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IUBMB Comments This is the last common enzyme in the biosynthesis of chlorophylls and heme . Two isoenzymes exist in plants: one in plastids and the other in mitochondria. This is the target enzyme of phthalimide-type and diphenylether-type herbicides . The enzyme from oxygen-dependent species contains FAD . Also slowly oxidizes mesoporphyrinogen IX.
The taxonomic range for the selected organisms is: Bacillus subtilis The enzyme appears in selected viruses and cellular organisms
Synonyms
protoporphyrinogen oxidase, ppox, protox, protoporphyrinogen ix oxidase, mtppo, protox enzyme, protoporphyrinogen oxidase ix,
ppo1-1 , ppox i, protein yfex,
more
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protoporphyrinogen IX oxidase
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protoporphyrinogen IX oxidase
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protoporphyrinogen oxidase
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protoporphyrinogenase
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PPO
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protox
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protoporphyrinogen-IX:oxygen oxidoreductase
This is the last common enzyme in the biosynthesis of chlorophylls and heme [8]. Two isoenzymes exist in plants: one in plastids and the other in mitochondria. This is the target enzyme of phthalimide-type and diphenylether-type herbicides [8]. The enzyme from oxygen-dependent species contains FAD [9]. Also slowly oxidizes mesoporphyrinogen IX.
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protoporphyrinogen IX + 3 O2
protoporphyrin + 3 H2O2
protoporphyrinogen IX + 3 O2
protoporphyrin IX + 3 H2O2
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protoporphyrinogen IX + O2
protoporphyrin IX + H2O
20fold lower activity with protoporphyrinogen IX compared to coproporphyrinogen III
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protoporphyrinogen-IX + 3 O2
protoporphyrin-IX + 3 H2O2
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coproporphyrinogen-III + 3 O2
coproporphyrin-III + 3 H2O2
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mesoporphyrinogen-IX + 3 O2
mesoporphyrin-IX + 3 H2O2
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protoporphyrinogen IX + 3 O2
protoporphyrin + 3 H2O2
protoporphyrinogen-IX + 3 O2
protoporphyrin-IX + 3 H2O2
additional information
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protoporphyrinogen IX + 3 O2
protoporphyrin + 3 H2O2
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protoporphyrinogen IX + 3 O2
protoporphyrin + 3 H2O2
Bacillus subtilis PPO shows a broad substrate specificity involving residue Y366 at a site adjacent to substrate and FAD cofactor, modeling and docking studies and structure-function relationship, overview
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protoporphyrinogen IX + 3 O2
protoporphyrin + 3 H2O2
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protoporphyrinogen IX + 3 O2
protoporphyrin + 3 H2O2
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PPO catalyzes the oxygen-dependent six-electron oxidation of protoporphyrinogen IX, i.e. protogen IX, to the fully conjugated macrocycle of protoporphyrin IX, i.e. proto IX
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protoporphyrinogen-IX + 3 O2
protoporphyrin-IX + 3 H2O2
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protoporphyrinogen-IX + 3 O2
protoporphyrin-IX + 3 H2O2
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protoporphyrinogen-IX + 3 O2
protoporphyrin-IX + 3 H2O2
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protoporphyrinogen-IX + 3 O2
protoporphyrin-IX + 3 H2O2
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penultimate step of heme and chlorophyll biosynthesis
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protoporphyrinogen-IX + 3 O2
protoporphyrin-IX + 3 H2O2
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penultimate step of heme and chlorophyll biosynthesis
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protoporphyrinogen-IX + 3 O2
protoporphyrin-IX + 3 H2O2
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penultimate step before the chlorophyl and heme synthesis diverge in plants
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additional information
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bsPPO has a broader substrate specificity compared to other PPOs, substrate binding structure comparison of wild-type and mutant enzymes, overview
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additional information
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bsPPO has a broader substrate specificity compared to other PPOs, substrate binding structure comparison of wild-type and mutant enzymes, overview
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protoporphyrinogen IX + 3 O2
protoporphyrin + 3 H2O2
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protoporphyrinogen IX + 3 O2
protoporphyrin IX + 3 H2O2
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protoporphyrinogen IX + O2
protoporphyrin IX + H2O
20fold lower activity with protoporphyrinogen IX compared to coproporphyrinogen III
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protoporphyrinogen-IX + 3 O2
protoporphyrin-IX + 3 H2O2
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protoporphyrinogen IX + 3 O2
protoporphyrin + 3 H2O2
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protoporphyrinogen-IX + 3 O2
protoporphyrin-IX + 3 H2O2
protoporphyrinogen-IX + 3 O2
protoporphyrin-IX + 3 H2O2
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penultimate step of heme and chlorophyll biosynthesis
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protoporphyrinogen-IX + 3 O2
protoporphyrin-IX + 3 H2O2
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penultimate step of heme and chlorophyll biosynthesis
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protoporphyrinogen-IX + 3 O2
protoporphyrin-IX + 3 H2O2
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penultimate step before the chlorophyl and heme synthesis diverge in plants
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FAD
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FAD
a FAD molecule is non-covalently bound to domain I, binding structure, overview
FAD
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FAD
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noncovalently bound
FAD
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protoporphyrinogen oxidase is a FAD-containing enzyme
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NaCl
inhibits recombinant wild-type enzyme and mutant V311M
oxyfluorfen
a diphenyl ether herbicide, competitive, the mutant V311M is slightly less sensitive to inhibition than the wild-type enzyme, inhibition kinetics
acifluorfen-methyl
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weak
carfentrazone-ethyl
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22% less inhibition is found in T3 transgenic lines
oxyfluorfen
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26% less inhibition is found in T3 transgenic lines
acifluorfen
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acifluorfen
a herbicide, binding structure, overview
acifluorfen
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no inhibition at 0.1 mM
acifluorfen
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competitive inhibition with respect to protoporphyrinogen IX
additional information
Bacillus subtilis PPO is unique because of its resistance to inhibition by diphenylethers involving residue Y366 at a site adjacent to substrate and FAD cofactor, modeling and docking studies, overview
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additional information
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Bacillus subtilis PPO is unique because of its resistance to inhibition by diphenylethers involving residue Y366 at a site adjacent to substrate and FAD cofactor, modeling and docking studies, overview
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additional information
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inhibited by diphenylether herbicides
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imidazole
activates recombinant wild-type enzyme and mutant V311M
Tween 20
activates recombinant wild-type enzyme and mutant V311M
n-octylglucopyranoside
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1 mM results in maximal activity
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0.00067 - 0.00354
protoporphyrinogen IX
0.0032
protoporphyrinogen-IX
recombinant wild-type enzyme and recombinant mutant V311M, pH 7.4, 25°C
0.0053
Coproporphyrinogen-III
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0.0049
Mesoporphyrinogen-IX
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0.007
protoporphyrinogen IX
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pH 7.5, 25°C
0.001 - 0.0063
protoporphyrinogen-IX
additional information
additional information
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steady-state kinetics, overview
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0.00067
protoporphyrinogen IX
pH 7.5, 22°C, recombinant wild-type enzyme
0.001
protoporphyrinogen IX
mutant F227R, pH 7.5, temperature not specified in the publication
0.001
protoporphyrinogen IX
mutant I176A, pH 7.5, temperature not specified in the publication
0.001
protoporphyrinogen IX
mutant K71A, pH 7.5, temperature not specified in the publication
0.001
protoporphyrinogen IX
mutant P64A, pH 7.5, temperature not specified in the publication
0.001
protoporphyrinogen IX
wild-type enzyme, pH 7.5, temperature not specified in the publication
0.00107
protoporphyrinogen IX
pH 7.5, 22°C, recombinant mutant Y366A
0.00234
protoporphyrinogen IX
pH 7.5, 22°C, recombinant mutant Y366E
0.00354
protoporphyrinogen IX
pH 7.5, 22°C, recombinant mutant Y366H
0.001
protoporphyrinogen-IX
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0.0063
protoporphyrinogen-IX
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0.00015 - 0.0181
protoporphyrinogen IX
12.9 - 14.1
protoporphyrinogen-IX
0.000833
Coproporphyrinogen-III
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0.0448
Mesoporphyrinogen-IX
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0.00000783 - 0.00317
protoporphyrinogen-IX
0.00015
protoporphyrinogen IX
pH 7.5, 22°C, recombinant mutant Y366E
0.0004
protoporphyrinogen IX
mutant K71A, pH 7.5, temperature not specified in the publication
0.00042
protoporphyrinogen IX
pH 7.5, 22°C, recombinant mutant Y366A
0.001
protoporphyrinogen IX
mutant I176A, pH 7.5, temperature not specified in the publication
0.0016
protoporphyrinogen IX
pH 7.5, 22°C, recombinant mutant Y366H
0.0027
protoporphyrinogen IX
mutant P64A, pH 7.5, temperature not specified in the publication
0.0034
protoporphyrinogen IX
pH 7.5, 22°C, recombinant wild-type enzyme
0.0131
protoporphyrinogen IX
wild-type enzyme, pH 7.5, temperature not specified in the publication
0.0181
protoporphyrinogen IX
mutant F227R, pH 7.5, temperature not specified in the publication
12.9
protoporphyrinogen-IX
recombinant mutant V311M, pH 7.4, 25°C
14.1
protoporphyrinogen-IX
recombinant wild-type enzyme, pH 7.4, 25°C
0.00000783
protoporphyrinogen-IX
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0.00317
protoporphyrinogen-IX
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0.016 - 0.784
protoporphyrinogen IX
0.016
protoporphyrinogen IX
mutant K71A, pH 7.5, temperature not specified in the publication
0.027
protoporphyrinogen IX
mutant I176A, pH 7.5, temperature not specified in the publication
0.057
protoporphyrinogen IX
mutant P64A, pH 7.5, temperature not specified in the publication
0.464
protoporphyrinogen IX
mutant F227R, pH 7.5, temperature not specified in the publication
0.784
protoporphyrinogen IX
wild-type enzyme, pH 7.5, temperature not specified in the publication
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0.029 - 0.154
acifluorfen
0.011 - 0.0177
oxyfluorfen
0.029
acifluorfen
pH 7.5, 22°C, recombinant mutant Y366A
0.033
acifluorfen
pH 7.5, 22°C, recombinant wild-type enzyme
0.053
acifluorfen
pH 7.5, 22°C, recombinant mutant Y366H
0.154
acifluorfen
pH 7.5, 22°C, recombinant mutant Y366E
0.011
oxyfluorfen
recombinant wild-type enzyme, pH 7.4, 25°C
0.0177
oxyfluorfen
recombinant mutant V311M, pH 7.4, 25°C
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0.133 - 0.617
acifluorfen
0.133
acifluorfen
Bacillus subtilis
pH 7.5, 22°C, recombinant mutant Y366H
0.173
acifluorfen
Bacillus subtilis
pH 7.5, 22°C, recombinant mutant Y366A
0.183
acifluorfen
Bacillus subtilis
pH 7.5, 22°C, recombinant wild-type enzyme
0.617
acifluorfen
Bacillus subtilis
pH 7.5, 22°C, recombinant mutant Y366E
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additional information
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additional information
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7.4
recombinant wild-type enzyme
7.5
assay at
7.5
recombinant mutant V311M
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22
assay at room temperature
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SwissProt
brenda
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Bacillus subtilis PPO is unique among PPO family members in that it is a soluble monomer
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brenda
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malfunction
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when PPO is inhibited, protoporphyrin IX accumulates to cause light-dependent membrane damage
metabolism
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protoporphyrinogen oxidase acts in the tetrapyrrole biosynthetic pathway that leads to the formation of both heme and chlorophylls
physiological function
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protoporphyrinogen oxidase is one of the most important action targets of commercial herbicides
metabolism
protoporphyrinogen IX oxidase is the last common enzyme of heme and chlorophyll biosynthesis
metabolism
PPO plays an important part in the heme/chlorophyll biosynthetic pathway
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53000
x * 53000, SDS-PAGE
56000
x * 56000, recombinant wild-type enzyme and mutant V311M, SDS-PAGE
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monomer
Bacillus subtilis PPO is unique among PPO family members in that it is a soluble monomer
monomer
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gel filtration, SDS-PAGE
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x * 53000, SDS-PAGE
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x * 56000, recombinant wild-type enzyme and mutant V311M, SDS-PAGE
additional information
modeling and docking studies and structure-function relationship, overview. Homology modelling and structure comparisons, overview
additional information
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modeling and docking studies and structure-function relationship, overview. Homology modelling and structure comparisons, overview
additional information
prototypical PPO enzyme structure consists of three domains: a FAD-binding domain, a substrate binding domain and a membrane-binding domain, structure analysis and comparison, overview
additional information
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prototypical PPO enzyme structure consists of three domains: a FAD-binding domain, a substrate binding domain and a membrane-binding domain, structure analysis and comparison, overview
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purified native and SeMet-labeled enzyme in complex with inhibitor acifluorfen, sitting-drop, vapor-diffusion method, 10 mg/ml wild-type bsPPO protein in 50 mM TrisHCl, pH 7.5, 200 mM sodium chloride, 5 mM DTT, 1 mM EDTA, and acifluorfen in a 1:5 ratio, equilibrating against a reservoir solution of 2.4 M ammonium phosphate dibasic, 0.1 M Tris-HCl, pH 7.5, 1 week, 20°C, X-ray diffraction structure determination and analysis at 2.8-3.5 A resolution
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F227R
the mutant shows reduced activity compared to the wild-type enzyme
I176A
the mutant shows reduced activity compared to the wild-type enzyme
K71A
the mutant shows reduced activity compared to the wild-type enzyme
P64A
the mutant shows reduced activity compared to the wild-type enzyme
V311M
site-directed mutagenesis, mutant shows similar kinetics compared to the wild-type enzyme, but slightly decreased activity dependent on pH, and NaCl, Tween 20, and imidazole concentrations
Y366A
site-directed mutagenesis, the mutant enzyme shows 10% of wild-type enzyme activity
Y366E
site-directed mutagenesis, the mutant enzyme shows 1% of wild-type enzyme activity
Y366H
site-directed mutagenesis, the mutant enzyme shows 10% of wild-type enzyme activity
additional information
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construction of transgenic Oryza sativa plants, enzyme is targeted to the cytoplasm or the chloroplasts, mutant plant show higher enzyme and photosynthetic activities, phenotype alterations compared to wild-type plants, e.g. narrower and more horizontal leaves or increased number of tiller buds, overview
additional information
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Bacillus subtilis Protox gene Agrobacterium-mediated transformation into rice T3 transgenic lines, Protox activity is 56% higher in the transgenic line than in wild-type rice, indicating that Bacillus subtilis Protox gene produces an enzyme that is functionally active in transgenic rice line
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Ni2+ affinity column chromatography
recombinant His-tagged wild-type and mutant V311M from Escherichia coli by nickel affinity chromatography
recombinant wild-type and mutant enzymes from Escherichia coli strain XL-1 Blue inclusion bodies
recombinant His-tagged enzyme from Escherichia coli by nickel affinity chromatography
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expression of wild-type and mutant enzymes in Escherichia coli strain XL-1 Blue in inclusion bodies
expression of wild-type and mutant V311M as His-tagged enzymes in Escherichia coli strain BL21(DE3)
the enzyme gene is fused in its 3'-end to a polynucleotide encoding six histidine residues and expressed in both Escherichia coli BL21(DE3) cells and Bacillus subtilis 168A cells
expression of His-tagged enzyme in Escherichia coli
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expression of the enzyme in transgenic rice plants using Agrobacterium tumefaciens transformation system
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in Escherichia coli, His-tag inserted for purification
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drug development
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protoporphyrinogen oxidase is one of the most important action targets of commercial herbicides
additional information
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transgenic rice lines are resistant to the herbicides carfentrazone-ethyl and oxyfluorfen
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Corrigall, A.V.; Siziba, K.B.; Maneli, M.H.; Shephard, E.G.; Ziman, M.; Dailey, T.A.; Dailey, H.A.; Kirsch, R.E.; Meissner, P.N.
Purification of and kinetic studies on a cloned protoporphyrinogen oxidase from the aerobic bacterium Bacillus subtilis
Arch. Biochem. Biophys.
358
251-256
1998
Bacillus subtilis
brenda
Jeong, E.; Han, O.
Purification and characterization of Bacillus subtilis protoporphyrinogen oxidase and pre-equilibrium behavior during oxidation of protoporphyrinogen IX
J. Biochem. Mol. Biol.
34
39-42
2001
Bacillus subtilis
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brenda
Jeong, E.; Houn, T.; Kuk, Y.; Kim, E.S.; Chandru, H.K.; Baik, M.; Back, K.; Guh, J.O.; Han, O.
A point mutation of valine-311 to methionine in Bacillus subtilis protoporphyrinogen oxidase does not greatly increase resistance to the diphenyl ether herbicide oxyfluorfen
Bioorg. Chem.
31
389-397
2003
Bacillus subtilis (P32397), Bacillus subtilis
brenda
Jung, S.; Chung, J.S.; Chon, S.U.; Kuk, Y.I.; Lee, H.J.; Guh, J.O.; Back, K.
Expression of recombinant protoporphyrinogen oxidase influences growth and morphological characteristics in transgenic rice
Plant Growth Regul.
42
283-288
2004
Bacillus subtilis
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brenda
Kuk, Y.I.; Lee, H.J.; Chung, J.S.; Kim, K.M.; Lee, S.B.; Ha, S.B.; Back, K.; Guh, J.O.
Expression of a Bacillus subtilis protoporphyrinogen oxidase gene in rice plants reduces sensitivity to peroxidizing herbicides
Biol. Plant.
49
577-583
2005
Bacillus subtilis, Oryza sativa
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brenda
Sun, L.; Wen, X.; Tan, Y.; Li, H.; Yang, X.; Zhao, Y.; Wang, B.; Cao, Q.; Niu, C.; Xi, Z.
Site-directed mutagenesis and computational study of the Y366 active site in Bacillus subtilis protoporphyrinogen oxidase
Amino Acids
37
523-530
2009
Bacillus subtilis (P32397), Bacillus subtilis
brenda
Tan, Y.; Sun, L.; Xi, Z.; Yang, G.F.; Jiang, D.Q.; Yan, X.P.; Yang, X.; Li, H.Y.
A capillary electrophoresis assay for recombinant Bacillus subtilis protoporphyrinogen oxidase
Anal. Biochem.
383
200-204
2008
Bacillus subtilis
brenda
Qin, X.; Sun, L.; Wen, X.; Yang, X.; Tan, Y.; Jin, H.; Cao, Q.; Zhou, W.; Xi, Z.; Shen, Y.
Structural insight into unique properties of protoporphyrinogen oxidase from Bacillus subtilis
J. Struct. Biol.
170
76-82
2010
Bacillus subtilis (P32397), Bacillus subtilis
brenda
Hansson, M.; Gustafsson, M.C.; Kannangara, C.G.; Hederstedt, L.
Isolated Bacillus subtilis HemY has coproporphyrinogen III to coproporphyrin III oxidase activity
Biochim. Biophys. Acta
1340
97-104
1997
Bacillus subtilis (P32397), Bacillus subtilis 168 (P32397)
brenda