Information on EC 1.17.1.8 - 4-hydroxy-tetrahydrodipicolinate reductase

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The expected taxonomic range for this enzyme is: Bacteria, Eukaryota

EC NUMBER
COMMENTARY hide
1.17.1.8
-
RECOMMENDED NAME
GeneOntology No.
4-hydroxy-tetrahydrodipicolinate reductase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
(S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + NAD(P)+ + H2O = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + NAD(P)H + H+
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
oxidation
-
-
-
-
redox reaction
-
-
-
-
reduction
-
-
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
L-lysine biosynthesis I
-
-
L-lysine biosynthesis II
-
-
L-lysine biosynthesis III
-
-
L-lysine biosynthesis VI
-
-
lysine metabolism
-
-
Monobactam biosynthesis
-
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Lysine biosynthesis
-
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Metabolic pathways
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Biosynthesis of secondary metabolites
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Microbial metabolism in diverse environments
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Biosynthesis of antibiotics
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SYSTEMATIC NAME
IUBMB Comments
(S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate:NAD(P)+ 4-oxidoreductase
Studies [2] of the enzyme from the bacterium Escherichia coli have shown that the enzyme accepts (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate and not (S)-2,3-dihydrodipicolinate as originally thought [1].
CAS REGISTRY NUMBER
COMMENTARY hide
9055-46-3
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
UniProt
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
PCI 219
-
-
Manually annotated by BRENDA team
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SwissProt
Manually annotated by BRENDA team
ATCC 10068 and asporogenic mutant BH 7
-
-
Manually annotated by BRENDA team
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SwissProt
Manually annotated by BRENDA team
-
SwissProt
Manually annotated by BRENDA team
recombinant enzyme
SwissProt
Manually annotated by BRENDA team
NCTC 9602
-
-
Manually annotated by BRENDA team
-
SwissProt
Manually annotated by BRENDA team
wild-type GR4 and natural mutant strain GR45B
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-
Manually annotated by BRENDA team
methicillin-resistant strain, MRSA-DHDPR, gene dapB
-
-
Manually annotated by BRENDA team
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Uniprot
Manually annotated by BRENDA team
Thermotoga maritima MSB8 / DSM 3109 / ATCC 43589
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Uniprot
Manually annotated by BRENDA team
-
UniProt
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
metabolism
physiological function
additional information
-
NMR studies uncover that dihydrodipicolinate reductase is also a dehydratase, overview
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
(2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + NAD(P)H + H+
(S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + NAD(P)+ + H2O
show the reaction diagram
(2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + NADH + H+
(S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + NAD+ + H2O
show the reaction diagram
(2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + NADPH + H+
(S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + NADP+ + H2O
show the reaction diagram
(S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + NAD(P)+ + H2O
(2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + NAD(P)H + H+
show the reaction diagram
(S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + NAD+ + H2O
(2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + NADH + H+
show the reaction diagram
(S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + NADP+ + H2O
(2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + NADPH + H+
show the reaction diagram
2,3-dihydrodipicolinate + NAD(P)H
2,3,4,5-tetrahydrodipicolinate + NAD(P)+
show the reaction diagram
2,3-dihydrodipicolinate + reduced 3-acetylpyridine adenine dinucleotide
2,3,4,5-tetrahydrodipicolinate + oxidized 3-acetylpyridine adenine dinucleotide
show the reaction diagram
-
-
-
?
dihydrodipicolinate + NADH + H+
tetrahydrodipicolinate + NAD+
show the reaction diagram
-
substrate dihydrodipicolinate is instable
-
-
?
pyridine dicarboxylate + NADH + H+
reduced pyridine dicarboxylate + NAD+
show the reaction diagram
-
stable substrate analog, 25 mM phosphate D2O (deuterium water) buffer, pH 7.8 for NMR analysis of binding interactions with saturation transfer difference titration studies at 298 K (25°C)
-
-
?
additional information
?
-
-
DHDPR accepts (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinic acid as true substrate rather than dihydrodipicolinate, suggesting that DHDPR catalyzes an overall deoxygenation reaction, likely by a dehydratase-reductase route, substrate specificity, overview. A critical role is played by residue His 159 in the catalytic mechanism of DHDPR. Replacement of this residue with an alanine or a glutamine is reported to result in a 150-200fold reduction in catalytic rate as well as a 6fold increase in KM. His 159 has been proposed to act as a general acid during catalysis, providing the proton required after hydride addition. No activity with beta-hydroxypyruvate and 3-fluoropyruvate
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-
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NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
(2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + NAD(P)H + H+
(S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + NAD(P)+ + H2O
show the reaction diagram
(S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + NAD(P)+ + H2O
(2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + NAD(P)H + H+
show the reaction diagram
2,3-dihydrodipicolinate + NAD(P)H
2,3,4,5-tetrahydrodipicolinate + NAD(P)+
show the reaction diagram
dihydrodipicolinate + NADH + H+
tetrahydrodipicolinate + NAD+
show the reaction diagram
-
substrate dihydrodipicolinate is instable
-
-
?
additional information
?
-
-
DHDPR accepts (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinic acid as true substrate rather than dihydrodipicolinate, suggesting that DHDPR catalyzes an overall deoxygenation reaction, likely by a dehydratase-reductase route, substrate specificity, overview. A critical role is played by residue His 159 in the catalytic mechanism of DHDPR. Replacement of this residue with an alanine or a glutamine is reported to result in a 150-200fold reduction in catalytic rate as well as a 6fold increase in KM. His 159 has been proposed to act as a general acid during catalysis, providing the proton required after hydride addition. No activity with beta-hydroxypyruvate and 3-fluoropyruvate
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
additional information
-
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate
(4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate
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-
1,10-phenanthroline
2,3-dihydrodipicolinate
the enzyme is inhibited by high concentrations of 2,3-dihydrodipicolinate
2,6-pyridine dicarboxylate
-
stable analog of the dihydrodipicolinate substrate, the binding affinity is not affected by the presence of NADH or NAD+
2,6-pyridinedicarboxylate
competitive, binding site structure
2,6-pyridinedicarboxylic acid
2-pyridine carboxylic acid
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-
3-acetyl-NAD+
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-
alpha-picolinic acid
catechol rhodanine acetic acid
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binds to the NADH cofactor site
DELTA3-tetrahydroisophthalic acid
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moderate inhibition
dihydrodipicolinate
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the enzyme is inhibited by high concentrations of dihydrodipicolinate when using NADPH as a cofactor, but not with NADH
dipicolinate
isocinchomeronic acid
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Isophthalic acid
L-Pipecolic acid
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higher concentration
NADP+
pyridine 2,6-dicarboxylic acid
sulfonamide derivatives
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-
additional information
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
aspartate-beta-semialdehyde
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crude extract
NADPH
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similar affinity as NADH
pyruvate
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crude extract
additional information
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0031 - 3.6
(2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate
0.529
(4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate
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-
0.0076 - 0.013
2,3-dihydrodipicolinate
0.08
3'-NADPH
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-
0.004
3-acetylpyridine
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-
0.052
alpha-NADPH
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-
0.009 - 0.77
dihydrodipicolinate
0.05
L-dihydrodipicolinate
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-
0.0005 - 0.31
NADH
0.0006 - 0.83
NADPH
0.009
nicotinamide hypoxanthine dinucleotide phosphate reduced
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-
0.0021
thio-NADPH
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-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
14 - 77
(2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate
8.1 - 19
2,3-dihydrodipicolinate
0.093 - 21
NADH
2.6 - 17
NADPH
additional information
additional information
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-
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Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.032 - 5.5
(2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate
0.435
(4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate
-
-
0.33
2,6-pyridinedicarboxylic acid
-
-
0.085 - 0.9
dipicolinate
5.5 - 15
Isophthalic acid
0.0051 - 0.0081
NADH
24
NADP+
-
-
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.01 - 0.079
-
depending on growth phase, similar course but lower activity for asporogenic mutant BH 7
0.029
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during stationary phase
0.04
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during late exponential phase
1.153
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pH 7.5, 30°C, recombinant enzyme
10.1
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purified recombinant enzyme, pH not specified in the publication, temperature not specified in the publication
56.4
-
purified enzyme
135
-
purified enzyme
300
-
purified enzyme
398
-
purified enzyme
additional information
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5.2 - 7.5
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6.5 - 7.5
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7 - 9
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at pH 7.0 and 9.0, approyimately 75% and 90% of the enzymatic activity is retained. Below pH 7.0 and above pH 9.0 a significant drop in activity is observed. At pH 11.0 an almost complete loss of activity is observed
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
30 - 50
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at 30°C and 50°C, approximately 57% and 85% of the enzymatic activity is retained. Between 50 and 60°C a fast decrease in activity is observed with increasing temperature. Complete loss of activity occurs above 60°C
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
-
specifically expressed in leaves
Manually annotated by BRENDA team
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-
Manually annotated by BRENDA team
additional information
-
not found in roots
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
additional information
-
not in the thylakoid membranes
-
Manually annotated by BRENDA team
PDB
SCOP
CATH
UNIPROT
ORGANISM
Q3MFY8
Anabaena variabilis (strain ATCC 29413 / PCC 7937);
Q8LB01
Arabidopsis thaliana;
Q6G2G3
Bartonella henselae (strain ATCC 49882 / DSM 28221 / Houston 1);
Q2SZ94
Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CIP 106301 / E264);
Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025);
P24703
Coxiella burnetii (strain RSA 493 / Nine Mile phase I);
Escherichia coli (strain K12);
Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra);
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv);
Q5F5Y7
Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090);
Q9K1F1
Neisseria meningitidis serogroup B (strain MC58);
P38103
Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1);
Q5HG24
Staphylococcus aureus (strain COL);
Q9X1K8
Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099);
Vibrio vulnificus (strain CMCP6);
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
18500
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4 * 18500, SDS-PAGE
26668
-
4 * 26668, mass spectrometry and gel filtration
27622
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4 * 27622, calculated from amino acid sequence; 4 * 27622, ESI-TOF mass spectrometry
28500
x * 28500, calculated
28798
-
4 * 28798, nucleotide sequence
28820
-
by MALDI-TOF mass spectrometry; MALDI-TOF, 28756 Da expected
29200
-
predicted molecular weight of mature CRR1
30000
-
4 * 30000, His-tagged enzyme, SDS-PAGE
30780
SDS-PAGE
34000
-
? * 34000, SDS-PAGE
62900
calculated
74000
-
gel filtration
80000 - 84000
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gel filtration
110000
113000
calculated
114000
size-exclusion chromatography
120000
-
gel filtration
139000
analytical ultracentrifugation
150000
-
gel filtration
155000
-
gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
homotetramer
monomer
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x * 28000, SDS-PAGE
tetramer
additional information
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
crystals are grown using the hanging-drop vapour-diffusion method. The crystals belong to the orthorhombic space group P222, with unit-cell parameters a: 80.0, b: 100.8, c: 147.6 A, and contain four molecules in the asymmetric unit
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crystal structure is determined at 1.92 A
vapour-diffusion method
sitting-drop vapor-diffusion, protein crystals are grown in conditions consisting of 5%(w/v) PEG 4000, 200 mM sodium acetate, 100 mM sodium citrate tribasic pH 5.5 and are shown to diffract to about 2.3 A resolution. They belong to space group P4(3)22, with unit cell parameters a = 109.38, b = 109.38, c = 176.95 A
crystal structure of the enzyme in the apoform and in complex with its cofactor NADP+, determined at 2.5 A resolution. The crystal belongs to the I4(1)22 space group, and the asymmetric unit of the crystal contains two CgDapB molecules; crystal structure of the enzyme in the apoform and in complex with its cofactor NADP+, hanging-drop vapor-diffusion method at 20°C, crystal structure of the enzyme is determined at 2.5 A resolution
hanging drop vapour diffusion method, crystal structure x-ray analysis and binding study with NADPH, NADH, 3-acetyl-NADH, and reduced nicotinamide hypoxanthine dinucleotide phosphate and other pyridine nucleotide derivatives in complex with the enzyme
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R-factor 18.6%, structure model of enzyme complexed with NADPH, analysis of cofactor binding site
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R-factor 21.4%, three-dimensional structure analysis , homotetramer with 3 molecules of NADH, 3 molecules of inhibitor 2,6-pyridinedicarboxylic acid, 1 phosphate ion and 186 water molecules per asymmetric unit in the model
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in complex with NADH
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purified recombinant wild-type enzyme in ternary complex with inhibitor 2,6-pyridinedicarboxylate and NADH or NADPH, hanging drop vapour diffusion method, room temperature, 0.003 ml protein solution containing 20 mg/ml enzyme, 2 mM NADH or NADPH, and 30 mM 2,6-pyridinedicarboxylate, mixed with 0.003 ml precipitant solution containing 2.2 M ammonium sulfate, 0.1 M HEPES, pH 7.5, 3% PEG 400, 3 days, X-ray diffraction strcuture determination at 16°C and 2.2 A resolution and analysis
sitting-drop vapour-diffusion method
purified recombinant enzyme, sitting-drop vapour-diffusion method, 100 ml drops of 9-10 mg/ml protein in 20 mM Tris-HCl, pH 8.0, and 150 mM NaCl with 10 mM 2,6-PDC and 10 mM NADPH are mixed with 100 ml of reservoir solution containing 2.4 M ammonium sulfate, 0.2 M sodium fluoride, and 0.1 M bis-tris propane, pH 7.5, and ethanol added to 10% v/v, 8°C, X-ray diffraction structure determination and analysis at 3.65 A resolution
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using 2.0 M ammonium sulfate and 0.2 M sodium acetate pH 4.5
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
45
-
5 min, 31% activity
65
-
both the native and His-tagged recombinant enzymes show an apparent melting temperature of approximately 65°C
70
-
3 min stable
80 - 95
the enzyme is stable for up to 48 h at 80°C, the melting temperature of DHDPR is at 95.7°C
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-15°C, several months
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-20°C, 0.04 M Tris buffer, pH 8.1, precipitate in 65% w/v ammonium sulfate, several months
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
cells grown in M9 medium containing 2H, 15N, and 13C-labeled sources, collected, lysed, and protein purified with a QA52 anion exchange column and a Blue Trisacryl affinity column with gravity gradient chromatography, fractions with activity pooled and concentrated using an Amicon ultrafiltration device with YM10 membrane, desalted and loaded onto the Blue Trisacryl affinity column and eluted with a linear gradient of 0-2 M NaCl, 25 mM Tris buffer, pH 7.5, pooled, concentrated and buffer ecxchanged; protein is purified using a QA52 anion exchange column and a Blue Trisacryl affinity column with gravity gradient chromatography
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His-Trap column chromatography
Ni-NTA agarose column chromatography
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Ni2+ affinity column chromatography and Superose 12 gel filtration
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Ni2+-NTA affinity column chromatography and DEAE-Sepharose column chromatography
overexpression in Escherichia coli from plasmid
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partial
purified from wild-type
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recombinant enzyme 5.9fold from Escherichia coli BL21(DE3) by ion-exchange and hydrophobic interaction chromatography, and gel filtration
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recombinant enzyme expressed in Escherichia coli
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
dapB gene, expression in and complementation of a deficient Escherichia coli strain, sequence analysis, 53% sequence identity with Escherichia coli gene
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dapB gene, expression in Escherichia coli
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dapB gene, overexpression from plasmid in Escherichia coli
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dapB gene, sequence determination, expression in Escherichia coli from plasmids
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expressed in Escherichia coli
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expressed in Escherichia coli (BL21); expression of pET11a expression construct in Escherichia coli (BL21)
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expressed in Escherichia coli BL21 (DE3)
expressed in Escherichia coli BL21(DE3) cells
expressed in Escherichia coli XL-1 Blue cells
expression in an Escherichia coli B834 strain
expression in Escherichia coli as His-tagged construct
expression in Escherichia coli BL21 (DE3) cells
expression in Escherichia coli BL21 (DE3) R3 Rosetta cells
expression of the histidine-tagged enzyme in Escherichia coli BL21 (DE3)
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functional complementation in Escherichia coli
gene dapB from strain MRSA252, expression in Escherichia coli BL21(DE3)
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gene dapB, expression of wild-type and mutant enzymes in Escherichia coli strain BL21(DE3)
subclone of gene dapB overexpressed in Corynebacterium glutamicum irrespective of orientation of the insert in the expression vector
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the dapB open reading frame is cloned in the expression vector pET28a for expression as N-terminal 6x His-tagged protein
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
K11A
site-directed mutagenesis, increased activity with and specificty for NADH as cofactor, reduced activity with NADPH compared to the wild-type enzyme
K9A
site-directed mutagenesis, increased specificty for NADH as cofactor, reduced activity with NADPH compared to the wild-type enzyme
additional information
-
natural mutant strain GR45B with an additional plasmid encoded dapB gene evokes a different phenotype in alfalfa plants after nodulation, yellow plants in nitrogen-free medium
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
agriculture
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potential herbicide target, leads for herbicide development are inhibitors: dipicolinic acid, isophthalic acid, and DELTA3-tetrahydroisophthalic acid
drug development
-
enzyme is a potential target for new antimicrobial and herbicidal compounds
medicine
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