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Information on EC 1.3.3.4 - protoporphyrinogen oxidase and Organism(s) Myxococcus xanthus and UniProt Accession P56601

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     1 Oxidoreductases
         1.3 Acting on the CH-CH group of donors
             1.3.3 With oxygen as acceptor
                1.3.3.4 protoporphyrinogen oxidase
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.
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This record set is specific for:
Myxococcus xanthus
UNIPROT: P56601
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Word Map
The taxonomic range for the selected organisms is: Myxococcus xanthus
The enzyme appears in selected viruses and cellular organisms
Synonyms
protoporphyrinogen oxidase, ppox, protox, protoporphyrinogen ix oxidase, mtppo, ppo1-1, protox enzyme, protoporphyrinogen oxidase ix, protoporphyrinogen ix oxidase 1, lmjf_06_1280, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
MxProtox
-
-
protoporphyrinogen IX oxidase
protoporphyrinogen oxidase
-
-
-
-
protoporphyrinogenase
-
-
-
-
protox
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
redox reaction
-
-
-
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oxidation
-
-
-
-
reduction
-
-
-
-
SYSTEMATIC NAME
IUBMB Comments
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.
CAS REGISTRY NUMBER
COMMENTARY hide
53986-32-6
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
protoporphyrinogen IX + 3 O2
protoporphyrin + 3 H2O2
show the reaction diagram
-
-
-
?
protoporphyrinogen IX + 3 O2
protoporphyrin IX + 3 H2O2
show the reaction diagram
-
-
-
?
protoporphyrinogen-IX + 3 O2
protoporphyrin-IX + 3 H2O2
show the reaction diagram
-
-
-
?
protoporphyrinogen IX + 3 O2
protoporphyrin IX + 3 H2O2
show the reaction diagram
-
-
-
-
?
protoporphyrinogen-IX + 3 O2
protoporphyrin-IX + 3 H2O2
show the reaction diagram
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
protoporphyrinogen IX + 3 O2
protoporphyrin + 3 H2O2
show the reaction diagram
-
-
-
?
protoporphyrinogen IX + 3 O2
protoporphyrin IX + 3 H2O2
show the reaction diagram
-
-
-
?
protoporphyrinogen IX + 3 O2
protoporphyrin IX + 3 H2O2
show the reaction diagram
-
-
-
-
?
protoporphyrinogen-IX + 3 O2
protoporphyrin-IX + 3 H2O2
show the reaction diagram
-
penultimate step of heme and chlorophyll biosynthesis
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
FAD
-
one noncovalently bound FAD per dimer
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2,2'-[[4-(5,7-dimethyl-4-oxo-4,7-dihydro-3H-pyrazolo[3,4-d][1,2,3]triazin-3-yl)-5-fluorobenzene-1,2-diyl]bis(oxy)]bis(N-prop-2-en-1-ylacetamide)
-
2,2'-[[4-(5,7-dimethyl-4-oxo-4,7-dihydro-3H-pyrazolo[3,4-d][1,2,3]triazin-3-yl)-5-fluorobenzene-1,2-diyl]bis(oxy)]bis(N-prop-2-yn-1-ylacetamide)
-
2,2'-[[4-fluoro-5-(4-oxo-6-prop-2-en-1-yl-4,6-dihydro-3H-pyrazolo[3,4-d][1,2,3]triazin-3-yl)benzene-1,2-diyl]bis(oxy)]bis(N-prop-2-en-1-ylacetamide)
-
2,2'-[[4-fluoro-5-(4-oxo-6-prop-2-en-1-yl-4,6-dihydro-3H-pyrazolo[3,4-d][1,2,3]triazin-3-yl)benzene-1,2-diyl]bis(oxy)]bis(N-prop-2-yn-1-ylacetamide)
-
2,2'-[[4-fluoro-5-(4-oxo-6-propyl-4,6-dihydro-3H-pyrazolo[3,4-d][1,2,3]triazin-3-yl)benzene-1,2-diyl]bis(oxy)]bis(N-prop-2-en-1-ylacetamide)
-
2,2'-[[4-fluoro-5-(4-oxo-6-propyl-4,6-dihydro-3H-pyrazolo[3,4-d][1,2,3]triazin-3-yl)benzene-1,2-diyl]bis(oxy)]bis(N-prop-2-yn-1-ylacetamide)
-
2,2'-[[4-fluoro-5-(4-oxo-7-prop-2-en-1-yl-4,7-dihydro-3H-pyrazolo[3,4-d][1,2,3]triazin-3-yl)benzene-1,2-diyl]bis(oxy)]bis(N-prop-2-en-1-ylacetamide)
-
2,2'-[[4-fluoro-5-(4-oxo-7-prop-2-en-1-yl-4,7-dihydro-3H-pyrazolo[3,4-d][1,2,3]triazin-3-yl)benzene-1,2-diyl]bis(oxy)]bis(N-prop-2-yn-1-ylacetamide)
-
2,2'-[[4-fluoro-5-(4-oxo-7-propyl-4,7-dihydro-3H-pyrazolo[3,4-d][1,2,3]triazin-3-yl)benzene-1,2-diyl]bis(oxy)]bis(N-prop-2-en-1-ylacetamide)
-
2,2'-[[4-fluoro-5-(4-oxo-7-propyl-4,7-dihydro-3H-pyrazolo[3,4-d][1,2,3]triazin-3-yl)benzene-1,2-diyl]bis(oxy)]bis(N-prop-2-yn-1-ylacetamide)
-
2,2'-[[4-fluoro-5-(7-methyl-4-oxo-4,7-dihydro-3H-pyrazolo[3,4-d][1,2,3]triazin-3-yl)benzene-1,2-diyl]bis(oxy)]bis(N-prop-2-en-1-ylacetamide)
-
2,2'-[[4-fluoro-5-(7-methyl-4-oxo-4,7-dihydro-3H-pyrazolo[3,4-d][1,2,3]triazin-3-yl)benzene-1,2-diyl]bis(oxy)]bis(N-prop-2-yn-1-ylacetamide)
-
2,2'-[[4-fluoro-5-(7-methyl-4-oxo-4,7-dihydro-3H-pyrazolo[3,4-d][1,2,3]triazin-3-yl)benzene-1,2-diyl]bis(oxy)]bis(N-propylacetamide)
-
2,2'-[[4-fluoro-5-[7-methyl-4-oxo-5-(trifluoromethyl)-4,7-dihydro-3H-pyrazolo[3,4-d][1,2,3]triazin-3-yl]benzene-1,2-diyl]bis(oxy)]bis(N-prop-2-en-1-ylacetamide)
-
2,2'-[[4-fluoro-5-[7-methyl-4-oxo-5-(trifluoromethyl)-4,7-dihydro-3H-pyrazolo[3,4-d][1,2,3]triazin-3-yl]benzene-1,2-diyl]bis(oxy)]bis(N-prop-2-yn-1-ylacetamide)
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3-(4-chloro-2-fluoro-5-hydroxyphenyl)-7-methyl-3,7-dihydro-4H-pyrazolo[3,4-d][1,2,3]triazin-4-one
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3-(4-chloro-2-fluoro-5-methoxyphenyl)-7-methyl-3,7-dihydro-4H-pyrazolo[3,4-d][1,2,3]triazin-4-one
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3-(4-chloro-2-fluoro-5-propoxyphenyl)-7-methyl-3,7-dihydro-4H-pyrazolo[3,4-d][1,2,3]triazin-4-one
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3-(4-chloro-5-ethoxy-2-fluorophenyl)-7-methyl-3,7-dihydro-4H-pyrazolo[3,4-d][1,2,3]triazin-4-one
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3-(5-butoxy-4-chloro-2-fluorophenyl)-7-methyl-3,7-dihydro-4H-pyrazolo[3,4-d][1,2,3]triazin-4-one
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3-[4-chloro-2-fluoro-5-(pentyloxy)phenyl]-7-methyl-3,7-dihydro-4H-pyrazolo[3,4-d][1,2,3]triazin-4-one
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3-[4-chloro-2-fluoro-5-(prop-2-en-1-yloxy)phenyl]-5,7-dimethyl-3,7-dihydro-4H-pyrazolo[3,4-d][1,2,3]triazin-4-one
-
3-[4-chloro-2-fluoro-5-(prop-2-en-1-yloxy)phenyl]-6-prop-2-en-1-yl-3,6-dihydro-4H-pyrazolo[3,4-d][1,2,3]triazin-4-one
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3-[4-chloro-2-fluoro-5-(prop-2-en-1-yloxy)phenyl]-7-methyl-3,7-dihydro-4H-pyrazolo[3,4-d][1,2,3]triazin-4-one
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3-[4-chloro-2-fluoro-5-(prop-2-en-1-yloxy)phenyl]-7-prop-2-en-1-yl-3,7-dihydro-4H-pyrazolo[3,4-d][1,2,3]triazin-4-one
-
3-[4-chloro-2-fluoro-5-(prop-2-yn-1-yloxy)phenyl]-5,7-dimethyl-3,7-dihydro-4H-pyrazolo[3,4-d][1,2,3]triazin-4-one
-
3-[4-chloro-2-fluoro-5-(prop-2-yn-1-yloxy)phenyl]-6-prop-2-en-1-yl-3,6-dihydro-4H-pyrazolo[3,4-d][1,2,3]triazin-4-one
-
3-[4-chloro-2-fluoro-5-(prop-2-yn-1-yloxy)phenyl]-7-methyl-3,7-dihydro-4H-pyrazolo[3,4-d][1,2,3]triazin-4-one
-
3-[4-chloro-2-fluoro-5-(prop-2-yn-1-yloxy)phenyl]-7-methyl-5-(trifluoromethyl)-3,7-dihydro-4H-pyrazolo[3,4-d][1,2,3]triazin-4-one
-
3-[4-chloro-2-fluoro-5-(prop-2-yn-1-yloxy)phenyl]-7-prop-2-en-1-yl-3,7-dihydro-4H-pyrazolo[3,4-d][1,2,3]triazin-4-one
-
3-[4-chloro-2-fluoro-5-[(2-methoxyethoxy)methoxy]phenyl]-7-methyl-3,7-dihydro-4H-pyrazolo[3,4-d][1,2,3]triazin-4-one
-
3-[4-chloro-5-[(2-chloroprop-2-en-1-yl)oxy]-2-fluorophenyl]-7-methyl-3,7-dihydro-4H-pyrazolo[3,4-d][1,2,3]triazin-4-one
-
3-[4-chloro-5-[(3-chloroprop-2-en-1-yl)oxy]-2-fluorophenyl]-7-methyl-3,7-dihydro-4H-pyrazolo[3,4-d][1,2,3]triazin-4-one
-
oxyfuorfen
all wild-type and transgenic rice lines have a significant decrease in Protox activity, all transgenic rice lines expressing native Protox show enhanced resistance to oxyfluorfen as compared to nontransgenic rice
[2-chloro-4-fluoro-5-(7-methyl-4-oxo-4,7-dihydro-3H-pyrazolo[3,4-d][1,2,3]triazin-3-yl)phenoxy]acetonitrile
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acifluorfen
butafenacil
-
0.0001 mM
carfentrazone
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-
carfentrazone-ethyl
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-
imazapyr
-
-
oxyfluorfen
oxyXuorfen
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transgenic rice lines TTS3 and TTS4 exhibit a reduced Protox activity, however, it is much greater than that of uninhibited Protox activity of wild type, seeds from all transgenic lines are able to germinate when treated with up to 0.5 mM, whereas seeds from the wild-type fail to germinate even when treated at levels as low as 0.001 mM, great accumulation of photodynamic protoporphyrin IX only in oxyfuorfen-treated wild-type plants, not in oxyfuorfen-treated TTS lines
paraquat
-
-
additional information
molecular docking and 3D QSAR studies of protoporphyrinogen oxidase inhibitor 3H-pyrazolo[3,4-d][1,2,3]triazin-4-one derivatives using crystal structure PDB ID 2IVD, detailed overview
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.00038 - 0.00149
protoporphyrinogen IX
0.0016 - 0.0036
protoporphyrinogen-IX
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.08 - 1.52
protoporphyrinogen IX
0.0867
protoporphyrinogen-IX
-
-
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
154.4 - 2576.3
protoporphyrinogen IX
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
additional information
additional information
pI50 values of 3H-pyrazolo[3,4-d][1,2,3]triazin-4-one derivative inhibitors, overview
-
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
-
prominent increase of Protox activity in transgenic rice plant lines TTS3 and TTS4 relative to the wild-type, increase is lower than that in transgenic line M4
Manually annotated by BRENDA team
-
membrane interaction/orientation
Manually annotated by BRENDA team
-
prominent increase of Protox activity in transgenic rice plant lines TTS3 and TTS4 relative to the wild-type, increase is lower than that in transgenic line M4
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
protoporphyrinogen oxidase (PPOX) i the penultimate enzyme in the heme biosynthetic pathway catalysing the six electron oxidation of protoporphyrinogen-IX to protoporphyrin-IX, in the presence of flavin adenine dinucleotide (FAD) and oxygen
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
PGOX_MYXXA
471
0
49388
Swiss-Prot
-
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
100000
-
gel filtration
48000
-
immunoblot analysis, transgenic lines TTS3 and TTS4, presumably breakdown products of Protox
49390
-
calculated from amino acid sequence
50000
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimer
-
2 * 50000, SDS-PAGE, gel filtration
monomer
-
crystallographic studies
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
by the hanging drop vapor diffusion method at 16°C in the dark
-
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
E39A
site-directed mutagenesis, inactive mutant
E39D
site-directed mutagenesis, the enzyme mutant shows 81% reduced activity compared to the wild-type enzyme
E39K
site-directed mutagenesis, inactive mutant
E39Q
site-directed mutagenesis, inactive mutant
N441I
site-directed mutagenesis, the enzyme mutant shows 84% reduced activity compared to the wild-type enzyme
N441Q
site-directed mutagenesis, the enzyme mutant shows 73% reduced activity compared to the wild-type enzyme
S20A
site-directed mutagenesis, the enzyme mutant shows 93% reduced activity compared to the wild-type enzyme
S20T
site-directed mutagenesis, the enzyme mutant shows 90% reduced activity compared to the wild-type enzyme
W408L
site-directed mutagenesis, the enzyme mutant shows 48% reduced activity compared to the wild-type enzyme
W408Y
site-directed mutagenesis, the enzyme mutant shows 82% reduced activity compared to the wild-type enzyme
additional information
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20°C, Tris-HCl buffer, pH 7.0, 50% glycerol
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His6-tagged wild-type and mutant enzymes from Escherichia coli strain JM109 by metal ion affinity chromatography
by gel filtration
-
cloned enzyme
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in transgenic rice plant lines M4 and and M7
gene hemeY, recombinant expression of His6-tagged wild-type and mutant enzymes in Escherichia coli strain JM109, growth at 30°C (rather than at 37°C) improves expression, and yield is increased by doubling the number of cells inoculated in 1 l growth media
gene hemY, recombinant expression in Oryza sativa cv. Dongjin constitutively under control of a ubiquitin promoter and nopaline synthase terminator. A hygromycin phosphotransferase (hpt) gene is used as a selectable marker, the transgenic line is reported to be strongly resistant to oxyfluorfen, a PPO-inhibiting herbicide
a modified, low G+C-content MxProtox gene construct pGA1611:synthetic MxProtox is transformed into Oryza sativa using Agrobacterium tumefaciens-mediated transformation altering the sensitivity of rice plants to herbicide oxyfluorfen, quantitative reverse transcriptase PCR expression analysis. Oxyfluorfen induces changes in the expression of the modified MxProtox gene, constitutive OsProtox gene, and other key genes encoding the porphyrin pathway, in leaves of the Oryza sativa wild-type and transgenic lines, overview
-
expressed in Oryza sativa cultivar Dongjin
-
expressed in Oryza sativa line M4 chloroplasts and mitochondria
-
full-length cDNA encoding Protox fused to a plastidal transit sequence at its N-terminus and subcloned into pGA1611 under the control of the constitutive maize ubiquitin promoter, with the hygromycin phosphotransferase gene as a selectable marker, overexpression in transgenic rice plants
-
in Escherichia coli His-tag inserted for purification
-
overexpression in Escherichia coli JM109 cells
-
overexpression in T2 homozygous transgenic plants under the control of the constitutive maize ubiquitin promoter
-
pMx-PPO vector transfected into and maintained in Escherichia coli JM109 cells
-
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
analysis
-
advantages of the continuous spectrofluorimetric assay over the discontinuous assay is of importance for both the kinetic characterization of recombinant PPOs and the detection of low concentrations of this enzyme in biological samples
medicine
-
conserved structural features in relation to a number of South African variegate porphyria-causing mutations in the human enzyme
additional information
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Dailey, H.A.; Dailey, T.A.
Protoporphyrinogen oxidase of Myxococcus xanthus. Expression, purification, and characterization of the cloned enzyme
J. Biol. Chem.
271
8714-8718
1996
Myxococcus xanthus
Manually annotated by BRENDA team
Shepherd, M.; Dailey, H.A.
A continuous fluorimetric assay for protoporphyrinogen oxidase by monitoring porphyrin accumulation
Anal. Biochem.
344
115-121
2005
Aquifex aeolicus, Homo sapiens, Mus musculus, Myxococcus xanthus
Manually annotated by BRENDA team
Corradi, H.R.; Corrigall, A.V.; Boix, E.; Mohan, C.G.; Sturrock, E.D.; Meissner, P.N.; Acharya, K.R.
Crystal structure of protoporphyrinogen oxidase from Myxococcus xanthus and its complex with the inhibitor acifluorfen
J. Biol. Chem.
281
38625-38633
2006
Myxococcus xanthus
Manually annotated by BRENDA team
Yang, K.; Jung, S.; Lee, Y.; Back, K.
Modifying Myxococcus xanthus protoporphyrinogen oxidase to plant codon usage and high level of oxyfluorfen resistance in transgenic rice
Pestic. Biochem. Physiol.
86
186-194
2006
synthetic construct (AY916795), Myxococcus xanthus (P56601)
-
Manually annotated by BRENDA team
Jung, S.; Lee, Y.; Back, K.
A tobacco plastidal transit sequence cannot override the dual targeting capacity of Myxococcus xanthus protoporphyrinogen oxidase in transgenic rice
Pestic. Biochem. Physiol.
86
49-56
2006
Myxococcus xanthus
-
Manually annotated by BRENDA team
Jung, S.; Back, K.
Herbicidal and antioxidant responses of transgenic rice overexpressing Myxococcus xanthus protoporphyrinogen oxidase
Plant Physiol. Biochem.
43
423-430
2005
Myxococcus xanthus, Oryza sativa
Manually annotated by BRENDA team
Lee, K.; Yang, K.; Kang, K.; Kang, S.; Lee, N.; Back, K.
Use of Myxococcus xanthus protoporphyrinogen oxidase as a selectable marker for transformation of rice
Pestic. Biochem. Physiol.
88
31-35
2007
Myxococcus xanthus
-
Manually annotated by BRENDA team
Jung, H.I.; Kuk, Y.I.; Back, K.; Burgos, N.R.
Resistance pattern and antioxidant enzyme profiles of protoporphyrinogen oxidase (PROTOX) inhibitor-resistant transgenic rice
Pestic. Biochem. Physiol.
91
53-65
2008
Myxococcus xanthus
-
Manually annotated by BRENDA team
Roy, K.; Paul, S.
Docking and 3D QSAR studies of protoporphyrinogen oxidase inhibitor 3H-pyrazolo[3,4-d][1,2,3]triazin-4-one derivatives
J. Mol. Model.
16
137-153
2010
Myxococcus xanthus (P56601)
Manually annotated by BRENDA team
Boateng, M.; Corrigall, A.; Sturrock, E.; Meissner, P.
Characterisation of the flavin adenine dinucleotide binding region of Myxococcus xanthus protoporphyrinogen oxidase
Biochem. Biophys. Rep.
4
306-311
2015
Myxococcus xanthus (P56601)
Manually annotated by BRENDA team
Park, J.; Tran, L.; Jung, S.
A protoporphyrinogen oxidase gene expression influences responses of transgenic rice to oxyfluorfen
Biol. Plant.
61
659-666
2017
Myxococcus xanthus
-
Manually annotated by BRENDA team
Chun, Y.; Kim, D.; Park, K.; Jeong, S.; Park, S.; Back, K.; Kim, C.
Fitness cost and competitive ability of transgenic herbicide-tolerant rice expressing a protoporphyrinogen oxidase gene
J. Ecol. Environ.
36
39-47
2013
Myxococcus xanthus (P56601)
-
Manually annotated by BRENDA team