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5.3.1.5: xylose isomerase

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

Word Map on EC 5.3.1.5

Reaction

alpha-D-xylopyranose
=
alpha-D-xylufuranose

Synonyms

D-XI, D-xylose aldose-ketose-isomerase, D-xylose isomerase, D-Xylose ketoisomerase, D-xylose ketol isomerase, D-xylose ketol-isomerase, D-xylose: ketol-isomerase, D-xylulose keto-isomerase, glucose isomerase, glucose/xylose isomerase, GXI, Isomerase, xylose, Maxazyme, Optisweet, SDXyI, Spezyme, Sweetase, Sweetzyme, Sweetzyme Q, Swetase, T80 xylose isomerase, TcaXI, TNXI, TthXI, XI, XYLA, XylC, xylose (glucose) isomerase, xylose isomerase

ECTree

     5 Isomerases
         5.3 Intramolecular oxidoreductases
             5.3.1 Interconverting aldoses and ketoses, and related compounds
                5.3.1.5 xylose isomerase

Crystallization

Crystallization on EC 5.3.1.5 - xylose isomerase

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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
structure of a number of binary and ternary complexes involving wild-type and mutant enzymes, the divalent cations Mg2+, Co2+, or Mn2+ and either the substrate xylose or substrate analogs
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crystal structure of complexes of D-xylose isomerase with deoxysugars
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structures of the enzyme containing the inhibitors xylitol and D-sorbitol at 2.5 A and 2.3 A resolution respectively
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wild-type and mutant enzymes
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sitting drop vapor diffusion method, using 100 mM sodium chloride, 100 mM bicine pH 9.0, 20% (v/v) PEG MME 550
sitting drop vapor diffusion method, using 0.2 M CaCl2, 20% (w/v) polyethylene glycol 3350
sitting drop vapour diffusion method at room temperature, space group 21212 with a: 87.976 A, b: 98.836 and c: 93.927 A
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3.0 A crystal structure
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D-threonohydroxamic acid soaked into the crystal, crystallographic structure at 1.6 A resolution
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X-ray crystallographic structure of the metal-activated enzyme with the substrates D-glucose, 3-O-methyl-D-glucose and in the absence of substrate at 1.96 A, 2.19 A, and 1.81 A
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analysis of the location of hydrogen atoms by time-of-flight neutron Laue technique. The neutron structure of crystalline XI with bound product, D-xylulose, shows, that O5 of D-xylulose is not protonated but is hydrogen-bonded to doubly protonated His54. Also, Lys289, which is neutral in native XI, is protonated, while the catalytic water in native XI has become activated to a hydroxyl anion which is in the proximity of C1 and C2, the molecular site of isomerization of xylose
cooling crystallization from 0.17 M MgSO4 solution
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in complex with D-glyceraldehyde, hanging drop vapor diffusion method, using 0.2-0.3 M Mg-formate at pH 7.0 and 22°C
neutron diffraction, largest crystals at 18°C, 95 mg/ml xylose isomerase, 16.9% ammonium sulfate, mathematical analysis to determine optimal conditions for crystallization
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neutron quasi-Laue diffraction, resolution: 2.2 A - clear visibility of deuterium atoms, clarification of critical residues at the active site and their protonation states
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structure of E186Q mutant with cyclic glucose bound at the active site, to 2.2 A resolution. Residue His54 is doubly protonated and is poised to protonate the glucose O5 position, while Lys289, which is neutral, promotes deprotonation of the glucose O1H hydroxyl group via an activated water molecule. An extended hydrogen-bonding network connects the conserved residues Lys289 and Lys183 through three structurally conserved water molecules and residue 186
study on the dynamics of solute transport in orthorhombic D-xylose isomerase crystals by means of Brownian dynamics and molecular dynamics simulations and investigation of the diffusion of S-phenylglycine molecules inside XI crystals. The S-phenylglycine molecules mostly interact with residues His54, Asp287, and Lys183. In general, the diffusivities of solute species are found to be 1 to 2 orders of magnitude lower than those of the corresponding free molecules in water
the mechanism of ring-opening for L-arabinose is the same as for the reaction with D-xylose. In the reactive Michaelis complex L-arabinose is distorted to the high-energy 5S1 conformation. Amino acid substitutions in a hydrophobic pocket near C5 of L-arabinose can enhance sugar binding. L-ribulose and L-ribose are found in furanose forms when bound to the enzyme
time-of-flight neutron diffraction at 1.8 A resolution, metal-free enzyme - emphasis on the active site of xylose isomerase, especially of protonation states of His, Lys and H2O
ammonium sulfate as precipitant, orthorhombic space group P212121 with a: 84.35 A, b: 123.6 A, c: 140.24 A
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ortjorhombic space group P212121 with a: 84.35 A, b: 123.60 A and c: 140.24 A
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at room temperature with polyethylene glycol 4000 as precipitant, orthorhombic space group P212121 with a: 73.34 A, b: 144.05 A and c 155.07 A
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ortjorhombic space group P212121 with a: 73.34 A, b: 144.05 A and c: 155.07 A
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