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Information on EC 1.2.1.92 - 3,6-anhydro-alpha-L-galactose dehydrogenase
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1.2.1.92 3,6-anhydro-alpha-L-galactose dehydrogenaseIUBMB Comments
The enzyme, characterized from the marine bacterium Vibrio sp. EJY3, is involved in a degradation pathway for 3,6-anhydro-alpha-L-galactose, a major component of the polysaccharides produced by red macroalgae, such as agarose and porphyran.
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The enzyme appears in viruses and cellular organisms
Reaction Schemes
Synonyms
vvahgd, sco3486, ahg dehydrogenase, vejahgd, anhydrogalactose dehydrogenase, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
3,6-anhydro-L-galactose dehydrogenase
AHG dehydrogenase
AHGD
SCO3486
VvAHGD
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
3,6-anhydro-alpha-L-galactopyranose + NAD(P)+ + H2O = 3,6-anhydro-L-galactonate + NAD(P)H + H+
3,6-anhydro-alpha-L-galactopyranose + NAD(P)+ + H2O = 3,6-anhydro-L-galactonate + NAD(P)H + H+
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-
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-
3,6-anhydro-alpha-L-galactopyranose + NAD(P)+ + H2O = 3,6-anhydro-L-galactonate + NAD(P)H + H+
catalytic mechanism, detailed overview. The catalytic process of VvAHGD involves both the two catalytic residues, Cys282 and Glu248, which not only undergo conformational changes but also function as gatekeepers between the cofactor channel and the substrate channel. The conformational changes of Cys282 and Glu248 lead to the connection and interruption of the cofactor channel and the substrate channel, which promotes the productive binding of NADPþ/L-AHG and the efficient release of NADPH and L-AHGA during the catalysis and therefore leads to the high catalytic activity of VvAHGD
3,6-anhydro-alpha-L-galactopyranose + NAD(P)+ + H2O = 3,6-anhydro-L-galactonate + NAD(P)H + H+
catalytic mechanism, detailed overview. The catalytic process of VvAHGD involves both the two catalytic residues, Cys282 and Glu248, which not only undergo conformational changes but also function as gatekeepers between the cofactor channel and the substrate channel. The conformational changes of Cys282 and Glu248 lead to the connection and interruption of the cofactor channel and the substrate channel, which promotes the productive binding of NADPþ/L-AHG and the efficient release of NADPH and L-AHGA during the catalysis and therefore leads to the high catalytic activity of VvAHGD
Vibrio variabilis JCM 19239
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SYSTEMATIC NAME
IUBMB Comments
3,6-anhydro-alpha-L-galactopyranose:NAD(P)+ 1-oxidoredutase
The enzyme, characterized from the marine bacterium Vibrio sp. EJY3, is involved in a degradation pathway for 3,6-anhydro-alpha-L-galactose, a major component of the polysaccharides produced by red macroalgae, such as agarose and porphyran.
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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
3,6-anhydro-alpha-L-galactopyranose + NAD(P)+ + H2O
3,6-anhydro-alpha-L-galactonate + NAD(P)H + H+
D-glyceraldehyde + NADP+ + H2O
?
less than 20% activity compared to 3,6-anhydro-alpha-L-galactopyranose
-
-
?
D-lyxose + NADP+ + H2O
?
about 15% activity compared to 3,6-anhydro-alpha-L-galactopyranose
-
-
?
D-ribose + NADP+ + H2O
?
about 45% activity compared to 3,6-anhydro-alpha-L-galactopyranose
-
-
?
L-fucose + NADP+ + H2O
?
25% activity compared to 3,6-anhydro-alpha-L-galactopyranose
-
-
?
L-glyceraldehyde + NADP+ + H2O
?
less than 10% activity compared to 3,6-anhydro-alpha-L-galactopyranose
-
-
?
L-rhamnose + NADP+ + H2O
?
less than 1% activity compared to 3,6-anhydro-alpha-L-galactopyranose
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-
?
3,6-anhydro-alpha-L-galactopyranose + NAD(P)+ + H2O
3,6-anhydro-alpha-L-galactonate + NAD(P)H + H+
the enzyme is involved in a degradation pathway for 3,6-anhydro-alpha-L-galactose, a major component of the polysaccharides produced by red macroalgae, such as agarose and porphyran
-
-
?
3,6-anhydro-alpha-L-galactopyranose + NAD(P)+ + H2O
3,6-anhydro-alpha-L-galactonate + NAD(P)H + H+
among the cofactors, NADP+, NAD+ and NADPH, the highest abundances of reaction products are observed when NADP+ is added to the crude enzyme reaction mixture
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-
?
3,6-anhydro-alpha-L-galactopyranose + NAD+ + H2O
3,6-anhydro-L-galactonate + NADH + H+
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-
-
?
3,6-anhydro-alpha-L-galactopyranose + NAD+ + H2O
3,6-anhydro-L-galactonate + NADH + H+
Vibrio variabilis JCM 19239
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-
-
?
3,6-anhydro-alpha-L-galactopyranose + NADP+ + H2O
3,6-anhydro-L-galactonate + NADPH + H+
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-
-
?
3,6-anhydro-alpha-L-galactopyranose + NADP+ + H2O
3,6-anhydro-L-galactonate + NADPH + H+
100% activity
-
-
?
3,6-anhydro-alpha-L-galactopyranose + NADP+ + H2O
3,6-anhydro-L-galactonate + NADPH + H+
-
-
-
?
3,6-anhydro-alpha-L-galactopyranose + NADP+ + H2O
3,6-anhydro-L-galactonate + NADPH + H+
100% activity
-
-
?
3,6-anhydro-alpha-L-galactopyranose + NADP+ + H2O
3,6-anhydro-L-galactonate + NADPH + H+
the enzyme is highly specific to 3,6-anhydro-alpha-L-galactopyranose
-
-
?
3,6-anhydro-alpha-L-galactopyranose + NADP+ + H2O
3,6-anhydro-L-galactonate + NADPH + H+
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-
-
?
3,6-anhydro-alpha-L-galactopyranose + NADP+ + H2O
3,6-anhydro-L-galactonate + NADPH + H+
L-AHG is the preferred substrate, and NADP+ is the preferred cofactor
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-
?
3,6-anhydro-alpha-L-galactopyranose + NADP+ + H2O
3,6-anhydro-L-galactonate + NADPH + H+
Vibrio variabilis JCM 19239
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-
-
?
3,6-anhydro-alpha-L-galactopyranose + NADP+ + H2O
3,6-anhydro-L-galactonate + NADPH + H+
Vibrio variabilis JCM 19239
L-AHG is the preferred substrate, and NADP+ is the preferred cofactor
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?
D-fructose + NADP+ + H2O
?
about 55% activity compared to 3,6-anhydro-alpha-L-galactopyranose
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-
?
D-fructose + NADP+ + H2O
?
about 55% activity compared to 3,6-anhydro-alpha-L-galactopyranose
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-
?
D-galactose + NADP+ + H2O
?
about 50% activity compared to 3,6-anhydro-alpha-L-galactopyranose
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-
?
D-galactose + NADP+ + H2O
?
about 50% activity compared to 3,6-anhydro-alpha-L-galactopyranose
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-
?
D-glucose + NADP+ + H2O
?
20% activity compared to 3,6-anhydro-alpha-L-galactopyranose
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-
?
D-glucose + NADP+ + H2O
?
20% activity compared to 3,6-anhydro-alpha-L-galactopyranose
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?
additional information
?
-
no activity with D-glucose, D-galactose, D-fructose, sucrose, maltose, arabinose, xylose, agarohexose, agarotetrose and neoagarobiose
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-
additional information
?
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-
enzyme VvAHGD shows high activity toward 3,6-anhydro-L-galactose (L-AHG). VvAHGD hardly oxidizes lactaldehyde, D-AHG, galactose, or glucose, no or poor activity. Substrate specificity and substrate binding mode in VvAHGD, overview. VvAHGD oxidizes L-AHG using both NADP+ and NAD+ as the cofactor
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additional information
?
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enzyme VvAHGD shows high activity toward 3,6-anhydro-L-galactose (L-AHG). VvAHGD hardly oxidizes lactaldehyde, D-AHG, galactose, or glucose, no or poor activity. Substrate specificity and substrate binding mode in VvAHGD, overview. VvAHGD oxidizes L-AHG using both NADP+ and NAD+ as the cofactor
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additional information
?
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the enzyme hardly oxidizes lactaldehyde, 3,6-anhydro-alpha-D-galactopyranose, D-galactose, or D-glucose
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additional information
?
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the enzyme hardly oxidizes lactaldehyde, 3,6-anhydro-alpha-D-galactopyranose, D-galactose, or D-glucose
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-
additional information
?
-
Vibrio variabilis JCM 19239
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the enzyme hardly oxidizes lactaldehyde, 3,6-anhydro-alpha-D-galactopyranose, D-galactose, or D-glucose
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-
additional information
?
-
Vibrio variabilis JCM 19239
the enzyme hardly oxidizes lactaldehyde, 3,6-anhydro-alpha-D-galactopyranose, D-galactose, or D-glucose
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additional information
?
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Vibrio variabilis JCM 19239
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enzyme VvAHGD shows high activity toward 3,6-anhydro-L-galactose (L-AHG). VvAHGD hardly oxidizes lactaldehyde, D-AHG, galactose, or glucose, no or poor activity. Substrate specificity and substrate binding mode in VvAHGD, overview. VvAHGD oxidizes L-AHG using both NADP+ and NAD+ as the cofactor
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additional information
?
-
Vibrio variabilis JCM 19239
enzyme VvAHGD shows high activity toward 3,6-anhydro-L-galactose (L-AHG). VvAHGD hardly oxidizes lactaldehyde, D-AHG, galactose, or glucose, no or poor activity. Substrate specificity and substrate binding mode in VvAHGD, overview. VvAHGD oxidizes L-AHG using both NADP+ and NAD+ as the cofactor
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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
3,6-anhydro-alpha-L-galactopyranose + NAD(P)+ + H2O
3,6-anhydro-alpha-L-galactonate + NAD(P)H + H+
the enzyme is involved in a degradation pathway for 3,6-anhydro-alpha-L-galactose, a major component of the polysaccharides produced by red macroalgae, such as agarose and porphyran
-
-
?
3,6-anhydro-alpha-L-galactopyranose + NAD+ + H2O
3,6-anhydro-L-galactonate + NADH + H+
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-
-
?
3,6-anhydro-alpha-L-galactopyranose + NAD+ + H2O
3,6-anhydro-L-galactonate + NADH + H+
Vibrio variabilis JCM 19239
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-
-
?
3,6-anhydro-alpha-L-galactopyranose + NADP+ + H2O
3,6-anhydro-L-galactonate + NADPH + H+
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-
-
?
3,6-anhydro-alpha-L-galactopyranose + NADP+ + H2O
3,6-anhydro-L-galactonate + NADPH + H+
-
-
-
?
3,6-anhydro-alpha-L-galactopyranose + NADP+ + H2O
3,6-anhydro-L-galactonate + NADPH + H+
the enzyme is highly specific to 3,6-anhydro-alpha-L-galactopyranose
-
-
?
3,6-anhydro-alpha-L-galactopyranose + NADP+ + H2O
3,6-anhydro-L-galactonate + NADPH + H+
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-
-
?
3,6-anhydro-alpha-L-galactopyranose + NADP+ + H2O
3,6-anhydro-L-galactonate + NADPH + H+
Vibrio variabilis JCM 19239
-
-
-
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
NAD+
among the cofactors, NADP+, NAD+ and NADPH, the highest abundances of reaction products are observed when NADP+ is added to the crude enzyme reaction mixture
NAD+
the enzyme prefers NADP+, showing an activity 3.6fold higher than that with NAD+
NADP+
among the cofactors, NADP+, NAD+ and NADPH, the highest abundances of reaction products are observed when NADP+ is added to the crude enzyme reaction mixture
NADP+
NADP+-binding mode in enzyme VvAHGD, overview. One molecule of NADP+ is bound in the active site of each monomer, occupying the cofactor channel. The substrate channel is on the opposite side of the cofactor channel. The catalytic residues Cys282 and Glu248 are located at the junction of these two channels. These two channels are disconnected in the apo structure of VvAHGD, but connected in the structure of the VvAHGD-NADP complex. The cofactor channel has a wide opening on the protein surface, which is mostly positively charged to hold the adenosine monophosphate (AMP) moiety and the diphosphate group of NADP+. The internal part of this channel is negatively charged to accommodate the nicotinamide riboside moiety of NADP+. In the complex, the cofactor NADP+ adopts an extended conformation, which is typical for oxidized NADP+. The VvAHGD-NADP complex, NADP+ is stabilized mainly by hydrogen bond interactions
NADP+
the enzyme prefers NADP+, showing an activity 3.6fold higher than that with NAD+
additional information
-
VvAHGD oxidizes L-AHG using both NADP+ and NAD+ as the cofactor, but VvAHGD prefers NADP+ showing an activity 3.6fold higher compared to NAD+
-
additional information
VvAHGD oxidizes L-AHG using both NADP+ and NAD+ as the cofactor, but VvAHGD prefers NADP+ showing an activity 3.6fold higher compared to NAD+
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
Mg2+, Na+ and K+ have no effect on the enzyme activity
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
NaCl
about 50% residual activity at 0.5 M, complete inhibition at 2 M
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
1.11
3,6-anhydro-alpha-L-galactopyranose
mutant enzyme L249A, at pH 7.0 and 40°C
1.11
3,6-anhydro-alpha-L-galactopyranose
pH 7.0, 40°C, recombinant mutant L249A
1.2
3,6-anhydro-alpha-L-galactopyranose
wild type enzyme, at pH 7.0 and 40°C
1.2
3,6-anhydro-alpha-L-galactopyranose
pH 7.0, 40°C, recombinant wild-type enzyme
1.26
3,6-anhydro-alpha-L-galactopyranose
mutant enzyme S227A, at pH 7.0 and 40°C
1.26
3,6-anhydro-alpha-L-galactopyranose
pH 7.0, 40°C, recombinant mutant S227A
1.35
3,6-anhydro-alpha-L-galactopyranose
mutant enzyme S233A, at pH 7.0 and 40°C
1.35
3,6-anhydro-alpha-L-galactopyranose
pH 7.0, 40°C, recombinant mutant S233A
1.45
3,6-anhydro-alpha-L-galactopyranose
mutant enzyme S176A, at pH 7.0 and 40°C
1.45
3,6-anhydro-alpha-L-galactopyranose
pH 7.0, 40°C, recombinant mutant S176A
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
10.67
3,6-anhydro-alpha-L-galactopyranose
mutant enzyme S176A, at pH 7.0 and 40°C
10.67
3,6-anhydro-alpha-L-galactopyranose
pH 7.0, 40°C, recombinant mutant S176A
35.99
3,6-anhydro-alpha-L-galactopyranose
mutant enzyme S227A, at pH 7.0 and 40°C
35.99
3,6-anhydro-alpha-L-galactopyranose
pH 7.0, 40°C, recombinant mutant S227A
52.77
3,6-anhydro-alpha-L-galactopyranose
mutant enzyme L249A, at pH 7.0 and 40°C
52.77
3,6-anhydro-alpha-L-galactopyranose
pH 7.0, 40°C, recombinant mutant L249A
58.29
3,6-anhydro-alpha-L-galactopyranose
pH 7.0, 40°C, recombinant wild-type enzyme
58.29
3,6-anhydro-alpha-L-galactopyranose
wild type enzyme, at pH 7.0 and 40°C
63.18
3,6-anhydro-alpha-L-galactopyranose
mutant enzyme S233A, at pH 7.0 and 40°C
63.18
3,6-anhydro-alpha-L-galactopyranose
pH 7.0, 40°C, recombinant mutant S233A
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
7.36
3,6-anhydro-alpha-L-galactopyranose
mutant enzyme S176A, at pH 7.0 and 40°C
7.36
3,6-anhydro-alpha-L-galactopyranose
pH 7.0, 40°C, recombinant mutant S176A
28.56
3,6-anhydro-alpha-L-galactopyranose
mutant enzyme S227A, at pH 7.0 and 40°C
28.56
3,6-anhydro-alpha-L-galactopyranose
pH 7.0, 40°C, recombinant mutant S227A
46.8
3,6-anhydro-alpha-L-galactopyranose
mutant enzyme S233A, at pH 7.0 and 40°C
46.8
3,6-anhydro-alpha-L-galactopyranose
pH 7.0, 40°C, recombinant mutant S233A
47.54
3,6-anhydro-alpha-L-galactopyranose
mutant enzyme L249A, at pH 7.0 and 40°C
47.54
3,6-anhydro-alpha-L-galactopyranose
pH 7.0, 40°C, recombinant mutant L249A
48.575
3,6-anhydro-alpha-L-galactopyranose
pH 7.0, 40°C, recombinant wild-type enzyme
48.58
3,6-anhydro-alpha-L-galactopyranose
wild type enzyme, at pH 7.0 and 40°C
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
57.4
purified recombinant enzyme, substrate 3,6-anhydro-L-galactose (L-AHG), pH 7.0, 40°C
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
5 - 8
the enzyme shows 44% and 42% activity at pH 5.0 and 8.0, respectively
6 - 12
the enzyme shows over 90% of its maximum within a small pH range from 8.0 to 11.0 and more than 60% activity between pH 6.0 and 12.0. At pH values lower than 5.0, activity of the enzyme is drastically reduced
6.5 - 8
more than 60% activity at pH 6.5, more than 90% activity from pH 7.0-8.0, 30% activity at pH 9.0
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
40 - 70
the enzyme maintains above 50% activity between 40 and 70°C
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
Vibrio variabilis JCM 19239
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
VvAHGD lacks an N-terminal signal peptide sequence based on SignalP 4.1 prediction, consistent with its intracellular location
brenda
Vibrio variabilis JCM 19239
-
VvAHGD lacks an N-terminal signal peptide sequence based on SignalP 4.1 prediction, consistent with its intracellular location
-
brenda
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
malfunction
the enzyme is involved in a degradation pathway for 3,6-anhydro-alpha-L-galactose, a major component of the polysaccharides produced by red macroalgae, such as agarose and porphyran
additional information
evolution
evolutionary relationship between VvAHGD and other ALDHs, a phylogenetic tree and analysis, including VvAHGD and its homologues, lactaldehyde dehydrogenases, succinic semialdehyde dehydrogenases from family ALDH5, betaine aldehyde dehydrogenases from family ALDH25, cytosolic aldehyde dehydrogenases from family ALDH2, and retinaldehyde dehydrogenases from family ALDH1
evolution
Vibrio variabilis JCM 19239
-
evolutionary relationship between VvAHGD and other ALDHs, a phylogenetic tree and analysis, including VvAHGD and its homologues, lactaldehyde dehydrogenases, succinic semialdehyde dehydrogenases from family ALDH5, betaine aldehyde dehydrogenases from family ALDH25, cytosolic aldehyde dehydrogenases from family ALDH2, and retinaldehyde dehydrogenases from family ALDH1
-
additional information
-
the catalytic residues of VvAHGD are Cys282 and Glu248
additional information
the catalytic residues of VvAHGD are Cys282 and Glu248
additional information
Vibrio variabilis JCM 19239
-
the catalytic residues of VvAHGD are Cys282 and Glu248
-
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UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). A0A2Z2NHZ6_9GAMM
478
0
51559
TrEMBL
-
Q9RKF1_STRCO
Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)
492
0
52173
TrEMBL
-
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
AHGD enzyme structure comparisons, overview
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
apo form and in complex with NADP+, hanging drop vapor diffusion method, using 0.2 M NaAC, 0.1 M sodium cacodylate trihydrate (pH 6.5), and 30% (w/v) PEG 8000
purified enzyme in apoform and in complex with NADP+, X-ray diffraction structure determination and analysis at 2.70 A and 2.37 A resolution, respectively, molecular replacement using the structure of Patl_2553 (PDB ID 3K2W) as the starting model
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PROTEIN VARIANTS
ORGANISM