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show all sequences of 1.1.1.107

Identification of a new tetrameric pyridoxal 4-dehydrogenase as the second enzyme in the degradation pathway for pyridoxine in a nitrogen-fixing symbiotic bacterium, Mesorhizobium loti

Yokochi, N.; Nishimura, S.; Yoshikane, Y.; Ohnishi, K.; Yagi, T.; Arch. Biochem. Biophys. 452, 1-8 (2006)

Data extracted from this reference:

Cloned(Commentary)
Commentary
Organism
expression in Escherichia coli; recombinant enzyme expressed in Escherichia coli
Mesorhizobium loti
KM Value [mM]
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
0.091
-
pyridoxal
30C, pH 9.2; pH 9.2, 30C
Mesorhizobium loti
0.28
-
NAD+
30C, pH 9.2; pH 9.2, 30C
Mesorhizobium loti
Localization
Localization
Commentary
Organism
GeneOntology No.
Textmining
Molecular Weight [Da]
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
25531
-
4 * 25531, calculated from sequence
Mesorhizobium loti
26000
-
4 * 26000; 4 * 26000, SDS-PAGE
Mesorhizobium loti
97000
-
gel filtration
Mesorhizobium loti
98000
-
non-denaturing PAGE
Mesorhizobium loti
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
pyridoxal + NAD+
Mesorhizobium loti
PLDH is essential for assimilation of vitamin B6 compounds and is the second step enzyme in the degradation pathway for pyridoxine
4-pyridoxolactone + NADH + H+
-
-
?
pyridoxal + NAD+
Mesorhizobium loti
PLDH is essential for the assimilation of vitamin B6 compounds and the second step enzyme in their degradation pathway
4-pyridoxolactone + NADH + H+
-
-
ir
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Mesorhizobium loti
-
; MAFF303099
-
Purification (Commentary)
Commentary
Organism
recombinant
Mesorhizobium loti
Specific Activity [micromol/min/mg]
Specific Activity Minimum [mol/min/mg]
Specific Activity Maximum [mol/min/mg]
Commentary
Organism
88
-
-
Mesorhizobium loti
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
additional information
the enzyme shows less than 0.01% of the activity of pyridoxal toward pyridoxal 5'-phosphate (0.5 mM), pyridoxine (0.8 mM), and pyridoxamine, pyridoxamine 5'-phosphate, 4-phthalaldehyde, 2-nitrobenzaldehyde, 3-nitrobenzaldehyde, 4-nitrobenzaldehyde, pyridine, formaldehyde, and 2-carboxybenzaldehyde (1.0 mM each). The enzyme shows less than 0.01% of the activity of pyridoxal toward DL-glyceraldehyde, D-xylose, L-xylose, D-ribose, D-glucose, D-arabinose, L-arabinose, L-fucose, and D-galactose (250 mM each)
667329
Mesorhizobium loti
?
-
-
-
-
pyridoxal + NAD+
PLDH is essential for assimilation of vitamin B6 compounds and is the second step enzyme in the degradation pathway for pyridoxine
667329
Mesorhizobium loti
4-pyridoxolactone + NADH + H+
-
-
-
?
pyridoxal + NAD+
PLDH is essential for the assimilation of vitamin B6 compounds and the second step enzyme in their degradation pathway
667329
Mesorhizobium loti
4-pyridoxolactone + NADH + H+
-
-
-
ir
pyridoxal + NAD+
very low activity toward NADP+. 0.16% of the maximal activity obtained with NAD+ is observed when 5.0 mM NADP+ is used. The enzyme does not catalyze the reduction of 4-pyridoxolactone with NADH + H+ to pyridoxal even when a 100fold higher concentration of the enzyme is used for the reverse reaction
667329
Mesorhizobium loti
4-pyridoxolactone + NADH + H+
-
-
-
ir
Subunits
Subunits
Commentary
Organism
tetramer
4 * 25531, calculated from sequence; 4 * 26000; 4 * 26000, SDS-PAGE
Mesorhizobium loti
Temperature Optimum [C]
Temperature Optimum [C]
Temperature Optimum Maximum [C]
Commentary
Organism
50
-
-
Mesorhizobium loti
Temperature Range [C]
Temperature Minimum [C]
Temperature Maximum [C]
Commentary
Organism
30
55
30C: 37% of maximal activity, 55C: 33% of maximal activity
Mesorhizobium loti
Temperature Stability [C]
Temperature Stability Minimum [C]
Temperature Stability Maximum [C]
Commentary
Organism
45
-
10 min, stable below
Mesorhizobium loti
50
-
10 min, 76% of original activity
Mesorhizobium loti
60
-
10 min, 1.3% of original activity
Mesorhizobium loti
Turnover Number [1/s]
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
136
-
NAD+
30C, pH 9.2; pH 9.2, 30C
Mesorhizobium loti
149
-
pyridoxal
30C, pH 9.2; pH 9.2, 30C
Mesorhizobium loti
pH Optimum
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
9.2
-
; 50 mM CHES-NaOH buffer
Mesorhizobium loti
pH Range
pH Minimum
pH Maximum
Commentary
Organism
8.6
10
pH 8.6: 66% of maximal activity, pH 10.0: 57% of maximal activity, 50 mM CHES-NaOH buffer
Mesorhizobium loti
Cofactor
Cofactor
Commentary
Organism
Structure
NAD+
-
Mesorhizobium loti
Cloned(Commentary) (protein specific)
Commentary
Organism
expression in Escherichia coli; recombinant enzyme expressed in Escherichia coli
Mesorhizobium loti
Cofactor (protein specific)
Cofactor
Commentary
Organism
Structure
NAD+
-
Mesorhizobium loti
KM Value [mM] (protein specific)
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
0.091
-
pyridoxal
30C, pH 9.2; pH 9.2, 30C
Mesorhizobium loti
0.28
-
NAD+
30C, pH 9.2; pH 9.2, 30C
Mesorhizobium loti
Localization (protein specific)
Localization
Commentary
Organism
GeneOntology No.
Textmining
Molecular Weight [Da] (protein specific)
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
25531
-
4 * 25531, calculated from sequence
Mesorhizobium loti
26000
-
4 * 26000; 4 * 26000, SDS-PAGE
Mesorhizobium loti
97000
-
gel filtration
Mesorhizobium loti
98000
-
non-denaturing PAGE
Mesorhizobium loti
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
pyridoxal + NAD+
Mesorhizobium loti
PLDH is essential for assimilation of vitamin B6 compounds and is the second step enzyme in the degradation pathway for pyridoxine
4-pyridoxolactone + NADH + H+
-
-
?
pyridoxal + NAD+
Mesorhizobium loti
PLDH is essential for the assimilation of vitamin B6 compounds and the second step enzyme in their degradation pathway
4-pyridoxolactone + NADH + H+
-
-
ir
Purification (Commentary) (protein specific)
Commentary
Organism
recombinant
Mesorhizobium loti
Specific Activity [micromol/min/mg] (protein specific)
Specific Activity Minimum [mol/min/mg]
Specific Activity Maximum [mol/min/mg]
Commentary
Organism
88
-
-
Mesorhizobium loti
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
additional information
the enzyme shows less than 0.01% of the activity of pyridoxal toward pyridoxal 5'-phosphate (0.5 mM), pyridoxine (0.8 mM), and pyridoxamine, pyridoxamine 5'-phosphate, 4-phthalaldehyde, 2-nitrobenzaldehyde, 3-nitrobenzaldehyde, 4-nitrobenzaldehyde, pyridine, formaldehyde, and 2-carboxybenzaldehyde (1.0 mM each). The enzyme shows less than 0.01% of the activity of pyridoxal toward DL-glyceraldehyde, D-xylose, L-xylose, D-ribose, D-glucose, D-arabinose, L-arabinose, L-fucose, and D-galactose (250 mM each)
667329
Mesorhizobium loti
?
-
-
-
-
pyridoxal + NAD+
PLDH is essential for assimilation of vitamin B6 compounds and is the second step enzyme in the degradation pathway for pyridoxine
667329
Mesorhizobium loti
4-pyridoxolactone + NADH + H+
-
-
-
?
pyridoxal + NAD+
PLDH is essential for the assimilation of vitamin B6 compounds and the second step enzyme in their degradation pathway
667329
Mesorhizobium loti
4-pyridoxolactone + NADH + H+
-
-
-
ir
pyridoxal + NAD+
very low activity toward NADP+. 0.16% of the maximal activity obtained with NAD+ is observed when 5.0 mM NADP+ is used. The enzyme does not catalyze the reduction of 4-pyridoxolactone with NADH + H+ to pyridoxal even when a 100fold higher concentration of the enzyme is used for the reverse reaction
667329
Mesorhizobium loti
4-pyridoxolactone + NADH + H+
-
-
-
ir
Subunits (protein specific)
Subunits
Commentary
Organism
tetramer
4 * 25531, calculated from sequence; 4 * 26000; 4 * 26000, SDS-PAGE
Mesorhizobium loti
Temperature Optimum [C] (protein specific)
Temperature Optimum [C]
Temperature Optimum Maximum [C]
Commentary
Organism
50
-
-
Mesorhizobium loti
Temperature Range [C] (protein specific)
Temperature Minimum [C]
Temperature Maximum [C]
Commentary
Organism
30
55
30C: 37% of maximal activity, 55C: 33% of maximal activity
Mesorhizobium loti
Temperature Stability [C] (protein specific)
Temperature Stability Minimum [C]
Temperature Stability Maximum [C]
Commentary
Organism
45
-
10 min, stable below
Mesorhizobium loti
50
-
10 min, 76% of original activity
Mesorhizobium loti
60
-
10 min, 1.3% of original activity
Mesorhizobium loti
Turnover Number [1/s] (protein specific)
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
136
-
NAD+
30C, pH 9.2; pH 9.2, 30C
Mesorhizobium loti
149
-
pyridoxal
30C, pH 9.2; pH 9.2, 30C
Mesorhizobium loti
pH Optimum (protein specific)
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
9.2
-
; 50 mM CHES-NaOH buffer
Mesorhizobium loti
pH Range (protein specific)
pH Minimum
pH Maximum
Commentary
Organism
8.6
10
pH 8.6: 66% of maximal activity, pH 10.0: 57% of maximal activity, 50 mM CHES-NaOH buffer
Mesorhizobium loti
Other publictions for EC 1.1.1.107
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Temperature Optimum [C]
Temperature Range [C]
Temperature Stability [C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [C] (protein specific)
Temperature Range [C] (protein specific)
Temperature Stability [C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
721873
Chu
The crystal structure of SDR-t ...
Mesorhizobium loti
Biosci. Biotechnol. Biochem.
75
388-390
2011
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1
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1
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2
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1
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1
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1
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2
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3
3
-
-
-
710764
Chu
Crystallization and preliminar ...
Mesorhizobium loti
Acta Crystallogr. Sect. F
66
718-720
2010
-
-
1
1
-
-
-
-
-
-
1
-
-
4
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-
1
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-
1
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1
1
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1
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1
1
1
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1
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1
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1
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1
1
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-
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-
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688568
Nishimura
Determination of individual vi ...
Saccharomyces cerevisiae
J. Nutr. Sci. Vitaminol.
54
18-24
2008
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1
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1
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1
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2
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1
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2
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1
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1
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1
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1
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-
-
2
-
1
-
-
-
2
-
-
-
-
-
-
-
-
-
699047
Tamura
Synthesis of 4-pyridoxolactone ...
Escherichia coli, Escherichia coli JM109
J. Biosci. Bioeng.
106
460-465
2008
-
-
1
-
-
-
-
-
-
-
-
-
-
30
-
-
-
-
-
-
2
-
2
-
-
-
-
-
-
-
-
1
-
-
-
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1
1
-
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2
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2
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-
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-
-
-
-
-
667329
Yokochi
Identification of a new tetram ...
Mesorhizobium loti
Arch. Biochem. Biophys.
452
1-8
2006
-
-
1
-
-
-
-
2
1
-
4
2
-
3
-
-
1
-
-
-
1
-
4
1
1
1
3
2
1
1
-
1
-
-
-
-
-
1
1
-
-
-
-
-
-
2
1
-
4
2
-
-
-
1
-
-
1
-
4
1
1
1
3
2
1
1
-
-
-
-
-
-
-
-
654111
Yokochi
Crystallization and preliminar ...
Microbacterium luteolum
Acta Crystallogr. Sect. D
60
2061-2062
2004
-
-
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1
-
-
-
-
-
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2
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1
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656239
Yokochi
Molecular cloning, expression, ...
Microbacterium luteolum, Microbacterium luteolum YK-1
J. Biol. Chem.
279
37377-37384
2004
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-
1
-
-
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-
7
-
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2
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5
-
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1
-
11
1
1
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2
4
2
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2
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1
2
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7
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2
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1
-
11
1
1
-
2
4
2
-
-
-
-
-
-
-
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-
655029
Trongpanich
Purification and characterizat ...
Microbacterium luteolum
Biosci. Biotechnol. Biochem.
66
543-548
2002
-
-
-
-
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3
3
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2
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4
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1
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1
4
2
1
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1
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2
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3
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1
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1
4
2
1
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1
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2
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80781
Burg
The bacterial oxidation of vit ...
Pseudomonas sp.
J. Biol. Chem.
244
2585-2589
1969
1
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11
2
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2
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1
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1
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4
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1
1
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11
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2
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2
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1
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4
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1
1
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