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D-glyceraldehyde 3-phosphate
dihydroxyacetone 3-phosphate
-
-
-
?
D-glyceraldehyde 3-phosphate
dihydroxyacetone phosphate
D-Glyceraldehyde 3-phosphate
Glycerone phosphate
dihydroxyacetone 3-phosphate
D-glyceraldehyde 3-phosphate
-
-
-
?
D-glyceraldehyde 3-phosphate
dihydroxyacetone 3-phosphate
-
-
-
-
r
D-glyceraldehyde 3-phosphate
dihydroxyacetone phosphate
D-Glyceraldehyde 3-phosphate
Glycerone phosphate
dihydroxyacetone 3-phosphate
D-glyceraldehyde 3-phosphate
-
-
-
-
r
additional information
?
-
D-glyceraldehyde 3-phosphate
dihydroxyacetone phosphate
-
-
-
?
D-glyceraldehyde 3-phosphate
dihydroxyacetone phosphate
-
-
-
r
D-Glyceraldehyde 3-phosphate
Glycerone phosphate
-
-
-
?
D-Glyceraldehyde 3-phosphate
Glycerone phosphate
substrate binding perturbs residues Asn10, His95, Ser100, Glu129-Glu133, Val167-Ala186, Asn213, and Leu230-Leu126 that either are near the ligand or have direct contact with the ligand
-
-
?
D-glyceraldehyde 3-phosphate
dihydroxyacetone phosphate
-
-
-
-
?
D-glyceraldehyde 3-phosphate
dihydroxyacetone phosphate
-
-
-
-
r
D-Glyceraldehyde 3-phosphate
Glycerone phosphate
-
-
-
?
D-Glyceraldehyde 3-phosphate
Glycerone phosphate
-
-
-
?
D-Glyceraldehyde 3-phosphate
Glycerone phosphate
-
r
-
?
additional information
?
-
the effect of bound phosphite dianion on the activation barrier is small, in comparison to the much larger intrinsic phosphodianion and phosphite dianion binding energy utilized to stabilize the transition states for TIM-catalyzed deprotonation of glyceraldehyde-3-phosphate and glyceraldehyde-phosphite dianion complex, respectively
-
-
?
additional information
?
-
the substrate is locked in a protein cage with the phosphodianion occluded from interaction with solvent water, and ion-paired to the surface alkyl ammonium side chain of residue K12. The neutral imidazole side chain of H95 interacts with the carbonyl oxygen of dihydroxyacetone phosphate and glyceraldehyde 3-phosphate
-
-
?
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0.7 - 12
D-glyceraldehyde 3-phosphate
1.7 - 25
dihydroxyacetone 3-phosphate
0.3 - 50
D-glyceraldehyde 3-phosphate
2.3
dihydroxyacetone 3-phosphate
-
at pH 7.5 and 37°C
0.6 - 2.1
dihydroxyacetone phosphate
1.23
glycerone phosphate
-
-
additional information
additional information
-
-
-
0.7
D-glyceraldehyde 3-phosphate
mutant Y208T/S211G, pH 7.5, 25°C
1
D-glyceraldehyde 3-phosphate
wild-type, pH 7.5, 25°C
1.09
D-glyceraldehyde 3-phosphate
mutant K17A/Y46A/D48F/Q82A/D85S , pH 7.4, 25°C
1.2
D-glyceraldehyde 3-phosphate
mutant K17L/Y46F/D48F/Q82F/D85L, pH 7.4, 25°C
1.26
D-glyceraldehyde 3-phosphate
mutant K17L/Y46F/D48Y/Q82A/D85A, pH 7.4, 25°C
1.4
D-glyceraldehyde 3-phosphate
wild-type, pH 7.4, 25°C
1.8
D-glyceraldehyde 3-phosphate
mutant S211G, pH 7.5, 25°C
2.4
D-glyceraldehyde 3-phosphate
mutant Y208F, pH 7.5, 25°C
2.44
D-glyceraldehyde 3-phosphate
mutant K17P/Y46A/D48L/Q82T/D85A, pH 7.4, 25°C
2.9
D-glyceraldehyde 3-phosphate
mutant Y208A, pH 7.5, 25°C
3.4
D-glyceraldehyde 3-phosphate
mutant Y208T, pH 7.5, 25°C
3.9
D-glyceraldehyde 3-phosphate
mutant Y208S, pH 7.5, 25°C
12
D-glyceraldehyde 3-phosphate
mutant S211A, pH 7.5, 25°C
1.7
dihydroxyacetone 3-phosphate
wild-type, pH 7.5, 25°C
3.2
dihydroxyacetone 3-phosphate
mutant S211G, pH 7.5, 25°C
4
dihydroxyacetone 3-phosphate
mutant Y208T/S211G, pH 7.5, 25°C
11
dihydroxyacetone 3-phosphate
mutant Y208T, pH 7.5, 25°C
17
dihydroxyacetone 3-phosphate
mutant Y208A, pH 7.5, 25°C
17
dihydroxyacetone 3-phosphate
mutant Y208F, pH 7.5, 25°C
25
dihydroxyacetone 3-phosphate
mutant Y208S, pH 7.5, 25°C
0.3
D-glyceraldehyde 3-phosphate
-
25°C, pH 7.4, mutant enzyme C126S
0.8
D-glyceraldehyde 3-phosphate
-
25°C, pH 7.4, mutant enzyme C126A
0.91
D-glyceraldehyde 3-phosphate
-
mutant D225Q, pH 7.4, 25°C
1.1
D-glyceraldehyde 3-phosphate
-
25°C, pH 7., wild-type enzyme
1.1
D-glyceraldehyde 3-phosphate
-
wild type enzyme, in 30 mM TEA at pH 7.5, at 25°C
1.13
D-glyceraldehyde 3-phosphate
-
wild-type, pH 7.4, 25°C
1.27
D-glyceraldehyde 3-phosphate
-
-
1.5
D-glyceraldehyde 3-phosphate
-
at pH 7.5 and 37°C
50
D-glyceraldehyde 3-phosphate
-
mutant enzyme K12G, in 30 mM TEA at pH 7.5, at 25°C
0.6
dihydroxyacetone phosphate
-
25°C, pH 7.4, mutant enzyme C126S
2.1
dihydroxyacetone phosphate
-
25°C, pH 7.4, wild-type enzyme
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0.69 - 8900
D-glyceraldehyde 3-phosphate
4.5 - 860
dihydroxyacetone 3-phosphate
0.6 - 16700
D-glyceraldehyde 3-phosphate
327
dihydroxyacetone 3-phosphate
-
at pH 7.5 and 37°C
60 - 500
dihydroxyacetone phosphate
additional information
additional information
-
-
-
0.69
D-glyceraldehyde 3-phosphate
mutant K17L/Y46F/D48F/Q82F/D85L, pH 7.4, 25°C
1.04
D-glyceraldehyde 3-phosphate
mutant K17L/Y46F/D48Y/Q82A/D85A, pH 7.4, 25°C
13
D-glyceraldehyde 3-phosphate
mutant Y208F, pH 7.5, 25°C
520
D-glyceraldehyde 3-phosphate
mutant Y208T/S211G, pH 7.5, 25°C
740
D-glyceraldehyde 3-phosphate
mutant Y208A, pH 7.5, 25°C
940
D-glyceraldehyde 3-phosphate
mutant Y208S, pH 7.5, 25°C
2800
D-glyceraldehyde 3-phosphate
mutant S211A, pH 7.5, 25°C
3700
D-glyceraldehyde 3-phosphate
mutant Y208T, pH 7.5, 25°C
4160
D-glyceraldehyde 3-phosphate
mutant K17P/Y46A/D48L/Q82T/D85A, pH 7.4, 25°C
6400
D-glyceraldehyde 3-phosphate
wild-type, pH 7.4, 25°C
7020
D-glyceraldehyde 3-phosphate
mutant K17A/Y46A/D48F/Q82A/D85S , pH 7.4, 25°C
7500
D-glyceraldehyde 3-phosphate
mutant S211G, pH 7.5, 25°C
8900
D-glyceraldehyde 3-phosphate
wild-type, pH 7.5, 25°C
4.5
dihydroxyacetone 3-phosphate
mutant Y208F, pH 7.5, 25°C
135
dihydroxyacetone 3-phosphate
mutant Y208T/S211G, pH 7.5, 25°C
210
dihydroxyacetone 3-phosphate
mutant Y208A, pH 7.5, 25°C
250
dihydroxyacetone 3-phosphate
mutant Y208S, pH 7.5, 25°C
580
dihydroxyacetone 3-phosphate
mutant Y208T, pH 7.5, 25°C
810
dihydroxyacetone 3-phosphate
mutant S211G, pH 7.5, 25°C
860
dihydroxyacetone 3-phosphate
wild-type, pH 7.5, 25°C
0.6
D-glyceraldehyde 3-phosphate
-
mutant enzyme K12G, in 30 mM TEA at pH 7.5, at 25°C
1100
D-glyceraldehyde 3-phosphate
-
25°C, pH 7.4, mutant enzyme C126S
3100
D-glyceraldehyde 3-phosphate
-
25°C, pH 7.4, mutant enzyme C126A
4600
D-glyceraldehyde 3-phosphate
-
mutant D225Q, pH 7.4, 25°C
4700
D-glyceraldehyde 3-phosphate
-
25°C, pH 7., wild-type enzyme
6900
D-glyceraldehyde 3-phosphate
-
wild-type, pH 7.4, 25°C
7300
D-glyceraldehyde 3-phosphate
-
wild type enzyme, in 30 mM TEA at pH 7.5, at 25°C
8700
D-glyceraldehyde 3-phosphate
-
at pH 7.5 and 37°C
16700
D-glyceraldehyde 3-phosphate
-
-
60
dihydroxyacetone phosphate
-
25°C, pH 7.4, mutant enzyme C126S
500
dihydroxyacetone phosphate
-
25°C, pH 7.4, wild-type enzyme
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5.4 - 8900
D-glyceraldehyde 3-phosphate
0.26 - 510
dihydroxyacetone 3-phosphate
0.012 - 6600
D-glyceraldehyde 3-phosphate
750
dihydroxyacetone 3-phosphate
-
at pH 7.5 and 37°C
5.4
D-glyceraldehyde 3-phosphate
mutant Y208F, pH 7.5, 25°C
230
D-glyceraldehyde 3-phosphate
mutant S211A, pH 7.5, 25°C
240
D-glyceraldehyde 3-phosphate
mutant Y208S, pH 7.5, 25°C
260
D-glyceraldehyde 3-phosphate
mutant Y208A, pH 7.5, 25°C
730
D-glyceraldehyde 3-phosphate
mutant Y208T/S211G, pH 7.5, 25°C
1100
D-glyceraldehyde 3-phosphate
mutant Y208T, pH 7.5, 25°C
4200
D-glyceraldehyde 3-phosphate
mutant S211G, pH 7.5, 25°C
8900
D-glyceraldehyde 3-phosphate
wild-type, pH 7.5, 25°C
0.26
dihydroxyacetone 3-phosphate
mutant Y208F, pH 7.5, 25°C
10
dihydroxyacetone 3-phosphate
mutant S211A, pH 7.5, 25°C
10
dihydroxyacetone 3-phosphate
mutant Y208S, pH 7.5, 25°C
12
dihydroxyacetone 3-phosphate
mutant Y208A, pH 7.5, 25°C
34
dihydroxyacetone 3-phosphate
mutant Y208T/S211G, pH 7.5, 25°C
53
dihydroxyacetone 3-phosphate
mutant Y208T, pH 7.5, 25°C
250
dihydroxyacetone 3-phosphate
mutant S211G, pH 7.5, 25°C
510
dihydroxyacetone 3-phosphate
wild-type, pH 7.5, 25°C
0.012
D-glyceraldehyde 3-phosphate
-
mutant enzyme K12G, in 30 mM TEA at pH 7.5, at 25°C
5800
D-glyceraldehyde 3-phosphate
-
at pH 7.5 and 37°C
6600
D-glyceraldehyde 3-phosphate
-
wild type enzyme, in 30 mM TEA at pH 7.5, at 25°C
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I170A
effect of the mutation on the relative electrostatic contribution of the residue is negligible. Mutation results in increases in the activation barriers for deprotonation of substrate
I170A/L230A
effect of the mutation on the relative electrostatic contribution of the residue is negligible. Mutation results in increases in the activation barriers for deprotonation of substrate
K17A/Y46A/D48F/Q82A/D85S
mutation of residues in the dimer interface of enzyme
K17L/Y46F/D48F/Q82F/D85L
mutation of residues in the dimer interface of enzyme. Decrease in catalytic efficiency by 4 orders of magnitude
K17L/Y46F/D48Y/Q82A/D85A
mutation of residues in the dimer interface of enzyme. Decrease in catalytic efficiency by 4 orders of magnitude
K17P/Y46A/D48L/Q82T/D85A
mutation of residues in the dimer interface of enzyme
L230A
effect of the mutation on the relative electrostatic contribution of the residue is negligible. Mutation results in increases in the activation barriers for deprotonation of substrate
S211A
mutation eliminates intraloop hydrogen bonds to the side-chain hydroxyl, 60fold decrease in kcat/Km
S211G
mutation eliminates intraloop hydrogen bonds to the side-chain hydroxyl, leading to small changes in the kinetic parameters
Y208A
main effect of mutations is to cause a reduction in the total intrinsic dianion binding energy
Y208F
mutation eliminates the intraloop hydrogen bond between the hydroxyl group of Y208 and the amide nitrogen of A176. Enzyme activity is reduced by ca. 50fold compared to the Y208A and Y208S mutants
Y208S
main effect of mutations is to cause a reduction in the total intrinsic dianion binding energy
Y208T
main effect of mutations is to cause a reduction in the total intrinsic dianion binding energy
Y208T/S211G
tenfold decrease in kcat/Km
C126A
-
turnover number for D-glyceraldehyde 3-phosphate is 1.5fold lower than the wild-type value, KM-value for D-glyceraldehyde 3-phosphate is 1.4fold lower than the wild-type value, turnover number for dihydroxyacetone phosphate is 4.3fold lower than the wild-type value, KM-value for dihydroxyacetone phosphate is 3.7fold lower than the wild-type value
C126S
-
mutant enzyme shows greater susceptibility to thermal denaturation than wild-type enzyme, turnover number for dihydroxyacetone phosphate is 8.3fold lower than the wild-type value, KM-value for dihydroxyacetone phosphate is 3.5fold lower than the wild-type value
D225Q
-
mutation causes minor drops in Km and kcat value without changes catalytic efficiency. Temperature-induced unfolding-refolding of both wild-type and mutant D225Q samples display hysteresis cycles, indicative of processes far from equilibrium. The rate constant for unfolding is about three-fold larger in the mutant than in wild-type. Upon mutation, the rate-limiting step changes from a second-order at submicromolar concentrations to a first-order reaction. Renaturation occurs through a uni-bimolecular mechanism in which refolding of the monomer most likely begins at the C-terminal half of its polypeptide chain
K12G
-
the mutation results in a ca. 50fold increase in Km for the substrate glyceraldehyde 3-phosphate (GAP) and a 60fold increase in Ki for competitive inhibition by 2-phosphoglycolate, a 12000fold decrease in kcat for isomerization of GAP, and a 6000000fold decrease in kcat/Km for GAP
additional information
mutation of five residues in the dimer interface of enzyme. Obtained proteins are soluble, dimeric, and compact. Proteins obtained from direct evolution experiments show wild-type-like catalytic activity, while their stability is decreased. In silico-designed proteins are very stable dimers that bind substrate with a wild-type-like Km value, albeit they exhibit a very low kcat
additional information
-
mutation of five residues in the dimer interface of enzyme. Obtained proteins are soluble, dimeric, and compact. Proteins obtained from direct evolution experiments show wild-type-like catalytic activity, while their stability is decreased. In silico-designed proteins are very stable dimers that bind substrate with a wild-type-like Km value, albeit they exhibit a very low kcat
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Krietsch, W.K.G.
Triosephosphate isomerase from yeast
Methods Enzymol.
41B
434-438
1975
Saccharomyces cerevisiae
-
brenda
Nickbarg, E.B.; Knowles, J.R.
Triosephosphate isomerase: energetics of the reaction catalyzed by the yeast enzyme expressed in Escherichia coli
Biochemistry
27
5939-5947
1988
Saccharomyces cerevisiae
brenda
Carza-Ramos, G.; Perez-Montfort, R.; Rojo-Dominguez, A.; de Gomez-Puyou, M.T.; Gomez-Puyou, A.
Species-specific inhibition of homologous enzymes by modification of nonconserved amino acids residues. The cysteine residues of triosephosphate isomerase
Eur. J. Biochem.
241
114-120
1996
Saccharomyces cerevisiae, Gallus gallus, Oryctolagus cuniculus, Escherichia coli, Schizosaccharomyces pombe
brenda
Najera, H.; Costas, M.; Fernandez-Velasco, D.A.
Thermodynamic characterization of yeast triosephosphate isomerase refolding: insights into the interplay between function and stability as reasons for the oligomeric nature of the enzyme
Biochem. J.
370
785-792
2003
Saccharomyces cerevisiae
brenda
Benitez-Cardoza, C.G.; Rojo-Dominguez, A.; Hernandez-Arana, A.
Temperature-induced denaturation and renaturation of triosephosphate isomerase from Saccharomyces cerevisiae: evidence of dimerization coupled to refolding of the thermally unfolded protein
Biochemistry
40
9049-9058
2001
Saccharomyces cerevisiae (P00942), Saccharomyces cerevisiae
brenda
Gonzalez-Mondragon, E.; Zubillaga, R.A.; Saavedra, E.; Chanez-Cardenas, M.E.; Perez-Montfort, R.; Hernandez-Arana, A.
Conserved cysteine 126 in triosephosphate isomerase is required not for enzymatic activity but for proper folding and stability
Biochemistry
43
3255-3263
2004
Saccharomyces cerevisiae
brenda
Vazquez-Perez, A.R.; Fernandez-Velasco, D.A.
Pressure and denaturants in the unfolding of triosephosphate isomerase: the monomeric intermediates of the enzymes from Saccharomyces cerevisiae and Entamoeba histolytica
Biochemistry
46
8624-8633
2007
Saccharomyces cerevisiae, Entamoeba histolytica
brenda
Najera, H.; Dagdug, L.; Fernandez-Velasco, D.A.
Thermodynamic and kinetic characterization of the association of triosephosphate isomerase: The role of diffusion
Biochim. Biophys. Acta
1774
985-994
2007
Saccharomyces cerevisiae
brenda
Gonzalez-Mondragon, E.; Zubillaga, R.A.; Hernandez-Arana, A.
Effect of a specific inhibitor on the unfolding and refolding kinetics of dimeric triosephosphate isomerase: establishing the dimeric and similarly structured nature of the main transition states on the forward and backward reactions
Biophys. Chem.
125
172-178
2007
Saccharomyces cerevisiae
brenda
Rozovsky, S.; McDermott, A.E.
Substrate product equilibrium on a reversible enzyme, triosephosphate isomerase
Proc. Natl. Acad. Sci. USA
104
2080-2085
2007
Saccharomyces cerevisiae
brenda
Peimbert, M.; Dominguez-Ramirez, L.; Fernandez-Velasco, D.A.
Hydrophobic repacking of the dimer interface of triosephosphate isomerase by in silico design and directed evolution
Biochemistry
47
5556-5564
2008
Saccharomyces cerevisiae (P00942), Saccharomyces cerevisiae
brenda
Reyes-Lopez, C.A.; Gonzalez-Mondragon, E.; Benitez-Cardoza, C.G.; Chanez-Cardenas, M.E.; Cabrera, N.; Perez-Montfort, R.; Hernandez-Arana, A.
The conserved salt bridge linking two C-terminal beta /alpha units in homodimeric triosephosphate isomerase determines the folding rate of the monomer
Proteins Struct. Funct. Bioinform.
72
972-979
2008
Saccharomyces cerevisiae
brenda
Xu, Y.; Lorieau, J.; McDermott, A.E.
Triosephosphate isomerase: 15N and 13C chemical shift assignments and conformational change upon ligand binding by magic-angle spinning solid-state NMR spectroscopy
J. Mol. Biol.
397
233-248
2010
Saccharomyces cerevisiae (P00942), Saccharomyces cerevisiae
brenda
Go, M.K.; Koudelka, A.; Amyes, T.L.; Richard, J.P.
The role of Lys-12 in catalysis by triosephosphate isomerase: a two-part substrate approach
Biochemistry
49
5377-5389
2010
Saccharomyces cerevisiae
brenda
Wierenga, R.K.; Kapetaniou, E.G.; Venkatesan, R.
Triosephosphate isomerase: a highly evolved biocatalyst
Cell. Mol. Life Sci.
67
3961-3982
2010
Entamoeba histolytica (O02611), Oryctolagus cuniculus (P00939), Gallus gallus (P00940), Saccharomyces cerevisiae (P00942), Geobacillus stearothermophilus (P00943), Trypanosoma brucei brucei (P04789), Escherichia coli (P0A858), Giardia intestinalis (P36186), Thermotoga maritima (P36204), Leishmania mexicana (P48499), Moritella marina (P50921), Trypanosoma cruzi (P52270), Helicobacter pylori (P56076), Homo sapiens (P60174), Pyrococcus woesei (P62003), Mycobacterium tuberculosis (P9WG43), Plasmodium falciparum (Q07412), Caenorhabditis elegans (Q10657), Methanocaldococcus jannaschii (Q58923), Bartonella henselae (Q8L1Z5), Tenebrio molitor (Q8MPF2), Thermoproteus tenax (Q8NKN9), Mycobacterium tuberculosis H37Rv (P9WG43)
brenda
Sullivan, B.J.; Durani, V.; Magliery, T.J.
Triosephosphate isomerase by consensus design: dramatic differences in physical properties and activity of related variants
J. Mol. Biol.
413
195-208
2011
Saccharomyces cerevisiae
brenda
Aqvist, J.
Cold adaptation of triosephosphate isomerase
Biochemistry
56
4169-4176
2017
Saccharomyces cerevisiae (P00942), Saccharomyces cerevisiae, Moritella marina (P50921), Moritella marina, Saccharomyces cerevisiae 288c (P00942)
brenda
Labastida-Polito, A.; Garza-Ramos, G.; Camarillo-Cadena, M.; Zubillaga, R.; Hernández-Arana, A.
Complex kinetics and residual structure in the thermal unfolding of yeast triosephosphate isomerase
BMC Biochem.
16
20
2015
Saccharomyces cerevisiae
brenda
Zhai, X.; Amyes, T.L.; Richard, J.P.
Role of loop-clamping side chains in catalysis by triosephosphate isomerase
J. Am. Chem. Soc.
137
15185-15197
2015
Saccharomyces cerevisiae (P00942)
brenda
Kulkarni, Y.S.; Liao, Q.; Petrovi?, D.; Krueger, D.M.; Strodel, B.; Amyes, T.L.; Richard, J.P.; Kamerlin, S.C.L.
Enzyme architecture Modeling the operation of a hydrophobic clamp in catalysis by triosephosphate isomerase
J. Am. Chem. Soc.
139
10514-10525
2017
Saccharomyces cerevisiae (P00942), Saccharomyces cerevisiae 288c (P00942)
brenda
Kulkarni, Y.S.; Liao, Q.; Bylehn, F.; Amyes, T.L.; Richard, J.P.; Kamerlin, S.C.L.
Role of ligand-driven conformational changes in enzyme catalysis Modeling the reactivity of the catalytic cage of triosephosphate isomerase
J. Am. Chem. Soc.
140
3854-3857
2018
Saccharomyces cerevisiae (P00942), Saccharomyces cerevisiae 288c (P00942)
brenda