Literature summary for 1.1.1.431 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 .

Search for more literature for 1.1.1.431

Cloned(Commentary)

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

Crystallization (Commentary)

Crystallization (Comment)	Organism
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

Crystallization (Comment)

Organism

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

Inhibitors	Comment	Organism	Structure
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
meso-erythritol	inhibits DnXR via mixed inhibition mechanism	Debaryomyces nepalensis

KM Value [mM]

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

Natural Substrates/ Products (Substrates)

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

Organism

Organism	UniProt	Comment	Textmining
Debaryomyces nepalensis	A0A0M4HL56	-	-

Purification (Commentary)

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

Reaction

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

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
D-erythrose + NADPH + H+	-	Debaryomyces nepalensis	erythritol + NADP+	-	r
D-xylose + NADPH + H+	-	Debaryomyces nepalensis	xylitol + NADP+	-	r
L-threose + NADPH + H+	-	Debaryomyces nepalensis	threitol + NADP+	-	r
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

Subunits	Comment	Organism
dimer	-	Debaryomyces nepalensis

Synonyms

Synonyms	Comment	Organism
DnXR	-	Debaryomyces nepalensis
xylose reductase	-	Debaryomyces nepalensis

Temperature Optimum [°C]

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

Turnover Number [1/s]

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

pH Optimum

pH Optimum Minimum	pH Optimum Maximum	Comment	Organism
7	-	-	Debaryomyces nepalensis

Cofactor

Cofactor	Comment	Organism	Structure
NADP+	-	Debaryomyces nepalensis
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]

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

General Information

General Information	Comment	Organism
evolution	the xylose reductase (XR) belongs to the AKR2 family xylose reductase of aldo-keto reductase (AKR) superfamily	Debaryomyces nepalensis
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
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
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]

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