral Aqueous Solution

1. Dihydroxyacetone phosphate exists in neutral aqueous solution at 20°C as a mixture of keto, gem-diol and enolic forms in the ratio 55:44:1. 2. The three forms are freely interconvertible and rate constants for these reactions have been determined. 3. Keto-dihydroxyacetone phosphate is the primary reactive species in the reactions catalysed by α-glycerophosphate dehydrogenase, aldolase and triose phosphate isomerase. 4. The proportion of keto form to gem-diol forms of dihydroxyacetone phosphate is temperature-dependent. At 37°C, 83% is keto-dihydroxyacetone phosphate. 5. The enzymological and metabolic consequences of these results are discussed.

scholarly journals Perdeuteration, large crystal growth and neutron data collection ofLeishmania mexicanatriose-phosphate isomerase E65Q variant

2019 ◽  
Vol 75 (4) ◽  
pp. 260-269 ◽  
Author(s):  
Vinardas Kelpšas ◽  
Bénédicte Lafumat ◽  
Matthew P. Blakeley ◽  
Nicolas Coquelle ◽  
Esko Oksanen ◽  
...  
Keyword(s):  
Triose Phosphate Isomerase ◽  
Dihydroxyacetone Phosphate ◽  
Leishmania Mexicana ◽  
Large Crystal ◽  
Neutron Data ◽  
X Ray ◽  
Triose Phosphate ◽  
Catalytic Mechanisms ◽  
Crystal Volume ◽  
Neutron Crystallography

Triose-phosphate isomerase (TIM) catalyses the interconversion of dihydroxyacetone phosphate and glyceraldehyde 3-phosphate. Two catalytic mechanisms have been proposed based on two reaction-intermediate analogues, 2-phosphoglycolate (2PG) and phosphoglycolohydroxamate (PGH), that have been used as mimics of thecis-enediol(ate) intermediate in several studies of TIM. The protonation states that are critical for the mechanistic interpretation of these structures are generally not visible in the X-ray structures. To resolve these questions, it is necessary to determine the hydrogen positions using neutron crystallography. Neutron crystallography requires large crystals and benefits from replacing all hydrogens with deuterium.Leishmania mexicanatriose-phosphate isomerase was therefore perdeuterated and large crystals with 2PG and PGH were produced. Neutron diffraction data collected from two crystals with different volumes highlighted the importance of crystal volume, as smaller crystals required longer exposures and resulted in overall worse statistics.

scholarly journals A Mutation in CsYL2.1 Encoding a Plastid Isoform of Triose Phosphate Isomerase Leads to Yellow Leaf 2.1 (yl2.1) in Cucumber (Cucumis Sativus L.)

2020 ◽  
Vol 22 (1) ◽  
pp. 322
Author(s):  
Liangrong Xiong ◽  
Hui Du ◽  
Keyan Zhang ◽  
Duo Lv ◽  
Huanle He ◽  
...  
Keyword(s):  
Chloroplast Development ◽  
Leaf Growth ◽  
Nuclear Gene ◽  
Triose Phosphate Isomerase ◽  
Dihydroxyacetone Phosphate ◽  
Chromosome 2 ◽  
Leaf Color ◽  
Mesophyll Cells ◽  
Chlorophyll Metabolism ◽  
Triose Phosphate

The leaf is an important photosynthetic organ and plays an essential role in the growth and development of plants. Leaf color mutants are ideal materials for studying chlorophyll metabolism, chloroplast development, and photosynthesis. In this study, we identified an EMS-induced mutant, yl2.1, which exhibited yellow cotyledons and true leaves that did not turn green with leaf growth. The yl2.1 locus was controlled by a recessive nuclear gene. The CsYL2.1 was mapped to a 166.7-kb genomic region on chromosome 2, which contains 24 predicted genes. Only one non-synonymous single nucleotide polymorphism (SNP) was found between yl2.1 and wt-WD1 that was located in Exon 7 of Csa2G263900, resulting in an amino acid substitution. CsYL2.1 encodes a plastid isoform of triose phosphate isomerase (pdTPI), which catalyzes the reversible conversion of dihydroxyacetone phosphate (DHAP) to glyceraldehyde-3-phosphate (GAP) in chloroplasts. CsYL2.1 was highly expressed in the cotyledons and leaves. The mesophyll cells of the yl2.1 leaves contained reduced chlorophyll and abnormal chloroplasts. Correspondingly, the photosynthetic efficiency of the yl2.1 leaves was impaired. Identification of CsYL2.1 is helpful in elucidating the function of ptTPI in the chlorophyll metabolism and chloroplast development and understanding the molecular mechanism of this leaf color variant in cucumber.

scholarly journals Disequilibrium in the triose phosphate isomerase system in rat liver

1969 ◽  
Vol 115 (4) ◽  
pp. 837-842 ◽  
Author(s):  
R. L. Veech ◽  
L. Raijman ◽  
K. Dalziel ◽  
H. A. Krebs
Keyword(s):  
Rat Liver ◽  
Significant Proportion ◽  
Enzyme Concentration ◽  
Triose Phosphate Isomerase ◽  
Distribution Data ◽  
Dihydroxyacetone Phosphate ◽  
Triose Phosphate ◽  
High Enzyme Concentration ◽  
Resting Muscle

1. The equilibrium constant at 38° and I 0·25 of the triose phosphate isomerase reaction was found to be 22·0 and that of the aldolase reaction, 0·99×10−4m. The [dihydroxyacetone phosphate]/[glyceraldehyde phosphate] ratio was found to be 9·3 in rat liver. The causes of the apparent deviation of the triose phosphate isomerase system from equilibrium in vivo have been investigated. 2. The equilibria of the triose phosphate isomerase and aldolase reactions were studied with relatively large concentrations of crystalline enzymes and small concentrations of substrates, approximating to those found in rat liver and muscle. There was significant binding of fructose diphosphate by aldolase under these conditions. There was no evidence that binding of glyceraldehyde phosphate by either enzyme affected the equilibria. 3. The deviation from equilibrium of the triose phosphate isomerase system in rat liver can be accounted for by the low activity of the enzyme, in relation to the flux, at low physiological concentrations of glyceraldehyde phosphate (about 3μm). It has been calculated that a flux of 1·8μmoles/min./g. wet weight of liver would be expected to cause the measured degree of disequilibrium found in vivo. 4. The conclusion that the triose phosphate isomerase is not at equilibrium is in accordance with the situation postulated by Rose, Kellermeyer, Stjernholm & Wood (1962) on the basis of isotope-distribution data. 5. The triose phosphate isomerase system is closer to equilibrium in resting muscle probably because of a very low flux and a high enzyme concentration. 6. The aldolase system deviated from equilibrium in rat liver by a factor of about 10 and by a much greater factor in resting muscle. 7. The measurement of total dihydroxyacetone phosphate and glyceraldehyde phosphate content indicates the concentrations of the free metabolites in the tissue. This may not hold for fructose diphosphate, a significant proportion of which may be bound to aldolase.

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