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Information on EC 1.1.1.430 - D-xylose reductase (NADH)
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1.1.1.430 D-xylose reductase (NADH)IUBMB Comments
Xylose reductases catalyse the reduction of xylose to xylitol, the initial reaction in the fungal D-xylose degradation pathway. Most of the enzymes exhibit a strict requirement for NADPH (cf. EC 1.1.1.431, D-xylose reductase (NADPH)). Some D-xylose reductases have dual coenzyme specificity, though they still prefer NADPH to NADH (cf. EC 1.1.1.307, D-xylose reductase [NAD(P)H]). The enzyme from Candida parapsilosis is a rare example of a xylose reductase that significantly prefers NADH, with Km and Vmax values for NADH being 10-fold lower and 10-fold higher, respectively, than for NADPH.
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The enzyme appears in viruses and cellular organisms
Reaction Schemes
Synonyms
xyl1.2, nadh-dependent xr, xyl1.1, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
dsXR
-
Candida intermedia produces two isoforms of xylose reductase: one is NADPH-dependent (monospecific xylose reductase, msXR, cf. 1.1.1.431), and another prefers NADH about 4fold over NADPH (dual specific xylose reductase, dsXR)
NADPH-preferring xylose reductase
XYL1
xylose reductase
XYL1
-
-
-
-
XYL1
-
-
ambiguous
-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
xylitol + NAD(P)+ = D-xylose + NAD(P)H + H+
enzymic mechanism in which a catalytic proton bridge from the protonated side chain of Lys80 to the carbonyl group adjacent to the hydride acceptor carbonyl facilitates the chemical reaction step. His113 contributes to positioning of the 9,10-phenanthrenequinone substrate for catalysis. Tyr51 controls release of the hydroquinone product. The proposed chemistry involves delivery of both hydrogens required for reduction of the alpha-dicarbonyl substrate to the carbonyl group undergoing stereoselective transformation. Hydride transfer from NADH probably precedes the transfer of a proton from Tyr51
xylitol + NAD(P)+ = D-xylose + NAD(P)H + H+
-
-
-
-
xylitol + NAD+ = D-xylose + NADH + H+
-
-
-
-
xylitol + NAD+ = D-xylose + NADH + H+
chemical mechanism of carbonyl reduction by xylose reductase in which transfer of hydride ion is a partially rate-limiting step and precedes the proton-transfer step
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SYSTEMATIC NAME
IUBMB Comments
xylitol:NAD+ oxidoreductase
Xylose reductases catalyse the reduction of xylose to xylitol, the initial reaction in the fungal D-xylose degradation pathway. Most of the enzymes exhibit a strict requirement for NADPH (cf. EC 1.1.1.431, D-xylose reductase (NADPH)). Some D-xylose reductases have dual coenzyme specificity, though they still prefer NADPH to NADH (cf. EC 1.1.1.307, D-xylose reductase [NAD(P)H]). The enzyme from Candida parapsilosis is a rare example of a xylose reductase that significantly prefers NADH, with Km and Vmax values for NADH being 10-fold lower and 10-fold higher, respectively, than for NADPH.
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
2,4'-dichloroacetophenone + NADH + H+
? + NAD+
-
binding and transformation of unnatural 2,4-dichloroacetophenone is not as for good as natural substrates, although it is reduced with very high catalytic efficiency
-
-
?
2-deoxy-D-galactose + NADH + H+
?
-
dual specific xylose reductase (dsXR)
-
-
?
2-deoxy-D-ribose + NADH + H+
?
-
dual specific xylose reductase (dsXR)
-
-
?
DL-glyceraldehyde + NADH + H+
glycerol + NAD+
-
dual specific xylose reductase (dsXR)
-
-
?
L-arabinose + NADH + H+
L-arabinitol + NAD+
-
dual specific xylose reductase (dsXR)
-
-
?
propionaldehyde + NADH + H+
?
-
dual specific xylose reductase (dsXR)
-
-
?
D-xylose + NADH + H+
xylitol + NAD+
the enzyme specifically transfers the 4-pro-R hydrogen from the C-4 of the nicotinamide ring to the re face of the carbonyl carbon of the substrate
-
-
r
D-xylose + NADH + H+
xylitol + NAD+
the enzyme specifically transfers the 4-pro-R hydrogen from the C-4 of the nicotinamide ring to the re face of the carbonyl carbon of the substrate
-
-
r
D-xylose + NADH + H+
xylitol + NAD+
-
wild-type enzyme prefers NADPH over NADH
-
-
?
D-xylose + NADH + H+
xylitol + NAD+
-
using a modified iterative protein redesign and optimization workflow, a sets of mutations is identified that change the nicotinamide cofactor specificity of xylose reductase (CbXR) from its physiological preference for NADPH, to the alternate cofactor NADH
-
-
?
D-xylose + NADH + H+
xylitol + NAD+
-
reaction is catalyzed by dual specific xylose reductase (dsXR), reaction is not catalyzed by NADPH-dependent monospecific xylose reductase (msXR)
-
-
?
D-xylose + NADPH + H+
xylitol + NADP+
-
xylose reductase is one of the key enzymes for xylose fermentation
-
-
?
D-xylose + NADPH + H+
xylitol + NADP+
-
wild-type enzyme prefers NADPH over NADH
-
-
?
D-xylose + NADPH + H+
xylitol + NADP+
-
using a modified iterative protein redesign and optimization workflow, a sets of mutations is identified that change the nicotinamide cofactor specificity of xylose reductase (CbXR) from its physiological preference for NADPH, to the alternate cofactor NADH
-
-
?
D-xylose + NADPH + H+
xylitol + NADP+
-
reaction is catalyzed by NADPH-dependent monospecific xylose reductase (msXR), and by dual specific xylose reductase (dsXR)
-
-
?
additional information
?
-
-
substrates preferentially bind as alpha-anomers of the pyranose forms. The alpha-anomers are transformed faster, predominately leading to saturation transfer difference effects in the formed products, and can be better docked into the active site than the beta-anomer. The reduction is initiated by alpha-xylopyranose ring opening prior to hydride transfer from NADH
-
-
?
additional information
?
-
-
Candida intermedia produces two isoforms of xylose reductase: one is NADPH-dependent (monospecific xylose reductase, msXR, cf. 1.1.1.431), and another prefers NADH about 4fold over NADPH (dual specific xylose reductase, dsXR)
-
-
-
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
D-xylose + NADPH + H+
xylitol + NADP+
-
xylose reductase is one of the key enzymes for xylose fermentation
-
-
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
NADH
-
dual specific xylose reductase (dsXR) has an about 4fold higher specificity for NADH than NADPH
NADH
-
transient-state and steady-state kinetic studies of the mechanism of NADH-dependent aldehyde reduction
NADH
-
using a modified iterative protein redesign and optimization workflow, a sets of mutations is identified that change the nicotinamide cofactor specificity of xylose reductase (CbXR) from its physiological preference for NADPH, to the alternate cofactor NADH
NADH
-
wild-type enzyme prefers NADPH over NADH. Mutant enzyme K270S/N272P/S271G/R276F shows a 25fold preference toward NADH over NADPH by a factor of about 13fold, or an improvement of about 42fold, as measured by the ratio of the specificity constant kcat/Km coenzyme
NADPH
-
dual specific xylose reductase (dsXR) has an about 4fold higher specificity for NADH than NADPH. NADPH-dependent monospecific xylose reductase (msXR) shows non activity with NADH
NADPH
-
using a modified iterative protein redesign and optimization workflow, a sets of mutations is identified that change the nicotinamide cofactor specificity of xylose reductase (CbXR) from its physiological preference for NADPH, to the alternate cofactor NADH
NADPH
-
wild-type enzyme prefers NADPH over NADH. Mutant enzyme K270S/N272P/S271G/R276F shows a 25fold preference toward NADH over NADPH by a factor of about 13fold, or an improvement of about 42fold, as measured by the ratio of the specificity constant kcat/Km coenzyme
additional information
-
Kluyveromyces marxianus strains expressing Pichia stipitis Psxyl1 genes show reversed cofactor specificity, overview
-
additional information
most XRs are NADPH-dependent rather than NADH-dependent. CT-XR from Candida tenuis shows a similar preference for both NADH and NADPH
-
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
neither inhibited nor activated by EDTA at concentrations ranging from 1 to 10 mM
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
NADP+
-
for monospecific xylose reductase (msXR) and dual specific xylose reductase (dsXR) NADP+ behaves as a competitive inhibitor against NADPH. Competitive inhibition of is observed both at unsaturating and saturating concentrations of xylose
NADPH
-
for monospecific xylose reductase (msXR) and dual specific xylose reductase (dsXR) NADPH behaves as a competitive inhibitor against NADP+. Competitive inhibition of is observed both at unsaturating and saturating concentrations of xylitol
NAD+
-
for dual specific xylose reductase (dsXR) NAD+ behaves as a competitive inhibitor against NADH. Competitive inhibition of is observed both at unsaturating and saturating concentrations of xylose
NADH
-
for dual specific xylose reductase (dsXR) NADH behaves as a competitive inhibitor against NAD+. Competitive inhibition of is observed both at unsaturating and saturating concentrations of xylitol
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
neither inhibited nor activated by EDTA at concentrations ranging from 1 to 10 mM
-
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.126
2-deoxy-D-galactose
-
pH 7.0, 25°C, dual specific xylose reductase, cofactor: NADH
33
Butanal
-
pH 7.0, 25°C, dual specific xylose reductase, cofactor: NADH
0.007
D-fucose
-
pH 7.0, 25°C, dual specific xylose reductase, cofactor: NADH
0.015
D-galactose
-
pH 7.0, 25°C, dual specific xylose reductase, cofactor: NADH
0.033
D-glucose
-
pH 7.0, 25°C, dual specific xylose reductase, cofactor: NADH
2.43
DL-glyceraldehyde
-
pH 7.0, 25°C, dual specific xylose reductase, cofactor: NADH
0.028
L-arabinose
-
pH 7.0, 25°C, dual specific xylose reductase, cofactor: NADH
0.144
L-Lyxose
-
pH 7.0, 25°C, dual specific xylose reductase, cofactor: NADH
14.7
pentanal
-
pH 7.0, 25°C, dual specific xylose reductase, cofactor: NADH
13.2
propionaldehyde
-
pH 7.0, 25°C, dual specific xylose reductase, cofactor: NADH
0.02
D-erythrose
-
pH 7.0, 25°C, dual specific xylose reductase, cofactor: NADH
0.068
D-ribose
-
pH 7.0, 25°C, dual specific xylose reductase, cofactor: NADH
0.01
D-xylose
-
pH 7.0, 25°C, dual specific xylose reductase, cofactor: NADH
82
D-xylose
-
pH 6.0, temperature not specified in the publication, cofactor: NADPH, wild-type enzyme
90
D-xylose
-
pH 6.0, temperature not specified in the publication, cofactor: NADH, wild-type enzyme
168
D-xylose
-
pH 6.0, temperature not specified in the publication, cofactor: NADPH, mutant enzyme K270S/N272P/S271G/R276F
291
D-xylose
-
pH 6.0, temperature not specified in the publication, cofactor: NADH, mutant enzyme K270S/N272P/S271G/R276F
0.0106
NADH
-
pH 6.0, temperature not specified in the publication, wild-type enzyme, wild-type enzyme
0.147
NADH
-
pH 6.0, temperature not specified in the publication, mutant enzyme K270S/N272P/S271G/R276F
0.0062
NADPH
-
pH 6.0, temperature not specified in the publication, wild-type enzyme, wild-type enzyme
0.427
NADPH
-
pH 6.0, temperature not specified in the publication, mutant enzyme K270S/N272P/S271G/R276F
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
3.5
2-deoxy-D-galactose
-
pH 7.0, 25°C, dual specific xylose reductase, cofactor: NADH
5.4
Butanal
-
pH 7.0, 25°C, dual specific xylose reductase, cofactor: NADH
27.5
D-erythrose
-
pH 7.0, 25°C, dual specific xylose reductase, cofactor: NADH
10.2
D-fucose
-
pH 7.0, 25°C, dual specific xylose reductase, cofactor: NADH
9.4
D-galactose
-
pH 7.0, 25°C, dual specific xylose reductase, cofactor: NADH
5.6
D-glucose
-
pH 7.0, 25°C, dual specific xylose reductase, cofactor: NADH
4.9
D-ribose
-
pH 7.0, 25°C, dual specific xylose reductase, cofactor: NADH
14.1
DL-glyceraldehyde
-
pH 7.0, 25°C, dual specific xylose reductase, cofactor: NADH
13.5
L-arabinose
-
pH 7.0, 25°C, dual specific xylose reductase, cofactor: NADH
6.6
L-Lyxose
-
pH 7.0, 25°C, dual specific xylose reductase, cofactor: NADH
5.9
pentanal
-
pH 7.0, 25°C, dual specific xylose reductase, cofactor: NADH
4.6
propionaldehyde
-
pH 7.0, 25°C, dual specific xylose reductase, cofactor: NADH
2.6
D-xylose
-
pH 6.0, temperature not specified in the publication, cofactor: NADPH, mutant enzyme K270S/N272P/S271G/R276F
12
D-xylose
-
pH 6.0, temperature not specified in the publication, cofactor: NADH, mutant enzyme K270S/N272P/S271G/R276F
15.4
D-xylose
-
pH 6.0, temperature not specified in the publication, cofactor: NADH, wild-type enzyme
16.9
D-xylose
-
pH 7.0, 25°C, dual specific xylose reductase, cofactor: NADH
27.5
D-xylose
-
pH 6.0, temperature not specified in the publication, cofactor: NADPH, wild-type enzyme
12
NADH
-
pH 6.0, temperature not specified in the publication, mutant enzyme K270S/N272P/S271G/R276F
15.4
NADH
-
pH 6.0, temperature not specified in the publication, wild-type enzyme, wild-type enzyme
2.6
NADPH
-
pH 6.0, temperature not specified in the publication, mutant enzyme K270S/N272P/S271G/R276F
27.5
NADPH
-
pH 6.0, temperature not specified in the publication, wild-type enzyme, wild-type enzyme
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
28
2-deoxy-D-galactose
-
pH 7.0, 25°C, dual specific xylose reductase, cofactor: NADH
0.16
Butanal
-
pH 7.0, 25°C, dual specific xylose reductase, cofactor: NADH
1457
D-fucose
-
pH 7.0, 25°C, dual specific xylose reductase, cofactor: NADH
627
D-galactose
-
pH 7.0, 25°C, dual specific xylose reductase, cofactor: NADH
170
D-glucose
-
pH 7.0, 25°C, dual specific xylose reductase, cofactor: NADH
5.8
DL-glyceraldehyde
-
pH 7.0, 25°C, dual specific xylose reductase, cofactor: NADH
482
L-arabinose
-
pH 7.0, 25°C, dual specific xylose reductase, cofactor: NADH
46
L-Lyxose
-
pH 7.0, 25°C, dual specific xylose reductase, cofactor: NADH
0.4
pentanal
-
pH 7.0, 25°C, dual specific xylose reductase, cofactor: NADH
0.035
propionaldehyde
-
pH 7.0, 25°C, dual specific xylose reductase, cofactor: NADH
1380
D-erythrose
-
pH 7.0, 25°C, dual specific xylose reductase, cofactor: NADH
72
D-ribose
-
pH 7.0, 25°C, dual specific xylose reductase, cofactor: NADH
6.2
D-xylose
-
pH 6.0, temperature not specified in the publication, cofactor: NADPH, mutant enzyme K270S/N272P/S271G/R276F
81.7
D-xylose
-
pH 6.0, temperature not specified in the publication, cofactor: NADH, mutant enzyme K270S/N272P/S271G/R276F
1460
D-xylose
-
pH 6.0, temperature not specified in the publication, cofactor: NADH, wild-type enzyme
1690
D-xylose
-
pH 7.0, 25°C, dual specific xylose reductase, cofactor: NADH
4648
D-xylose
-
pH 6.0, temperature not specified in the publication, cofactor: NADPH, wild-type enzyme
81.7
NADH
-
pH 6.0, temperature not specified in the publication, mutant enzyme K270S/N272P/S271G/R276F
1460
NADH
-
pH 6.0, temperature not specified in the publication, wild-type enzyme, wild-type enzyme
6.2
NADPH
-
pH 6.0, temperature not specified in the publication, mutant enzyme K270S/N272P/S271G/R276F
4648
NADPH
-
pH 6.0, temperature not specified in the publication, wild-type enzyme, wild-type enzyme
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Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
5 - 7
pH 5.0: 81% of maximal activity, pH 7.0: about 65% of maximal activity