Information on EC 1.3.5.3 - protoporphyrinogen IX dehydrogenase (menaquinone)

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The expected taxonomic range for this enzyme is: Escherichia coli

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EC NUMBER
COMMENTARY hide
1.3.5.3
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RECOMMENDED NAME
GeneOntology No.
protoporphyrinogen IX dehydrogenase (menaquinone)
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REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
protoporphyrinogen IX + 3 menaquinone = protoporphyrin IX + 3 menaquinol
show the reaction diagram
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-
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
3,8-divinyl-chlorophyllide a biosynthesis II (anaerobic)
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heme b biosynthesis II (anaerobic)
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heme metabolism
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Porphyrin and chlorophyll metabolism
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Metabolic pathways
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Biosynthesis of secondary metabolites
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SYSTEMATIC NAME
IUBMB Comments
protoporphyrinogen IX:menadione oxidoreductase
This enzyme enables Escherichia coli to synthesize heme in both aerobic and anaerobic environments.
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
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the FMN enzyme protoporphyrinogen IX oxidase (HemG) of Escherichia coli abstracts six electrons from its substrate and transfers them via ubiquinone, cytochrome bo3 and cytochrome bd oxidase to oxygen. Under anaerobic conditions electrons are transferred via menaquinone, fumarate and nitrate reductase. Cytochrome bo3 , cytochrome bd, and nitrate reductase contribute to the proton motive force that drives ATP formation
additional information
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detailed model of heme biosynthesis coupled energy generation, overview
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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 menadione
protoporphyrin IX + 3 menadiol
show the reaction diagram
protoporphyrinogen IX + 3 menaquinone
protoporphyrin IX + 3 menaquinol
show the reaction diagram
protoporphyrinogen IX + 3 triphenyltetrazolium chloride
protoporphyrin IX + ?
show the reaction diagram
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artificial electron acceptor
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-
?
protoporphyrinogen IX + 3 ubiquinone
protoporphyrin IX + 3 ubiquinol
show the reaction diagram
additional information
?
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potential electron acceptors, i.e. 2, 6-dichloroindophenol, phenazine methosulfate, menadione, and vitamin K1, respectively, directly oxidize the substrate in the absence of HemG
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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
protoporphyrinogen IX + 3 menadione
protoporphyrin IX + 3 menadiol
show the reaction diagram
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the enzyme enables Escherichia coli to synthesize heme in both aerobic and anaerobic environments
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-
?
protoporphyrinogen IX + 3 menaquinone
protoporphyrin IX + 3 menaquinol
show the reaction diagram
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under anaerobic conditions
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?
protoporphyrinogen IX + 3 ubiquinone
protoporphyrin IX + 3 ubiquinol
show the reaction diagram
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under aerobic conditions
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?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.00376
menadione
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pH 8.0, 37°C
0.0173
menaquinone
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recombinant His-tagged enzyme, pH and temperature not specified in the publication
0.007
protoporphyrinogen IX
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pH 8.0, 37°C
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.281
menadione
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pH 8.0, 37°C
0.292
protoporphyrinogen IX
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pH 8.0, 37°C
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
74.73
menadione
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pH 8.0, 37°C
41.7
protoporphyrinogen IX
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pH 8.0, 37°C
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.0000042
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membrane associated enzyme with substrates protoporphyrinogen IX and triphenyltetrazolium chloride, pH and temperature not specified in the publication
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
8
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assay at
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
37
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assay at
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
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associated
Manually annotated by BRENDA team
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
22000
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4 * 22000, SDS-PAGE
22500
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4 * 22500, calculated from sequence
108000
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gel filtration
150000
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recombinant enzyme, gel filtration
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SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hexamer
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tetramer
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4 * 22000, SDS-PAGE; 4 * 22500, calculated from sequence
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
native enzyme solubilized from membranes by anion exchange chromatography, recombinant His-tagged enzyme from Bacillus megaterium byy affinity chromatography and gel filtration. Removal of the fused His-tag via protease digestion does not change the catalytic properties
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six histidine-tagged recombinant protein
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
gene hemG, expression of His-tagged enzyme in Bacillus megaterium
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
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Show AA Sequence (275 entries)
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LINKS TO OTHER DATABASES (specific for EC-Number 1.3.5.3)
ExplorEnz
ExPASy
KEGG
MetaCyc
SABIO-RK
NCBI: PubMed, Protein, Nucleotide, Structure, Genome, OMIM
IUBMB Enzyme Nomenclature
PROSITE Database of protein families and domains
InterPro (database of protein families, domains and functional sites)