Any feedback?
Please rate this page
(literature.php)
(0/150)

BRENDA support

Literature summary extracted from

  • Paidimuddala, B.; Mohapatra, S.B.; Gummadi, S.N.; Manoj, N.
    Crystal structure of yeast xylose reductase in complex with a novel NADP-DTT adduct provides insights into substrate recognition and catalysis (2018), FEBS J., 285, 4445-4464 .
    View publication on PubMed

Cloned(Commentary)

EC Number Cloned (Comment) Organism
1.1.1.431 recombinant expression of His-tagged enzyme in Escherichia coli strain Rosetta Debaryomyces nepalensis

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
1.1.1.431 purified xylose reductase (DnXR) in the apoform and as a ternary complex with a NADP-DTT adduct, covalent linkage between the C4N atom of the nicotinamide ring of the cosubstrate and the S1 sulfur atom of DTT and provides the first structural evidence for a protein mediated NADP-low-molecular-mass thiol adduct, the formation of the adduct is facilitated by an in-crystallo Michael addition of the DTT thiolate to the specific conformation of bound NADPH in the active site of DnXR. Hanging drop vapor diffusion method, mixing of 0.001 ml of 15 mg/ml protein in 20 mM Tris/HCl, pH 7.5, with 0.001 ml of reservoir solution containing 24% PEG 4000, 0.1 M sodium citrate, pH 6.2, and 0.15 M ammonium acetate, 20°C, for the complex crystals, 10 mM NADPH and 10 mM DTT are added to the protein solution and a reservoir solution containing 22% PEG 3350, 0.1 M HEPES, pH 7.5, and 0.2 M ammonium sulfate is used, X-ray diffraction structure determination and analysis at 1.7-2.0 A resolution, modeling Debaryomyces nepalensis

Inhibitors

EC Number Inhibitors Comment Organism Structure
1.1.1.431 DL-DTT inhibits DnXR via mixed inhibition mechanism, a covalent adduct is formed between the nicotinamide ring and enzyme-bound DTT (NADP-DTT). In the DnXR complex, DTT is bound in the substrate-binding pocket in an orientation expected for a four-carbon open chain sugar alcohol, reminiscent of a product-bound form. The tertiary structure has an eight stranded barrel (beta1-beta8) is flanked by eight helices (alpha1-alpha8). A beta-hairpin caps the N-terminal end of the barrel while the C-terminal end contains the conserved active site groove. The extended C-terminal region containing two helices reaches over the active site with the terminal loop that is stabilized by interactions with residues from loop 4. Sequence comparisons Debaryomyces nepalensis
1.1.1.431 meso-erythritol inhibits DnXR via mixed inhibition mechanism Debaryomyces nepalensis

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
1.1.1.431 additional information
-
 additional information Michaelis-Menten and Lineweaver-Burk plots by linear and nonlinear regression fitting Debaryomyces nepalensis
1.1.1.431 5.5
-
 D-erythrose recombinant His-tagged enzyme, pH 7.0, 45°C Debaryomyces nepalensis

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
1.1.1.431 D-xylose + NADPH + H+ Debaryomyces nepalensis
-
 xylitol + NADP+
-
 r

Organism

EC Number Organism UniProt Comment Textmining
1.1.1.431 Debaryomyces nepalensis A0A0M4HL56
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
1.1.1.431 recombinant His-tagged enzyme from Escherichia coli strain Rosetta by nickel affinity chromatography Debaryomyces nepalensis

Reaction

EC Number Reaction Comment Organism Reaction ID
1.1.1.431 xylitol + NAD(P)+ = D-xylose + NAD(P)H + H+ structure-function analysis, overview Debaryomyces nepalensis
a

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
1.1.1.431 D-erythrose + NADPH + H+
-
 Debaryomyces nepalensis erythritol + NADP+
-
 r
1.1.1.431 D-xylose + NADPH + H+
-
 Debaryomyces nepalensis xylitol + NADP+
-
 r
1.1.1.431 L-threose + NADPH + H+
-
 Debaryomyces nepalensis threitol + NADP+
-
 r
1.1.1.431 additional information the enzyme displays the highest catalytic efficiency for L-threose, followed by D-erythrose. DnXR exhibits broad substrate specificity, with the highest catalytic efficiency for C5 sugars like arabinose, xylose, and ribose and a strict preference for cosubstrate NADPH Debaryomyces nepalensis ?
-
-

Subunits

EC Number Subunits Comment Organism
1.1.1.431 dimer
-
 Debaryomyces nepalensis

Synonyms

EC Number Synonyms Comment Organism
1.1.1.431 DnXR
-
 Debaryomyces nepalensis
1.1.1.431 xylose reductase
-
 Debaryomyces nepalensis

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
1.1.1.431 45
-
-
 Debaryomyces nepalensis

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
1.1.1.431 165
-
 D-erythrose recombinant His-tagged enzyme, pH 7.0, 45°C Debaryomyces nepalensis

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
1.1.1.431 7
-
-
 Debaryomyces nepalensis

Cofactor

EC Number Cofactor Comment Organism Structure
1.1.1.431 NADP+
-
 Debaryomyces nepalensis
1.1.1.431 NADPH enzyme DnXR shows strict dependence on NADPH, specific conformation of bound NADPH in the active site of DnXR, crystal structure analysis, structure-function analysis, overview. A large number of specific nonbonded interactions are involved in the binding. Among these, the side chain of Tyr212 stacks with the nicotinamide ring and hydrogen bond interactions between the side chains of Ser164, Asn165, and Gln186 with the carboxamide group orient the A-side of the nicotinamide group toward the substrate binding cavity Debaryomyces nepalensis

Ki Value [mM]

EC Number Ki Value [mM] Ki Value maximum [mM] Inhibitor Comment Organism Structure
1.1.1.431 1.8
-
 DL-DTT recombinant His-tagged enzyme, pH 7.0, 45°C Debaryomyces nepalensis
1.1.1.431 1577
-
 meso-erythritol recombinant His-tagged enzyme, pH 7.0, 45°C Debaryomyces nepalensis

General Information

EC Number General Information Comment Organism
1.1.1.431 evolution the xylose reductase (XR) belongs to the AKR2 family xylose reductase of aldo-keto reductase (AKR) superfamily Debaryomyces nepalensis
1.1.1.431 metabolism enzyme XR is the first enzyme in the xylose utilization pathway. Debaryomyces nepalensis, a nonpathogenic Saccharomycetes yeast can utilize both hexose and pentose sugars to produce polyols. DnXR is a key metabolic enzyme in the D-xylose utilization pathway Debaryomyces nepalensis
1.1.1.431 additional information the catalytic site architecture of AKRs includes a highly conserved tetrad of residues Asp42, Tyr47, Lys76, and His109 (DnXR numbering) lining the bottom of a deep open cavity Debaryomyces nepalensis
1.1.1.431 physiological function xylose reductase is a key enzyme in the conversion of xylose to xylitol, it catalyzes the conversion of carbonyl substrates into their respective alcohols Debaryomyces nepalensis

kcat/KM [mM/s]

EC Number kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
1.1.1.431 30
-
 D-erythrose recombinant His-tagged enzyme, pH 7.0, 45°C Debaryomyces nepalensis
1.1.1.431 138
-
 L-threose recombinant His-tagged enzyme, pH 7.0, 45°C Debaryomyces nepalensis