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Information on EC 1.1.1.107 - pyridoxal 4-dehydrogenase
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1.1.1.107 pyridoxal 4-dehydrogenaseIUBMB Comments
The enzyme acts on the hemiacetal form of the substrate.
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Word Map
- 1.1.1.107
- pyridoxine
- loti
- luteolum
-
5'-phosphate
-
mesorhizobium
- microbacterium
-
monoclinic
-
sitting-drop
- nadp+
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4-oxidase
-
4-pyridoxic
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vapour-diffusion
- chaperonin
- analysis
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota
Synonyms
pyridoxal dehydrogenase, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
PLDH
pyridoxal dehydrogenase
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-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
pyridoxal + NAD+ = 4-pyridoxolactone + NADH + H+
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
oxidation
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redox reaction
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reduction
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PATHWAY SOURCE
PATHWAYS
MetaCyc
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SYSTEMATIC NAME
IUBMB Comments
pyridoxal:NAD+ 4-oxidoreductase
The enzyme acts on the hemiacetal form of the substrate.
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CAS REGISTRY NUMBER
COMMENTARY
37250-39-8
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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
pyridine-4-aldehyde + NAD+
4-pyridoxolactone + NADH + H+
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0.9% of the activity against pyridoxal
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-
?
pyridoxal + NAD+
4-pyridoxolactone + NADH + H+
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cells coexpressing pyridoxal 4-dehydrogenase and alcohol dehydrogenase show a higher conversion rate than those expressing pyridoxal 4-dehydrogenase alone
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-
?
pyridoxal + NAD+
4-pyridoxolactone + NADH + H+
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cells coexpressing pyridoxal 4-dehydrogenase and alcohol dehydrogenase show a higher conversion rate than those expressing pyridoxal 4-dehydrogenase alone
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-
?
pyridoxal + NAD+
4-pyridoxolactone + NADH + H+
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PLDH is essential for assimilation of vitamin B6 compounds and is the second step enzyme in the degradation pathway for pyridoxine
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-
?
pyridoxal + NAD+
4-pyridoxolactone + NADH + H+
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PLDH is essential for the assimilation of vitamin B6 compounds and the second step enzyme in their degradation pathway
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-
ir
pyridoxal + NAD+
4-pyridoxolactone + NADH + H+
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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
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ir
pyridoxal + NAD+
4-pyridoxolactone + NADH + H+
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via pyridoxal hemiacetal
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ir
pyridoxal + NAD+
4-pyridoxolactone + NADH + H+
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PLDH is essential for assimilation of vitamin B6 compounds and is the second step enzyme in the degradation pathway for pyridoxine
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-
?
pyridoxal + NAD+
4-pyridoxolactone + NADH + H+
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PLDH is essential for the assimilation of vitamin B6 compounds and the second step enzyme in their degradation pathway
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-
ir
pyridoxal + NAD+
4-pyridoxolactone + NADH + H+
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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
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ir
pyridoxal + NAD+
4-pyridoxolactone + NADH + H+
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specific conversion of vitamin B6
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ir
pyridoxal + NAD+
4-pyridoxolactone + NADH + H+
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development and evaluation of a method to determine vitamin B6, pyridoxal, involving the enzyme, overview
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ir
additional information
?
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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)
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additional information
?
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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)
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additional information
?
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no substrate: pyridoxal-5’-phosphate, pyridoxamine, pyridoxine, 2-nitrobenzaldehyde, 3-nitrobenzaldehyde, 4-nitrobenzaldehyde, o-phthalaldehyde, 5-nitrosalicylaldehyde, 2-carboxybenzaldehyde
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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
pyridoxal + NAD+
4-pyridoxolactone + NADH + H+
-
PLDH is essential for assimilation of vitamin B6 compounds and is the second step enzyme in the degradation pathway for pyridoxine
-
-
?
pyridoxal + NAD+
4-pyridoxolactone + NADH + H+
-
PLDH is essential for the assimilation of vitamin B6 compounds and the second step enzyme in their degradation pathway
-
-
ir
pyridoxal + NAD+
4-pyridoxolactone + NADH + H+
-
PLDH is essential for assimilation of vitamin B6 compounds and is the second step enzyme in the degradation pathway for pyridoxine
-
-
?
pyridoxal + NAD+
4-pyridoxolactone + NADH + H+
-
PLDH is essential for the assimilation of vitamin B6 compounds and the second step enzyme in their degradation pathway
-
-
ir
pyridoxal + NAD+
4-pyridoxolactone + NADH + H+
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specific conversion of vitamin B6
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ir
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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TURNOVER NUMBER [1/s]
SUBSTRATE
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
8.6 - 10
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pH 8.6: 66% of maximal activity, pH 10.0: 57% of maximal activity, 50 mM CHES-NaOH buffer
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
30
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TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
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the enzyme belongs to the short-chain dehydrogenase/reductase enzyme family
physiological function
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the enzyme is involved in the degradation pathway I of pyridoxine, a vitamin B6 compound
additional information
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structure analysis, homology modeling using the crystal structure of (S)-1-phenylethanol dehydrogenase, PDB ID 2EW8, molecular replacement, overview
Show AA Sequence and Transmembrane Helices (506 entries)
Please use the AA Sequence and Transmembrane Helices Search for a specific query.
Please use the AA Sequence and Transmembrane Helices Search for a specific query.
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PDB
SCOP
CATH
UNIPROT
ORGANISM
Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)
Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)
Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)
Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
26000
38000
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
tetramer
tetramer
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4 * 25531, calculated from sequence; 4 * 26000; 4 * 26000, SDS-PAGE
tetramer
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4 * 25531, calculated from sequence; 4 * 26000; 4 * 26000, SDS-PAGE
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CRYSTALLIZATION/commentary
ORGANISM
UNIPROT
LITERATURE
recombinant selenomethionine-substituted enzyme, crystallized by the sitting-drop vapour-diffusion method using PEG 4000 as precipitant, in the presence of 0.45 mM NAD+. The crystals diffract to 2.9 A resolution and belong to the monoclinic space group P21
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
45
50
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
4°C, 1% 2-mercaptoethanol, 24 h, no loss of activity, 2-mercaptoethanol is essential for stability
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PURIFICATION/commentary
ORGANISM
UNIPROT
LITERATURE
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CLONED/commentary
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli; recombinant enzyme expressed in Escherichia coli
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
analysis
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the enzyme is useful in determination of vitamin B6 contents, method development, overview
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Burg, R.W.; Snell, E.E.
The bacterial oxidation of vitamin B6. VI. Pyridoxal dehydrogenase and 4-pyridoxolactonase
J. Biol. Chem.
244
2585-2589
1969
Pseudomonas sp.
brenda
Yokochi, N.; Yoshikane, Y.; Yagi, T.; Yamasaki, M.; Mikami, B.
Crystallization and preliminary X-ray analysis of pyridoxal 4-dehydrogenase, the second enzyme in degradation pathway I of pyridoxine
Acta Crystallogr. Sect. D
60
2061-2062
2004
Microbacterium luteolum
brenda
Trongpanich, Y.; Abe, K.; Kaneda, Y.; Morita, T.; Yagi, T.
Purification and characterization of pyridoxal 4-dehydrogenase from Aureobacterium luteolum
Biosci. Biotechnol. Biochem.
66
543-548
2002
Microbacterium luteolum
brenda
Yokochi, N.; Yoshikane, Y.; Trongpanich, Y.; Ohnishi, K.; Yagi, T.
Molecular cloning, expression, and properties of an unusual aldo-keto reductase family enzyme, pyridoxal 4-dehydrogenase, that catalyzes irreversible oxidation of pyridoxal
J. Biol. Chem.
279
37377-37384
2004
Microbacterium luteolum (Q76KC2), Microbacterium luteolum YK-1, Microbacterium luteolum YK-1 (Q76KC2)
brenda
Yokochi, N.; Nishimura, S.; Yoshikane, Y.; Ohnishi, K.; Yagi, T.
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
Arch. Biochem. Biophys.
452
1-8
2006
Mesorhizobium loti, Mesorhizobium loti MAFF303099
brenda
Nishimura, S.; Nagano, S.; A Crai, C.; Yokochi, N.; Yoshikane, Y.; Ge, F.; Yagi, T.
Determination of individual vitamin B(6) compounds based on enzymatic conversion to 4-pyridoxolactone
J. Nutr. Sci. Vitaminol.
54
18-24
2008
Saccharomyces cerevisiae
brenda
Tamura, A.; Yoshikane, Y.; Yokochi, N.; Yagi, T.
Synthesis of 4-pyridoxolactone from pyridoxine using a combination of transformed Escherichia coli cells
J. Biosci. Bioeng.
106
460-465
2008
Escherichia coli, Escherichia coli JM109
brenda
Chu, H.N.; Kobayashi, J.; Yoshikane, Y.; Mikami, B.; Yagi, T.
Crystallization and preliminary X-ray analysis of SDR-type pyridoxal dehydrogenase from Mesorhizobium loti
Acta Crystallogr. Sect. F
66
718-720
2010
Mesorhizobium loti, Mesorhizobium loti (Q988B7), Mesorhizobium loti MAFF303099 (Q988B7)
brenda
Chu, H.N.; Kobayashi, J.; Mikami, B.; Yagi, T.
The crystal structure of SDR-type pyridoxal 4-dehydrogenase of Mesorhizobium loti
Biosci. Biotechnol. Biochem.
75
388-390
2011
Mesorhizobium loti
brenda
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