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Information on EC 1.13.11.9 - 2,5-dihydroxypyridine 5,6-dioxygenase
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EC Tree
1.13.11.9 2,5-dihydroxypyridine 5,6-dioxygenaseIUBMB Comments
Requires Fe2+.
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Word Map
- 1.13.11.9
- putida
-
copperi
- dopamine
-
deformylase
-
alpha-hydroxylating
- peptidylglycine
-
beta-monooxygenase
- biotechnology
The expected taxonomic range for this enzyme is: Bacteria, Archaea
Synonyms
2,5-DHP dioxygenase, 2,5-dihydroxypyridine dioxygenase, 2,5-dihydroxypyridine oxygenase, 2,5DHP dioxygenase, EC 1.13.1.9, NicX, NicX protein, oxygenase, 2,5-dihydroxypyridine 5,6-di-, pyridine-2,5-diol dioxygenase, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
2,5-DHP dioxygenase
2,5-dihydroxypyridine dioxygenase
2,5DHP dioxygenase
NicX
NicX protein
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
2,5-dihydroxypyridine + O2 = N-formylmaleamic acid
-
-
-
-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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PATHWAY SOURCE
PATHWAYS
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SYSTEMATIC NAME
IUBMB Comments
2,5-dihydroxypyridine:oxygen 5,6-oxidoreductase
Requires Fe2+.
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CAS REGISTRY NUMBER
COMMENTARY
9029-57-6
-
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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
2,5-dihydroxypyridine + O2
N-formylmaleamic acid
-
aerobic catabolism of nicotinic acid
-
-
?
2,5-dihydroxypyridine + O2
N-formylmaleamic acid
-
extradiol ring-cleavage dioxygenase cleaves between carbons 5 and 6
-
-
?
2,5-dihydroxypyridine + O2
N-formylmaleamic acid
-
aerobic catabolism of nicotinic acid
-
-
?
2,5-dihydroxypyridine + O2
N-formylmaleamic acid
-
extradiol ring-cleavage dioxygenase cleaves between carbons 5 and 6
-
-
?
2,5-dihydroxypyridine + O2 + H2O
maleamate + formate
Gram-negative rod
-
O2 cannot be replaced by methylene blue
-
-
?
2,5-dihydroxypyridine + O2 + H2O
maleamate + formate
-
nicotinic acid catabolism
-
-
?
2,5-dihydroxypyridine + O2 + H2O
maleamate + formate
-
nicotinic acid catabolism
-
-
?
2,5-dihydroxypyridine + O2 + H2O
maleamate + formate
-
strictly specific for 2,5-dihydroxypyridine
-
-
?
2,5-dihydroxypyridine + O2 + H2O
maleamate + formate
-
nicotinic acid catabolism
-
-
?
2,5-dihydroxypyridine + O2 + H2O
N-formylmaleamic acid
-
activation with 10 mM DTT and 0.5 mM FeSO4 (25 min, 25°C)
ring cleavage between carbon 5 and 6, further conversion to formic and maleamic acid is catalyzed by the NicD protein, a deformylase similar to some members of the alpha/beta-hydolase fold superfamily
-
?
2,5-dihydroxypyridine + O2 + H2O
N-formylmaleamic acid
-
activation with 10 mM DTT and 0.5 mM FeSO4 (25 min, 25°C)
ring cleavage between carbon 5 and 6, further conversion to formic and maleamic acid is catalyzed by the NicD protein, a deformylase similar to some members of the alpha/beta-hydolase fold superfamily
-
?
additional information
?
-
-
aerobic nicotinic acid degradation, nice gene cluster is responsible for the aerobic nicotinic acid degradation
-
-
?
additional information
?
-
-
no activity with: 2,3-dihydroxypyridine, 2,4-dihydroxypyridine, 2-hydroxypyridine, 3-hydroxypyridine, 4-hydroxypyridine, NA, 6HNA, 2-carboxypyridine, pyridoxamine, pyridoxal, catechol, protocatechuate, gentisate, gallate, resorcinol, hydroquinone, or pyrogallol
-
-
?
additional information
?
-
-
aerobic nicotinic acid degradation, nice gene cluster is responsible for the aerobic nicotinic acid degradation
-
-
?
additional information
?
-
-
no activity with: 2,3-dihydroxypyridine, 2,4-dihydroxypyridine, 2-hydroxypyridine, 3-hydroxypyridine, 4-hydroxypyridine, NA, 6HNA, 2-carboxypyridine, pyridoxamine, pyridoxal, catechol, protocatechuate, gentisate, gallate, resorcinol, hydroquinone, or pyrogallol
-
-
?
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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
2,5-dihydroxypyridine + O2
N-formylmaleamic acid
-
aerobic catabolism of nicotinic acid
-
-
?
2,5-dihydroxypyridine + O2
N-formylmaleamic acid
-
aerobic catabolism of nicotinic acid
-
-
?
2,5-dihydroxypyridine + O2 + H2O
maleamate + formate
-
nicotinic acid catabolism
-
-
?
2,5-dihydroxypyridine + O2 + H2O
maleamate + formate
-
nicotinic acid catabolism
-
-
?
2,5-dihydroxypyridine + O2 + H2O
maleamate + formate
-
nicotinic acid catabolism
-
-
?
2,5-dihydroxypyridine + O2 + H2O
N-formylmaleamic acid
-
activation with 10 mM DTT and 0.5 mM FeSO4 (25 min, 25°C)
ring cleavage between carbon 5 and 6, further conversion to formic and maleamic acid is catalyzed by the NicD protein, a deformylase similar to some members of the alpha/beta-hydolase fold superfamily
-
?
2,5-dihydroxypyridine + O2 + H2O
N-formylmaleamic acid
-
activation with 10 mM DTT and 0.5 mM FeSO4 (25 min, 25°C)
ring cleavage between carbon 5 and 6, further conversion to formic and maleamic acid is catalyzed by the NicD protein, a deformylase similar to some members of the alpha/beta-hydolase fold superfamily
-
?
additional information
?
-
-
aerobic nicotinic acid degradation, nice gene cluster is responsible for the aerobic nicotinic acid degradation
-
-
?
additional information
?
-
-
aerobic nicotinic acid degradation, nice gene cluster is responsible for the aerobic nicotinic acid degradation
-
-
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Fe2+
Iron
Fe2+
-
one mole per mole enzyme, activation of enzyme with 0.5 mM FeSO4 for 15 min at 25°C, replacement with other divalent cations do not lead to detectable 2,5-dihydroxypyridine dioxygenase activity
Fe2+
-
purified enzyme is inactive, Fe2+-dependent reactivation of the purified enzyme (0.025 mM), 0.0198 mM iron is detected, indicating that the ratio of mol of iron to mol of a monomer of NicX is near 1.0
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
L-cysteine
-
enzyme has a specific requirement for L-cysteine (6.7 mM), required to restore full activity after dialysis or treatment with chelating agents
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
0.13
-
pyridine-2,6-dicarboxylic acid-induced cells of strain 23K8, pH 7.2, 30°C
6
-
pH 8.0, 25°C, in cell extracts of Escherichia coli BL21(DE3) overexpressing the nicX gene
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
25
30
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
-
pyridine-2,6-dicarboxylic acid- and pyridine-2,3-dicarboxylic acid-induced strain 23K8 cells. The cells do not grow on pyridine-2,5-dicarboxylic acid
brenda
-
pyridine-2,6-dicarboxylic acid- and pyridine-2,3-dicarboxylic acid-induced strain 23K8 cells. The cells do not grow on pyridine-2,5-dicarboxylic acid
brenda
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
metabolism
metabolism
-
the enzyme catalyzes the last step of putative pathway of pyridine-2,3-dicarboxylic acid oxidation in Cupriavidus campinensis 23K8
metabolism
-
the enzyme catalyzes the last step of putative pathway of pyridine-2,3-dicarboxylic acid oxidation in Cupriavidus campinensis 23K8
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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). NICX_PSEPK
Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440)
350
0
39017
Swiss-Prot
-
A0A2S6TNC6_9PROT
358
0
39427
TrEMBL
-
A0A1V6JNU2_9BACT
368
0
40386
TrEMBL
-
A0A1V6A3N7_9FIRM
323
0
34281
TrEMBL
-
A0A2P5VLZ2_9PROT
348
0
37887
TrEMBL
-
A0A1V6KJK8_9SPIR
365
0
39289
TrEMBL
-
A0A2S6QNC9_9PROT
54
0
5946
TrEMBL
-
A0A0P8AYJ5_9RHOB
277
0
30298
TrEMBL
-
A0A1V6I304_9BACT
323
0
34879
TrEMBL
-
A0A423K8N9_9PSED
350
0
38704
TrEMBL
-
A0A2S6TNA9_9PROT
358
0
39674
TrEMBL
-
A0A644VRK0_9ZZZZ
355
0
38727
TrEMBL
other Location (Reliability: 2)
A0A1Q9N7G9_ODILC
Odinarchaeota archaeon (strain LCB_4)
348
0
38721
TrEMBL
-
A0A1V5T737_9SPIR
371
0
39840
TrEMBL
-
A0A2S6QF49_9PROT
360
0
39984
TrEMBL
-
A0A2C9D2S5_9RHIZ
347
0
38070
TrEMBL
-
A0A418SIN3_9RHOB
345
0
37970
TrEMBL
-
A0A645E6F3_9ZZZZ
234
0
25893
TrEMBL
other Location (Reliability: 1)
A0A2U9PKR9_MYCSE
Mycolicibacterium smegmatis (strain MKD8)
343
0
37334
TrEMBL
-
A0A2S6R6X5_9PROT
340
0
37395
TrEMBL
-
A0A259UKB1_9FIRM
354
0
38195
TrEMBL
-
A0A2U9PMX3_MYCSE
Mycolicibacterium smegmatis (strain MKD8)
343
0
37259
TrEMBL
-
A0A1Y5SN86_9RHOB
348
0
37960
TrEMBL
-
A0A1V5KAI7_9FIRM
294
0
30764
TrEMBL
-
A0A143X8U5_9ACTN
317
0
33818
TrEMBL
-
A0A1V6EE01_9PROT
94
0
10509
TrEMBL
-
A0A1V5JZ62_9FIRM
246
0
25677
TrEMBL
-
A0A0P0RRE3_9BURK
343
0
37062
TrEMBL
-
A0A347WFI1_9PROT
346
0
37608
TrEMBL
-
A0A1V5SWQ5_9BACT
348
0
38127
TrEMBL
-
A0A0S4IDT4_9PSED
350
0
38976
TrEMBL
-
A0A1V5WE85_9SPIR
372
0
40025
TrEMBL
-
A0A1V6E5W6_9SPIR
365
0
39367
TrEMBL
-
A0A075RI20_BRELA
316
0
33118
TrEMBL
-
A0A2S6RKK4_9PROT
344
0
37821
TrEMBL
-
A0A1V6A2I6_9FIRM
324
0
34081
TrEMBL
-
A0A1V5SXF5_9BACT
323
0
34853
TrEMBL
-
A0A2S6TB08_9PROT
111
0
12652
TrEMBL
-
A0A2S6TT88_9PROT
345
0
37513
TrEMBL
-
A0A1V6E3P5_9SPIR
326
0
36028
TrEMBL
-
A0A644VP57_9ZZZZ
355
0
38976
TrEMBL
other Location (Reliability: 2)
Show AA Sequence and Transmembrane Helices (210 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
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
242000
-
sucrose density gradient centrifugation (+ dithiothreitol)
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
hexamer
monomer
hexamer
-
6 * 38 883, a hexameric assembly composed of two cyclic trimers, gel filtration and mass spectrometry
hexamer
-
6 * 38 883, a hexameric assembly composed of two cyclic trimers, gel filtration and mass spectrometry
monomer
-
1 * 39000, amino acid sequence similarity to aminopeptidase S from Staphylococcus aureus and aminopeptidase T from Thermus thermophilus, 2 globular domains
monomer
-
1 * 39000, amino acid sequence similarity to aminopeptidase S from Staphylococcus aureus and aminopeptidase T from Thermus thermophilus, 2 globular domains
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified recombinant NicX, hanging drop vapour diffusion method, 0.001 ml of 14 mg/ml protein in 20 mM HEPES pH 7.5, 0.1 M NaCl, and 2 mM DTT, is mixed with 0.001 ml of reservoir solution, containing 22% w/v PEG 4000, 0.1 M sodium acetate and 0.1 M HEPES pH 7.5, 2 mM DTT, and with 1 ml 50 mM EDTA, 18°C, method optimization, X-ray diffraction structure determination and analysis at 2.0 A resolution
-
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
-
nic gene cluster knockout mutants do not grow on nicotinic acid as sole carbon source in contrary to the wild-type, this ability can be restored by introducing a broad-host-range plasmid harboring a 14 kb DNA cassette containing the complete nice cluster, NicX knockout mutant does not show 2,5DHP dioxygenase activity
additional information
-
nic gene cluster knockout mutants do not grow on nicotinic acid as sole carbon source in contrary to the wild-type, this ability can be restored by introducing a broad-host-range plasmid harboring a 14 kb DNA cassette containing the complete nice cluster, NicX knockout mutant does not show 2,5DHP dioxygenase activity
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
combination of dithiothreitol and FeSO4 is detrimental during long-term incubation at 0°C
-
incubation with or dialysis against 0.001 mM 8-hydroxyquinoline and by (NH4)2SO4 fractionation: complete loss of activity
-
L-cysteine: enzyme has a specific requirement for L-cysteine, 6.7 mM, required to restore full activity after dialysis or treatment with chelating agents
-
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OXIDATION STABILITY
ORGANISM
UNIPROT
LITERATURE
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
0°C, 20 mM sodium phosphate, pH 7.5, half-life: 2-3 days, addition of dithiothreitol extends half-life to about 2 weeks
-
4°C, purified recombinant enzyme, 20 mM HEPES pH 7.5, 0.1 M NaCl, and 2 mM DTT, maintains its activity for several days
-
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
Escherichia coli cells overexpressing NicX are harvested and disrupted by passage through a French press, supernatant applied to DEAE-cellulose column with 50 mM NaH2PO4 buffer, pH 7.5, washed with buffer (0.1-0.3 M) containing 0.1 M NaCl, fraction with 2,5-dihydroxypyridine deoxygenase activity pooled and dialyzed with 20 mM NaH2PO4 buffer, pH 7.5, loaded onto hydroxyapatite column, eluted with 20-100 mM NaH2PO4 buffer, pH 7.0, fractions with enzyme activity pooled, dialyzed in 20 mM NaH2PO4 buffer, pH 7.5, and concentrated
-
recombinant enzyme from Escherichia coli strain BL21(DE3) by anion exchange and hydroxyapatite chromatography
-
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
PCR-amplification of nicX gene, overexpression of nix gene in Escherichia coli BL21(DE3) cells with plasmid pETNicX, for knockout mutants transformation of pKnicX plasmid into Pseudomonas putida KT2440 as recipient, using Escherichia coli DH10B(pKnicX) as donor strain, Escherichia coli HB101 (pRK600) as helper strain
-
the nicX gene is overexpressed in Escherichia coli BL21(DE3) cells containing plasmid pETNicX
-
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
biotechnology
biotechnology
-
the enzyme catalyzes one step in a new process of detoxification/biotransformation of N-heterocyclic aromatic compounds
biotechnology
-
the enzyme catalyzes one step in a new process of detoxification/biotransformation of N-heterocyclic aromatic compounds
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Behrman, E.J.; Stanier, R.Y.
The bacterial oxidation of nicotinic acid
J. Biol. Chem.
228
923-945
1957
Pseudomonas fluorescens
brenda
Nozaki, M.
Nonheme iron dioxygenase
Mol. Mech. Oxygen Activ. (Hayaishi, O., ed.) Academic Press, New York
135-165
1974
Pseudomonas putida
-
brenda
Gauthier, J.J.; Rittenberg, S.C.
The metabolism of nicotinic acid. I. Purification and properties of 2,5-dihydroxypyridine oxygenase from Pseudomonas putida N-9
J. Biol. Chem.
246
3737-3742
1971
Pseudomonas putida
brenda
Orpin, C.G.; Knight, M.; Evans, W.C.
The bacterial oxidation of picolinamide, a photolytic product of Diquat
Biochem. J.
127
819-831
1972
Gram-negative rod
brenda
Cain, R.B.; Houghton, C.; Wright, K.A.
Microbial metabolism of the pyridine ring. Metabolism of 2- and 3-hydroxypyridines by the maleamate pathway in Achromobacter sp
Biochem. J.
140
293-300
1974
Achromobacter sp.
brenda
Jimenez, J.; Canales, A.; Jimenez-Barbero, J.; Ginalski, K.; Rychlewski, L.; Garcia, J.; Diaz, E.
Deciphering the genetic determinants for aerobic nicotinic acid degradation: The nic cluster from Pseudomonas putida KT2440
Proc. Natl. Acad. Sci. USA
105
11329-11334
2008
Pseudomonas putida, Pseudomonas putida KT 2240
brenda
Jimenez, J.I.; Acebron, I.; Garcia, J.L.; Diaz, E.; Mancheno, J.M.
A preliminary crystallographic study of recombinant NicX, an Fe2+-dependent 2,5-dihydroxypyridine dioxygenase from Pseudomonas putida KT2440
Acta Crystallogr. Sect. F
66
549-553
2010
Pseudomonas putida, Pseudomonas putida KT 2240
brenda
Kutanovas, S.; Karvelis, L.; Vaitekunas, J.; Stankeviciute, J.; Gasparaviciute, R.; Meskys, R.
Isolation and characterization of novel pyridine dicarboxylic acid-degrading microorganisms
Chemija
27
74-83
2016
Cupriavidus campinensis, Cupriavidus campinensis 23K8
-
brenda
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