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5.3.1.1: triose-phosphate isomerase

This is an abbreviated version!
For detailed information about triose-phosphate isomerase, go to the full flat file.

Word Map on EC 5.3.1.1

Reaction

D-glyceraldehyde 3-phosphate
=
glycerone phosphate

Synonyms

CP 25, CTIMC, cTPI, cytoplasmic TPI, cytoplasmic triosephosphate isomerase, cytoTPI, D-glyceraldehyde-3-phosphate ketol-isomerase, GlTIM, Isomerase, triose phosphate, Lactacin B inducer protein, monoTIM, PfTIM, PfuTIM, Phosphotriose isomerase, plastidic TPI, plastidic triosephosphate isomerase, pTPI, SSO2592, TcTIM, TIM, TIM1, TIM2, TonTIM, TpI, TPI1, TpiA, Triose phosphate isomerase, Triose phosphate mutase, Triose phosphoisomerase, Triosephosphate isomerase, Triosephosphate mutase, vTIM

ECTree

     5 Isomerases
         5.3 Intramolecular oxidoreductases
             5.3.1 Interconverting aldoses and ketoses, and related compounds
                5.3.1.1 triose-phosphate isomerase

Crystallization

Crystallization on EC 5.3.1.1 - triose-phosphate isomerase

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
sitting drop vapor diffusion method, using either 65% (v/v) 2-methyl-2,4-pentanediol 0.1 M HEPES, pH 7.5, or 6% (w/v) PEG 6000 0.1 M HEPES, pH 7.0, or 17.5% (w/v) PEG 3350, 0.1 M Bis-Tris, pH 5.5, or 15% (w/v) PEG 3350 0.1 M Bis-Tris, pH 5.0
using 100 mM Bis-Tris propane pH 7.5, 200 mM sodium sulfate, 20% (w/v) PEG 3350
crystals are grown at 18°C from hanging drops by mixing 0.005 ml of the enzyme, 5 mg/ml, with 0.005 ml of the reservoir solution, 28% w/v PEG 1500 and 0.001 ml of 30% v/v 1,6-hexanediol
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crystal structure of the recombinant enzyme complexed with phosphoglycolohydroxamate, at 1.8 A resolution
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simulation of both dimeric and monomeric (isolated from dimer) forms in explicit water at 27°C and 1 bar. Significant cross-correlations between residue fluctuations are observed in the dimer, which result from the global counter-rotations of the two identical subunits in the essential modes of the dimer. The first essential mode contributing to 34% of overall motion of the dimer is strongly coupled to the loop 6's closure over the active site. The monomeric structure maintains relatively localized motions of the loops in the essential modes
structures of mutants 170-173del and V167P/W168E
hanging drop vapor diffusion method
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triosephosphate isomerase complexed with the competitive inhibitor 2-phosphoglycolate, at 2.8 A resolution
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determination of intrinsic fluorescence of wild-type and mutants lacking Trp residues, interpretation based on crystal structure. Fluorescence of all Trp residues is quenched by aromatic-aromatic interactions due to the proximity and orientation of the indole groups of Trp196 and Tro162. Quenching is also due to energy transfer to the charged resiudes that surround Trp75, Trp173, and Trp196
determination by molecular replacement, at 2.3 A resolution and in the closed state. Phosphate acts as a competitive inhibitor and occupies the binding pocket. Binding pocket has a very stable conformation even without a substrate
monomer, to 2.3 A resolution
high resolution structure of crystal form 2 employing the gel-tube method in microgravity
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mutant E104D, at 1.85 A resolution. Mutant structure is similar to wild-type, mutant residue E104A is part of a conserved cluster of 10 residues, 5 from each subunit. This cluster forms a cavity that possesses an elaborate conserved network of buried water molecules that bridge the two subunits. In the E104D mutant, a disruption of contacts of the amino acid side chains in the conserved cluster leads to a perturbation of the water network in which the water-protein and water-water interactions that join the two monomers are significantly weakened and diminished
triosephosphate isomerase complexed with the competitive inhibitor 2-phosphoglycolate, at 2.8 A resolution
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crystal structure of triosephosphate isomerase complexed with 2-phosphoglycolate at 0.83-A resolution
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mutant enzyme E65Q, hanging drop vapor diffusion method, crystal structure of the enzyme complexed with 2-(N-formyl-N-hydroxy)-aminoethyl phosphonate
purified enzyme mutant E65Q in complex with reaction-intermediate analogue phosphoglycolohydroxamate, hanging drop method, TIM-PGH crystals are grown at room temperature, 0.004 ml of protein solution with 11 mg/ml protein in 20 mM Tris-HCl, pH 7.5, 25 mM NaCl, 10 mM PGH, 1 mM DTT, 1 mM EDTA, and 1 mM NaN3, are mixed with 0.004 ml of well solution containing 0.1M acetate, pH 5.0, 24% PEG6000, 1 mM DTT, 1 mM EDTA, and 1 mM NaN3, X-ray diffraction structure determination and analysis at 0.82 A resolution
unliganded enzyme. Complete absence of electron density for the loop 6 residues. Disorder of this loop due to a missing slat bridge between residues at the N-and C-terminal ends of the loop
crystal structures of the vTIM-sulfate complex and the vTIM-2-phosphoglycolate complex, at 2.7 A resolution
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hanging drop vapor diffusion method. Crystal structure of the enzyme-sulfate complex and the enzyme-2-phosphoglycolate complex at a 2.7 A resolution
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hanging drop vapor diffusion method, using 16% (w/v) PEG 3350 and 250 mM ammonium citrate
hanging drop vapor diffusion method, apo-enzyme structure, refined to 1.5 A resolution, in which the active site loop is either in the open or in the closed conformation in different subunits of the enzyme. The observation of both open and closed lid conformations in triosephosphate isomerase crystals might by related to a persistent conformational heterogeneity of the protein in solution
structure of TPI with bound phosphoenolpyruvate at 1.6 A resolution. Phosphoenolpyruvate is bound to the catalytic pocket of TPI and occludes substrate
two crystal forms, A and B, belonging to space group P212121 are obtained by hanging-drop method. Crystal form A has unit-cell parameters a = 65.14, b = 72.45, c = 93.24 A and diffracts to 2.25 A at -188°C, whereas form B has unit-cell parameters A = 73.02, b = 79.8 and c = 172.85
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crystal structure analysis
crystal structure analysis, overview
crystal structure of PfTIMat 2.2 A resolution or 2.8 A resolution, crystal structure of the enzyme in complex with phosphoglycolate at 1.9 A resolution, crystal structure of the enzyme in complex with glycerol phosphate at 2.4 A resolution, crystal structure of the enzyme in complex with 2-phosphoglycerate at 1.1 A resolution or 2.4 A resolution
E97Q and E97D mutant enzymes, hanging drop vapor diffusion method
enzyme in complex with 3-phosphoglycerate or glycerol 3-phosphate, hanging drop vapor diffusion method
mutant enzyme C126S in complex with PGA, hanging drop vapor diffusion method, using 20% (w/v) poly(ethylene glycol), 1 M HEPES buffer (pH 7.5), and 10 mM lithium sulfate, at 23°C. Unliganded mutant enzymes C126S and C126A, hanging drop vapor diffusion method, using 24% (w/v) poly(ethylene glycol), 1 M HEPES buffer (pH 7.0), and 10 mM lithium sulfate
structures of wild-type and mutants at residues T75 and Q64
wild-type and mutant enzymes in complex with inhibitor 3-phosphoglycerate, 0.003 ml of 10 mg/ml protein in 100 mM triethanolamine-HCl, pH 7.6, are mixed with an equal volume of reservoir solution, the crystallization cocktail contains 0.1 M sodium acetate pH 4.0-5.5 and PEG 1450 varying from 8% to 24% in the reservoir, X-ray diffraction structure determination and analysis at 1.4-2.25 A resolutions
hanging drop vapor diffusion method, diffraction quality can only be obtained in the presence of inhibitors, monoclinic crystal form is obtained by cocrystallization with 20 mM 2-carboxyethylphosphonic acid with sodium acetate, pH 4.0, and 7% PEG 4000 as the precipitant buffer. An orthorhombic crystal form is obtained by cocrystallization with 20 mM 2-phosphoglycolic acid with 0.1 M sodium acetate, pH 4.2, and 5% PEG 4000 as the precipitant buffer. Hexagonal crystal forms are obtained under the same conditions with 2-phosphoglycolic acid, but their diffraction shows high disorder
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hanging drop vapor diffusion method, using 0.1 M HEPES-Na, pH 7.5, and 1.4 M trisodium citrate dihydrate
purified recombinant enzyme, 200 mg/ml protein with ligand in a ratio of 5:1 in 50 mM Tris-HCl, 50 mM NaCl, and 1 mM EDTA, pH 6.8, 4°C, is mixed with 40% w/v PEG 4000 as precipitant, X-ray diffraction structure determination and analysis
enzyme alone and in complex with various phosphate containing ligands like glycerol 3-phosphate, glycerol 2-phosphate, 3-phosphoglyceric acid, and 2-phosphoglyceric acid, hanging drop vapor diffusion method
purified recombinant enzyme by hanging drop vapour diffusion method, from 1.6 M trisodium citrate dihydrate, pH 6.5, X-ray diffraction structure determination and analysis at1.9 A resolution, modeling
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purified recombinant C-terminally His6-tagged enzyme, sitting drop vapour diffusion method, room temperature, 0.003 ml of 18 mg/ml protein in 10 mM MES buffer, pH 6.5, and 15 mM NaCl, is mixed with 0.003 ml of reservoir solution containing 18% PEG MME 2000 as precipitant, X-ray diffraction structure determination and analysis at 2.0 A resolution
structures of apo- and glycerol-3-phosphate-bound TPI, to 1.94 and 2.17 A resolution, respectively. The protein adopts the canonical TIM-barrel fold with eight alpha-helices and parallel eight beta-strands
structure of both a hexagonal and an orthorhombic crystal form to resolutions of 2.5 A and 2.3 A. In both crystal forms the enzyme exists as a tetramer of the (betaalpha)8-barrel. Hexagonal crystal form (crystallisation conditions 0.1 M Hepes–KOH (pH 7.5), 0.8 M sodium potassium phosphate) diffracts to 2.5 A and belongs to spacegroup P6(5)22/P6(1)22 with cell dimensions a = b = 186.9 A, c = 287.8 A, alpha = beta = 90°, gamma = 120°, suggesting two tetramers in the asymmetric unit. Orthorhombic crystals with cell dimensions a = 154.1 A, b = 91.0 A, c = 141.2 A, alpha = beta = gamma = 90° are obtained in 0.1 M sodium acetate (pH 4.6), 0.2 M ammonium sulfate, with PEG4000 at any concentration between 20% and 30% (w/v). Crystals grew within 48 hours at 20°C
hanging drop vapor diffusion method
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hanging drop vapor diffusion method, crystal structure represents the most thermostable triosephosphate isomerase presently known in its 3D-structure
use of real time in situ atomic force microscopy to monitor the molecular processes that govern the crystallization of triosephosphate isomerase. Triosephosphate isomerase tetramers are the dominating growth units. The incorporation of growth units occurs through surface diffusion. Normal growth is dominated by the two-dimensional nucleation of triangular islands
monomeric enzyme variant with an engineered binding groove, m18bTIM, and the V233A mutant of this variant in complex with citrate, 2-phosphoglycolate, and glycerol 3-phosphate, to 1.89, 1.6, 2.3 and 2.0 A resolution, respectively
mutant A178L, unliganded and in complex with 2-phosphoglycolate, to 2.2 A and 1.89 A, respectively. Monomeric mutant mlA178L, unliganded and in complex with 2-phosphoglycolate, to 2.3 A and 1.18 A, respectively. Mutation A178L favors the closed conformation of the C-terminal hinge region
mutant enzyme R191S, hanging drop vapor diffusion method, crystal structure of the R191S mutant complexed with 2-phosphoglycolate is determined at 1.65 A resolution
mutant P168A, with and without 2-phosphoglycolate. Phosphate moiety of 2-phosphoglycolate is bound similarly as in wild-type, but interactions of the carboxylic acid moiety with the side chain of catalytic Glu167 differ
structures of wild-type and mutants Q65L and E23G/A70T/S96F/A178V. Mutation Q65L contributes to small structural rearrangements near Asn11 of loop 1, which correlate with different ligand-binding properties. Its Leu65 side chain is involved in van der Waals interactions with neighbouring hydrophobic side-chain moieties
hanging drop vapor diffusion method, a crystal of the dimeric enzyme is soaked and diffracted in hexane and its structure solved at 2 A resolution. Its overall structure and the dimer interface are not altered by hexane
hanging drop vapour diffusion method, crystals of the enzyme in complex with one molecule of 3-(2-benzothiazolylthio)-1-propanesulfonic acid diffract to a resolution of 2 A. Unit cell dimensions: a = 42.87, b = 75.57, c = 146.45
molecular docking studies with inhibitors
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purified recombinant monomeric enzyme by sitting drop method, 0.001 ml of protein solutioncontaining 25 mg/ml protein in 20 mM Tris-HCl , pH 7.4, and 1.0 mM EDTA is mixed with 0.001 ml of reservoir solution containing 100 mM HEPES, pH 7.5, 10% PEG 6000, and 5% MPD, X-ray diffraction structure determination and analysis
comparison of the structures and the crystal contacts of trypanosomal triosephosphate isomerase in four different crystal forms
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genetically engineered enzyme variant, at 2.6 A resolution
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resolution of 2.1 A in a new crystal form grown at pH 8.8 from PEG6000
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