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Enzyme Nomenclature
Information on EC 1.1.99.42 - 4-pyridoxic acid dehydrogenase
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EC Tree
1.1.99.42 4-pyridoxic acid dehydrogenaseIUBMB Comments
The enzyme, characterized from the bacteria Pseudomonas sp. MA-1 and Mesorhizobium loti, participates in the degradation of pyridoxine (vitamin B6). It is membrane bound and contains FAD. The enzyme has been assayed in vitro in the presence of the artificial electron acceptor dichloroindophenol (DCPIP).
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The expected taxonomic range for this enzyme is: Bacteria, Eukaryota
Reaction Schemes
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
mlr6739
mlr6792
mlr6792
-
-
locus name
-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
4-pyridoxate + acceptor = 5-formyl-3-hydroxy-2-methylpyridine-4-carboxylate + reduced acceptor
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-
-
-
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PATHWAY SOURCE
PATHWAYS
MetaCyc
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SYSTEMATIC NAME
IUBMB Comments
4-pyridoxate:acceptor 5-oxidoreductase
The enzyme, characterized from the bacteria Pseudomonas sp. MA-1 and Mesorhizobium loti, participates in the degradation of pyridoxine (vitamin B6). It is membrane bound and contains FAD. The enzyme has been assayed in vitro in the presence of the artificial electron acceptor dichloroindophenol (DCPIP).
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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
4-pyridoxate + 2,6-dichloroindophenol
5-formyl-3-hydroxy-2-methylpyridine-4-carboxylate + reduced 2,6-dichloroindophenol
4-pyridoxate + phenazine methosulfate
5-formyl-3-hydroxy-2-methylpyridine-4-carboxylate + reduced phenazine methosulfate
-
-
-
-
?
4-pyridoxate + 2,6-dichloroindophenol
5-formyl-3-hydroxy-2-methylpyridine-4-carboxylate + reduced 2,6-dichloroindophenol
-
-
-
?
4-pyridoxate + 2,6-dichloroindophenol
5-formyl-3-hydroxy-2-methylpyridine-4-carboxylate + reduced 2,6-dichloroindophenol
Mesorhizobium loti MAFF303099
-
-
-
?
4-pyridoxate + 2,6-dichloroindophenol
5-formyl-3-hydroxy-2-methylpyridine-4-carboxylate + reduced 2,6-dichloroindophenol
-
-
-
-
?
4-pyridoxate + NAD+
5-formyl-3-hydroxy-2-methylpyridine-4-carboxylate + NADH + H+
-
-
-
?
4-pyridoxate + NAD+
5-formyl-3-hydroxy-2-methylpyridine-4-carboxylate + NADH + H+
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-
-
?
4-pyridoxate + NAD+
5-formyl-3-hydroxy-2-methylpyridine-4-carboxylate + NADH + H+
Mesorhizobium loti MAFF303099
-
-
-
?
5-formyl-3-hydroxy-2-methylpyridine-4-carboxylate + NADH + H+
4-pyridoxate + NAD+
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-
-
?
5-formyl-3-hydroxy-2-methylpyridine-4-carboxylate + NADH + H+
4-pyridoxate + NAD+
Mesorhizobium loti MAFF303099
-
-
-
?
5-formyl-3-hydroxy-2-methylpyridine-4-carboxylate + NADH + H+
4-pyridoxate + NAD+
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?
additional information
?
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enzyme catalyzes oxidation of the hemiacetal form of 5-formyl-3-hydroxy-2-methylpyridine-4-carboxylate to 3-hydroxy-2-methylpyridine-4,5-dicarboxylate with NAD+, reaction of EC 1.2.1.100, and reduction of an aldehyde form of 5-formyl-3-hydroxy-2-methylpyridine-4-carboxylate to 4-pyridoxic acid with NADH. The Ser-His-Glu catalytic triad facilitates the two-way reactions. Ser116 assists protonation of His137 to drive the reduction reaction. His137 acts as a catalytic base to abstract a proton during oxidation. Glu149 likely neutralizes the positive charge on His137 after the deprotonation of the substrate
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-
?
additional information
?
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enzyme catalyzes practically irreversible oxidation of 5-formyl-3-hydroxy-2-methylpyridine-4-carboxylate by NAD+ to 3-hydroxy-2-methyl-pyridine 4, 5-dicarboxylic acid, i.e. reaction of EC 1.2.1.100, and practically irreversible reduction of 5-formyl-3-hydroxy-2-methylpyridine-4-carboxylate by NADH to 4-pyridoxic acid. When the enzyme reaction is started with the combination of 5-formyl-3-hydroxy-2-methylpyridine-4-carboxylate and NAD+ or that of 5-formyl-3-hydroxy-2-methylpyridine-4-carboxylate and NADH, 3-hydroxy-2-methylpyridine-4,5-dicarboxylate and 4-pyridoxic acid are produced in an almost equimolar ratio throughout the reaction
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-
?
additional information
?
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enzyme catalyzes practically irreversible oxidation of 5-formyl-3-hydroxy-2-methylpyridine-4-carboxylate by NAD+ to 3-hydroxy-2-methyl-pyridine 4, 5-dicarboxylic acid, i.e. reaction of EC 1.2.1.100, and practically irreversible reduction of 5-formyl-3-hydroxy-2-methylpyridine-4-carboxylate by NADH to 4-pyridoxic acid. When the enzyme reaction is started with the combination of 5-formyl-3-hydroxy-2-methylpyridine-4-carboxylate and NAD+ or that of 5-formyl-3-hydroxy-2-methylpyridine-4-carboxylate and NADH, 3-hydroxy-2-methylpyridine-4,5-dicarboxylate and 4-pyridoxic acid are produced in an almost equimolar ratio throughout the reaction
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-
?
additional information
?
-
very poor activity with substrates pyridoxal, pyridoxine and 4-pyridoxic acid lactone, and simple alpha-hydroxy acids, such as lactic acid and glycolic acid
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-
?
additional information
?
-
Mesorhizobium loti MAFF303099
very poor activity with substrates pyridoxal, pyridoxine and 4-pyridoxic acid lactone, and simple alpha-hydroxy acids, such as lactic acid and glycolic acid
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-
?
additional information
?
-
Mesorhizobium loti MAFF303099
enzyme catalyzes practically irreversible oxidation of 5-formyl-3-hydroxy-2-methylpyridine-4-carboxylate by NAD+ to 3-hydroxy-2-methyl-pyridine 4, 5-dicarboxylic acid, i.e. reaction of EC 1.2.1.100, and practically irreversible reduction of 5-formyl-3-hydroxy-2-methylpyridine-4-carboxylate by NADH to 4-pyridoxic acid. When the enzyme reaction is started with the combination of 5-formyl-3-hydroxy-2-methylpyridine-4-carboxylate and NAD+ or that of 5-formyl-3-hydroxy-2-methylpyridine-4-carboxylate and NADH, 3-hydroxy-2-methylpyridine-4,5-dicarboxylate and 4-pyridoxic acid are produced in an almost equimolar ratio throughout the reaction
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-
?
additional information
?
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2,6-dichloroindophenol, phenazine methosulfate, and menadione are effective electron acceptors. Ubiquinones are less active, while NAD, FAD, and O2 are inactive. In membrane fractions, oxygen supports 4-pyridoxic acid oxidation via a CN--sensitive electron transport chain
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-
?
additional information
?
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enzyme catalyzes with equal facility both the oxidation of formyl-3-hydroxy-2-methylpyridine-4-carboxylic-acid by NAD+ to 3-hydroxy-2-methylpyridine-4,5-dicarboxylic acid, i.e. reaction of EC 1.2.1.100, and the reduction of formyl-3-hydroxy-2-methylpyridine-4-carboxylic-acid by NADH to 4-pyridoxic acid. No oxidation of 4-pyridoxic acid is observed
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-
?
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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
4-pyridoxate + 2,6-dichloroindophenol
5-formyl-3-hydroxy-2-methylpyridine-4-carboxylate + reduced 2,6-dichloroindophenol
4-pyridoxate + 2,6-dichloroindophenol
5-formyl-3-hydroxy-2-methylpyridine-4-carboxylate + reduced 2,6-dichloroindophenol
-
-
-
?
4-pyridoxate + 2,6-dichloroindophenol
5-formyl-3-hydroxy-2-methylpyridine-4-carboxylate + reduced 2,6-dichloroindophenol
Mesorhizobium loti MAFF303099
-
-
-
?
4-pyridoxate + NAD+
5-formyl-3-hydroxy-2-methylpyridine-4-carboxylate + NADH + H+
-
-
-
?
4-pyridoxate + NAD+
5-formyl-3-hydroxy-2-methylpyridine-4-carboxylate + NADH + H+
Mesorhizobium loti MAFF303099
-
-
-
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
FAD
1 mol of FAD per mol of subunit. Purified protein is yellowish and shows absorption maxima near 380nm and 455 nm
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.029
4-pyridoxate
pH 8.0, temperature not specified in the publication
0.0058
4-pyridoxate
pH 8.0, temperature not specified in the publication
0.0093
4-pyridoxate
-
electron acceptor 2,6-dichloroindophenol, pH 8.0, 25°C
0.0084
4-pyridoxate
-
electron acceptor phenazine methosulfate, pH 8.0, 25°C
0.03
5-formyl-3-hydroxy-2-methylpyridine-4-carboxylate
mutant E149Q, pH 5.0, 30°C
0.02
5-formyl-3-hydroxy-2-methylpyridine-4-carboxylate
mutant E149Q, pH 8.0, 30°C
0.0249
5-formyl-3-hydroxy-2-methylpyridine-4-carboxylate
wild-type, pH 8.0, 30°C
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
11
4-pyridoxate
pH 8.0, temperature not specified in the publication
217
5-formyl-3-hydroxy-2-methylpyridine-4-carboxylate
wild-type, pH 8.0, 30°C
78
5-formyl-3-hydroxy-2-methylpyridine-4-carboxylate
mutant E149Q, pH 8.0, 30°C
300
5-formyl-3-hydroxy-2-methylpyridine-4-carboxylate
mutant E149Q, pH 5.0, 30°C
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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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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
enzyme additionally catalyzes the reaction of EC 1.2.1.100
UniProt
brenda
Mesorhizobium loti MAFF303099
enzyme additionally catalyzes the reaction of EC 1.2.1.100
UniProt
brenda
Mesorhizobium loti MAFF303099
enzyme additionally catalyzes the reaction of EC 1.2.1.100
UniProt
brenda
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
recombinant enzyme in Escherichia coli, integral monotopic protein, protruding into a cytoplasm side from the bacterial membrane
-
brenda
Mesorhizobium loti MAFF303099
-
recombinant enzyme in Escherichia coli, integral monotopic protein, protruding into a cytoplasm side from the bacterial membrane
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-
brenda
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
physiological function
physiological function
contrary to wild-type, mlr6793-disruptant cells cannot grow on pyridoxine, 4-pyridoxic acid or 5-formyl-3-hydroxy-2-methylpyridine-4-carboxylate as sole carbon and nitrogen source
physiological function
Mesorhizobium loti MAFF303099
-
contrary to wild-type, mlr6793-disruptant cells cannot grow on pyridoxine, 4-pyridoxic acid or 5-formyl-3-hydroxy-2-methylpyridine-4-carboxylate as sole carbon and nitrogen source
-
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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). 4PADH_RHILO
Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)
543
0
58988
Swiss-Prot
-
FHMCD_RHILO
Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)
309
0
33061
Swiss-Prot
other Location (Reliability: 5)
Q988H5_RHILO
Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)
319
0
34897
TrEMBL
-
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
-
undenatured preparations aggregate readily, leading to mass values of 148,000, 470,000, and more than 670000 obtained by density gradient centrifugation or by gel filtration
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
monomer
dimer
2 * 38900, SDS-PAGE, 2 * 33060, calculated from sequence, 2 * 33121, TOF-MS
dimer
Mesorhizobium loti MAFF303099
-
2 * 38900, SDS-PAGE, 2 * 33060, calculated from sequence, 2 * 33121, TOF-MS
-
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
structure determined by molecular replacement, to 1. 55 A resolution. Residues Ser116, His137 and Glu149 are connected by a hydrogen bonding network forming a catalytic triad
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
E149Q
mutant shows a showed a different pH optimum depending on the cosubstrate. With NAD+, the mutant shows very low activity with an optimum pH at 8.5 in the universal buffer. In contrast, the optimum pH is 5.5 with NADH
E149Q
Mesorhizobium loti MAFF303099
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mutant shows a showed a different pH optimum depending on the cosubstrate. With NAD+, the mutant shows very low activity with an optimum pH at 8.5 in the universal buffer. In contrast, the optimum pH is 5.5 with NADH
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additional information
additional information
deletion or mutation of a deduced transmembrane segment in 4-pyridoxic acid dehydrogenase makes it an inclusion body upon expression in Escherichia coli, and the enzyme protein is not found in the cell membrane
additional information
-
deletion or mutation of a deduced transmembrane segment in 4-pyridoxic acid dehydrogenase makes it an inclusion body upon expression in Escherichia coli, and the enzyme protein is not found in the cell membrane
additional information
Mesorhizobium loti MAFF303099
-
deletion or mutation of a deduced transmembrane segment in 4-pyridoxic acid dehydrogenase makes it an inclusion body upon expression in Escherichia coli, and the enzyme protein is not found in the cell membrane
-
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
4°C, half-life 3 days in absence of glycerol. In presence of glycerol 0-20% of the activity is lost in 1 week
-
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
from Pseudomonas MA-1 grown with pyridoxine as a sole source of carbon and nitrogen
-
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Mugo, A.N.; Kobayashi, J.; Mikami, B.; Yoshikane, Y.; Yagi, T.; Ohnishi, K.
Crystal structure of 5-formyl-3-hydroxy-2-methylpyridine 4-carboxylic acid 5-dehydrogenase, an NAD+-dependent dismutase from Mesorhizobium loti
Biochem. Biophys. Res. Commun.
456
35-40
2015
Mesorhizobium japonicum (Q988C8)
brenda
Mukherjee, T.; Kinsland, C.; Begley, T.P.
PLP catabolism identification of the 4-pyridoxic acid dehydrogenase gene in Mesorhizobium loti MAFF303099
Bioorg. Chem.
35
458-464
2007
Mesorhizobium loti (Q988H5), Mesorhizobium loti MAFF303099 (Q988H5)
brenda
Ge, F.; Yokochi, N.; Yoshikane, Y.; Ohnishi, K.; Yagi, T.
Gene identification and characterization of the pyridoxine degradative enzyme 4-pyridoxic acid dehydrogenase from the nitrogen-fixing symbiotic bacterium Mesorhizobium loti MAFF303099
J. Biochem.
143
603-609
2008
Mesorhizobium loti (Q988C9), Mesorhizobium loti MAFF303099 (Q988C9)
brenda
Yokochi, N.; Yoshikane, Y.; Matsumoto, S.; Fujisawa, M.; Ohnishi, K.; Yagi, T.
Gene identification and characterization of 5-formyl-3-hydroxy-2-methylpyridine 4-carboxylic acid 5-dehydrogenase, an NAD+-dependent dismutase
J. Biochem.
145
493-503
2009
Mesorhizobium loti (Q988H5), Mesorhizobium loti MAFF303099 (Q988H5), Mesorhizobium loti
brenda
Ge, F.; Yagi, T.
Topology of 4-pyridoxic acid dehydrogenase in transformed Escherichia coli cells
J. Biochem.
147
291-295
2010
Mesorhizobium loti (Q988C9), Mesorhizobium loti MAFF303099 (Q988C9), Mesorhizobium loti
brenda
Yagi, T.; Kishore, G.M.; Snell, E.E.
The bacterial oxidation of vitamin B6. 4-Pyridoxic acid dehydrogenase a membrane-bound enzyme from Pseudomonas MA-1
J. Biol. Chem.
258
9419-9425
1983
Pseudomonas sp. MA-1
brenda
Lee, Y.; Nelson, M.; Snell, E.
Enzymes of vitamin B6 degradation. Purification and properties of isopyridoxal dehydrogenase and 5-formyl-3-hydroxy-2-methylpyridine-4-carboxylic-acid dehydrogenase
J. Biol. Chem.
261
15106-15111
1986
Pseudomonas sp. MA-1
brenda
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