1.1.1.431: D-xylose reductase (NADPH)
This is an abbreviated version!
For detailed information about D-xylose reductase (NADPH), go to the full flat file.
Reaction
Synonyms
ALR1, Cb-XR, CbXR, CtXR, D-xylose reductase, D-xylose reductase 1, D-xylose reductase 2, D-xylose reductase 3, DnXR, GRE3, monospecific xylose reductase, More, msXR, NAD(P)H-dependent D-xylose reductase, NAD(P)H-dependent xylose reductase, NADPH dependent D-xylose reductase, NADPH-dependent D-xylose reductase II,III, NADPH-dependent xylose reductase, NADPH-preferring xylose reductase, NRRL3_10868, SsXR, Texr, TrxR, XR1, XR2, XR3, XRTL, XYL1, xylose reductase, xyr8, XyrA, XyrB
ECTree
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General Information
General Information on EC 1.1.1.431 - D-xylose reductase (NADPH)
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evolution
malfunction
metabolism
physiological function
additional information
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D-xylose reductase is a member of the aldo-keto reductase family. Its catalytic mechanism is likely conserved in other AKRs that contain these amino acids. Expression profiles for D-xylose reductase xyrA, D-xylose reductase xyrB and L-arabinose reductase larA from Aspergillus niger, overview
evolution
the xylose reductase (XR) belongs to the AKR2 family xylose reductase of aldo-keto reductase (AKR) superfamily
alteration in both secondary and tertiary structures cause enzyme deactivation in acidic pH, while increased deactivation rates at alkaline pH are attributed to the variation of tertiary structure over time
malfunction
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expression of gene xyrB is strongly reduced in the xlnR deletion strain on D-xylose and in the araR deletion strain on L-arabinose, indicating control of its expression by both regulators
malfunction
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alteration in both secondary and tertiary structures cause enzyme deactivation in acidic pH, while increased deactivation rates at alkaline pH are attributed to the variation of tertiary structure over time
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the redox balance between xylose reductase (XR) and xylitol dehydrogenase (XDH, EC 1.1.1.10) is thought to be an important factor in effective xylose fermentation
metabolism
biosynthesis of xylitol can be achieved from two distinctive routes, one occurs via the activity of NADPH-dependent xylose reductase (XR), reducing xylose directly into xylitol. The other one proceeds via formation of the intermediate xylulose through xylose isomerase (XI, EC 5.3.1.5) followed by NADH-dependent reduction via the xylitol dehydrogenase (XDH, EC 1.1.1.9). Both of the metabolic routes originate from xylose dissimilation and can lead to formation of xylulose-5-phosphtate, the entrance point of pentose phosphate pathway
metabolism
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D-xylose reductase is involved in D-xylose and L-arabinose conversion through the pentose catabolic pathway (PCP) in fungi
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
metabolism
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derivatives of D-xylose and D-glucose, in which the hydroxy groups at C-5, and C-5 and C-6 are replaced by fluorine, hydrogen and azide are reduced with up to 3000fold increased catalytic efficiencies. Azide introduced at C-5 or C-6 destabilizes the transition state of reduction of the corresponding hydrogen-substituted aldoses by approx. 4 kJ/mol
metabolism
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derivatives of D-xylose and D-glucose, in which the hydroxy groups at C-5, and C-5 and C-6 are replaced by fluorine, hydrogen and azide are reduced with up to 3000fold increased catalytic efficiencies. Azide introduced at C-5 or C-6 destabilizes the transition state of reduction of the corresponding hydrogen-substituted aldoses by approx. 4 kJ/mol
metabolism
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ordered mechanism in which coenzyme binds first and substrate second
strictly NADPH-dependent xylose reductase with mutated strict NADP+-dependent xylitol dehydrogenase, EC 1.1.1.10, are more effective in increasing bioethanol production and decreasing xylitol accumulation than the wild-type, overview
physiological function
xylitol production through whole-cell catalysis from pure xylose and glucose, and xylitol production from cornstalk hydrolysate
physiological function
xylitol production through whole-cell catalysis from pure xylose and glucose, and xylitol production from cornstalk hydrolysate, method optimization, overview
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
physiological function
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an enzyme mutant shows poor growth on D-xylose but normal growth on xylitol and D-glucose. Growth rate, growth yield, and D-xylose consumption rate of the mutant are less sensitive than those of the wild-type to changes in aeration rate. D-Xylose is utilized more efficiently in that less of a by-product, xylitol, is produced
physiological function
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Candida intermedia produces two different isoforms. Isoform I is strictly specific for NADPH, isoform II shows similar specificity constants for NADPH and NADH
physiological function
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D-xylose, L-arabinose and D-galactose serve as substrates for NADPH-linked reactions in extracts of cells grown in medium containing D-xylose, L-arabinose, or D-galactose. Xylitol, L-arabitol, and galactitol are the respective conversion products of these sugars
physiological function
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deletion of the XyrB gene in the D-xylose reductase/L-arabinose reductase LarA/XyrA deletion background completely abolishes growth on both pentoses. This mutant does not accumulate any pathway intermediates but accumulates high amounts of L-arabinose and D-xylose when grown on these sugars
physiological function
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isoform ALR1 is strictly specific for NADPH, EC 1.1.1.431, whereas isoform ALR2 utilises NADH and NADPH with similar specificity constants, EC 1.1.1.307
physiological function
Yamadazyma tenuis CBS 4435
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xylitol production through whole-cell catalysis from pure xylose and glucose, and xylitol production from cornstalk hydrolysate
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physiological function
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xylitol production through whole-cell catalysis from pure xylose and glucose, and xylitol production from cornstalk hydrolysate, method optimization, overview
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structure-function analysis, molecular docking simulation, overview. The SsXR structure in complex with the NADPH cofactor shows that the protein undergoes an open/closed conformation change upon NADPH binding. The substrate binding pocket of SsXR is somewhat hydrophobic, which seems to result in low binding affinity to the substrate. The monomeric structure of SsXR is composed of 15 alpha-helices (alpha1-alpha15) and 10 beta-strands (beta1-beta10). The monomeric structure of SsXR consists of a core domain and two auxiliary regions (ARs), AR-I and AR-II. The core domain consists of 13 alpha-helices (alpha1-alpha10, alpha12-alpha13, and alpha15) and eight beta-strands (beta3-beta10) and forms a TIM-barrel motif. As the conventional TIM-barrel motif, in SsXR eight parallel beta-strands (beta3-beta10) are arranged in a cylindrical shape with eight surrounding alpha-helices (alpha1, alpha3, alpha5-alpha8, and alpha12-alpha13). Four alpha-helices (alpha2, alpha9-alpha10, and alpha15) are located at the back of the TIM-barrel motif and contribute to binding of the NADPH cofactor. AR-I is composed of two beta-strands (beta1-beta2) and is located on the opposite side of the TIM-barrel. AR-II consists of two alpha-helices (alpha11 and alpha14) and is positioned next to the alpha12 helix. As reported in other enzymes belonging to AKR families, four catalytic residues, Asp43, Tyr48, Lys77, and His110, are also conserved in the SsXR, and involved in the catalytic mechanism
additional information
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structure-function analysis, molecular docking simulation, overview. The SsXR structure in complex with the NADPH cofactor shows that the protein undergoes an open/closed conformation change upon NADPH binding. The substrate binding pocket of SsXR is somewhat hydrophobic, which seems to result in low binding affinity to the substrate. The monomeric structure of SsXR is composed of 15 alpha-helices (alpha1-alpha15) and 10 beta-strands (beta1-beta10). The monomeric structure of SsXR consists of a core domain and two auxiliary regions (ARs), AR-I and AR-II. The core domain consists of 13 alpha-helices (alpha1-alpha10, alpha12-alpha13, and alpha15) and eight beta-strands (beta3-beta10) and forms a TIM-barrel motif. As the conventional TIM-barrel motif, in SsXR eight parallel beta-strands (beta3-beta10) are arranged in a cylindrical shape with eight surrounding alpha-helices (alpha1, alpha3, alpha5-alpha8, and alpha12-alpha13). Four alpha-helices (alpha2, alpha9-alpha10, and alpha15) are located at the back of the TIM-barrel motif and contribute to binding of the NADPH cofactor. AR-I is composed of two beta-strands (beta1-beta2) and is located on the opposite side of the TIM-barrel. AR-II consists of two alpha-helices (alpha11 and alpha14) and is positioned next to the alpha12 helix. As reported in other enzymes belonging to AKR families, four catalytic residues, Asp43, Tyr48, Lys77, and His110, are also conserved in the SsXR, and involved in the catalytic mechanism
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
additional information
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the enzyme contains an aldo/keto reductase (AKR) motif between positions 22-277. The mechanism of catalysis in AKRs involves a catalytic tetrad, His, Tyr, Lys and Asp, in which the tyrosine hydroxyl group is the general acid and appears to be a proton relay from the histidine or lysine
additional information
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structure-function analysis, molecular docking simulation, overview. The SsXR structure in complex with the NADPH cofactor shows that the protein undergoes an open/closed conformation change upon NADPH binding. The substrate binding pocket of SsXR is somewhat hydrophobic, which seems to result in low binding affinity to the substrate. The monomeric structure of SsXR is composed of 15 alpha-helices (alpha1-alpha15) and 10 beta-strands (beta1-beta10). The monomeric structure of SsXR consists of a core domain and two auxiliary regions (ARs), AR-I and AR-II. The core domain consists of 13 alpha-helices (alpha1-alpha10, alpha12-alpha13, and alpha15) and eight beta-strands (beta3-beta10) and forms a TIM-barrel motif. As the conventional TIM-barrel motif, in SsXR eight parallel beta-strands (beta3-beta10) are arranged in a cylindrical shape with eight surrounding alpha-helices (alpha1, alpha3, alpha5-alpha8, and alpha12-alpha13). Four alpha-helices (alpha2, alpha9-alpha10, and alpha15) are located at the back of the TIM-barrel motif and contribute to binding of the NADPH cofactor. AR-I is composed of two beta-strands (beta1-beta2) and is located on the opposite side of the TIM-barrel. AR-II consists of two alpha-helices (alpha11 and alpha14) and is positioned next to the alpha12 helix. As reported in other enzymes belonging to AKR families, four catalytic residues, Asp43, Tyr48, Lys77, and His110, are also conserved in the SsXR, and involved in the catalytic mechanism
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additional information
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structure-function analysis, molecular docking simulation, overview. The SsXR structure in complex with the NADPH cofactor shows that the protein undergoes an open/closed conformation change upon NADPH binding. The substrate binding pocket of SsXR is somewhat hydrophobic, which seems to result in low binding affinity to the substrate. The monomeric structure of SsXR is composed of 15 alpha-helices (alpha1-alpha15) and 10 beta-strands (beta1-beta10). The monomeric structure of SsXR consists of a core domain and two auxiliary regions (ARs), AR-I and AR-II. The core domain consists of 13 alpha-helices (alpha1-alpha10, alpha12-alpha13, and alpha15) and eight beta-strands (beta3-beta10) and forms a TIM-barrel motif. As the conventional TIM-barrel motif, in SsXR eight parallel beta-strands (beta3-beta10) are arranged in a cylindrical shape with eight surrounding alpha-helices (alpha1, alpha3, alpha5-alpha8, and alpha12-alpha13). Four alpha-helices (alpha2, alpha9-alpha10, and alpha15) are located at the back of the TIM-barrel motif and contribute to binding of the NADPH cofactor. AR-I is composed of two beta-strands (beta1-beta2) and is located on the opposite side of the TIM-barrel. AR-II consists of two alpha-helices (alpha11 and alpha14) and is positioned next to the alpha12 helix. As reported in other enzymes belonging to AKR families, four catalytic residues, Asp43, Tyr48, Lys77, and His110, are also conserved in the SsXR, and involved in the catalytic mechanism
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additional information
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structure-function analysis, molecular docking simulation, overview. The SsXR structure in complex with the NADPH cofactor shows that the protein undergoes an open/closed conformation change upon NADPH binding. The substrate binding pocket of SsXR is somewhat hydrophobic, which seems to result in low binding affinity to the substrate. The monomeric structure of SsXR is composed of 15 alpha-helices (alpha1-alpha15) and 10 beta-strands (beta1-beta10). The monomeric structure of SsXR consists of a core domain and two auxiliary regions (ARs), AR-I and AR-II. The core domain consists of 13 alpha-helices (alpha1-alpha10, alpha12-alpha13, and alpha15) and eight beta-strands (beta3-beta10) and forms a TIM-barrel motif. As the conventional TIM-barrel motif, in SsXR eight parallel beta-strands (beta3-beta10) are arranged in a cylindrical shape with eight surrounding alpha-helices (alpha1, alpha3, alpha5-alpha8, and alpha12-alpha13). Four alpha-helices (alpha2, alpha9-alpha10, and alpha15) are located at the back of the TIM-barrel motif and contribute to binding of the NADPH cofactor. AR-I is composed of two beta-strands (beta1-beta2) and is located on the opposite side of the TIM-barrel. AR-II consists of two alpha-helices (alpha11 and alpha14) and is positioned next to the alpha12 helix. As reported in other enzymes belonging to AKR families, four catalytic residues, Asp43, Tyr48, Lys77, and His110, are also conserved in the SsXR, and involved in the catalytic mechanism
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