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Literature summary for 1.3.3.4 extracted from
- Computational and experimental insights into the mechanism of substrate recognition and feedback inhibition of protoporphyrinogen oxidase (2013), PLoS ONE, 8, e69198.
Crystallization (Commentary)
| Crystallization (Comment) | Organism |
|---|---|
| crystal structure analysis | Homo sapiens |
Protein Variants
| Protein Variants | Comment | Organism |
|---|---|---|
| F331A | site-directed mutagenesis of ring A, the mutant shows decreased activity compared to the wild-type enzyme | Homo sapiens |
| F331T | site-directed mutagenesis of ring A, the mutant shows increased activity compared to the wild-type enzyme | Homo sapiens |
| F392E | site-directed mutagenesis | Nicotiana tabacum |
| G169A | site-directed mutagenesis of ring C, the mutant shows decreased activity compared to the wild-type enzyme | Homo sapiens |
| L166N | site-directed mutagenesis of ring C, the mutant shows decreased activity compared to the wild-type enzyme | Homo sapiens |
| L334V | site-directed mutagenesis of ring A, the mutant shows highly increased activity compared to the wild-type enzyme | Homo sapiens |
| L356N | site-directed mutagenesis | Nicotiana tabacum |
| L356V | site-directed mutagenesis | Nicotiana tabacum |
| L372N | site-directed mutagenesis | Nicotiana tabacum |
| L372V | site-directed mutagenesis | Nicotiana tabacum |
| M368K | site-directed mutagenesis of ring A, the mutant shows increased activity compared to the wild-type enzyme | Homo sapiens |
| M368Q | site-directed mutagenesis of ring A, the mutant shows decreased activity compared to the wild-type enzyme | Homo sapiens |
| R168S | site-directed mutagenesis of ring A, the mutant shows decreased activity compared to the wild-type enzyme | Homo sapiens |
| R97G | site-directed mutagenesis of ring A, the mutant shows increased activity compared to the wild-type enzyme | Homo sapiens |
| R98A | site-directed mutagenesis, the mutant has a 60fold increased catalytic activity compared to the wild-type enzyme | Nicotiana tabacum |
| R98E | site-directed mutagenesis | Nicotiana tabacum |
| R98K | site-directed mutagenesis | Nicotiana tabacum |
| V170T | site-directed mutagenesis of ring B, the mutant shows increased activity compared to the wild-type enzyme | Homo sapiens |
Inhibitors
| Inhibitors | Comment | Organism | Structure |
|---|---|---|---|
| additional information | mechanism of substrate recognition and feedback inhibition of protoporphyrinogen oxidase, overview | Homo sapiens | |
| additional information | mechanism of substrate recognition and feedback inhibition of protoporphyrinogen oxidase, overview | Nicotiana tabacum |
KM Value [mM]
| KM Value [mM] | KM Value Maximum [mM] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| additional information | - |
additional information | Michaelis-Menten kinetics | Homo sapiens | |
| additional information | - |
additional information | Michaelis-Menten kinetics | Nicotiana tabacum | |
| 0.00117 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, wild-type enzyme | Nicotiana tabacum |  |
| 0.0021 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, wild-type enzyme | Homo sapiens | |
| 0.0022 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, mutant G169A | Homo sapiens | |
| 0.003 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, mutant V170T | Homo sapiens | |
| 0.00302 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, mutant F331T | Homo sapiens | |
| 0.0051 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, mutant L166N | Homo sapiens | |
| 0.0056 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, mutant M368K | Homo sapiens | |
| 0.0066 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, mutant F331A | Homo sapiens | |
| 0.0071 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, mutant L334V | Homo sapiens | |
| 0.0083 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, mutant R98A | Nicotiana tabacum | |
| 0.0113 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, mutant R168S | Homo sapiens | |
| 0.014 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, mutant M368Q | Homo sapiens | |
| 0.0196 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, mutant R97G | Homo sapiens | |
Localization
| Localization | Comment | Organism | GeneOntology No. | Textmining |
|---|---|---|---|---|
| mitochondrion | - |
Nicotiana tabacum | 5739 | - |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| protoporphyrinogen IX + 3 O2 | Homo sapiens | - |
protoporphyrin IX + 3 H2O2 | - |
? | |
| protoporphyrinogen IX + 3 O2 | Nicotiana tabacum | - |
protoporphyrin IX + 3 H2O2 | - |
? | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Homo sapiens | - |
- |
- |
| Nicotiana tabacum | - |
- |
- |
Source Tissue
| Source Tissue | Comment | Organism | Textmining |
|---|---|---|---|
| leaf | - |
Nicotiana tabacum | - |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| protoporphyrinogen IX + 3 O2 | - |
Homo sapiens | protoporphyrin IX + 3 H2O2 | - |
? | |
| protoporphyrinogen IX + 3 O2 | - |
Nicotiana tabacum | protoporphyrin IX + 3 H2O2 | - |
? | |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| PPO | - |
Homo sapiens |
| PPO | - |
Nicotiana tabacum |
| protoporphyrinogen IX oxidase | - |
Homo sapiens |
| protoporphyrinogen IX oxidase | - |
Nicotiana tabacum |
Turnover Number [1/s]
| Turnover Number Minimum [1/s] | Turnover Number Maximum [1/s] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 0.0062 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, mutant G169A | Homo sapiens | |
| 0.0303 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, mutant L166N | Homo sapiens | |
| 0.05 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, wild-type enzyme | Homo sapiens | |
| 0.055 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, mutant R168S | Homo sapiens | |
| 0.073 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, mutant F331A | Homo sapiens | |
| 0.128 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, mutant V170T | Homo sapiens | |
| 0.151 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, mutant F331T | Homo sapiens | |
| 0.155 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, mutant M368Q | Homo sapiens | |
| 0.236 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, mutant M368K | Homo sapiens | |
| 0.853 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, mutant L334V | Homo sapiens | |
| 1.273 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, mutant R97G | Homo sapiens | |
| 6 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, wild-type enzyme | Nicotiana tabacum | |
| 365 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, mutant R98A | Nicotiana tabacum | |
pH Optimum
| pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
|---|---|---|---|
| 7.4 | - |
assay at | Homo sapiens |
| 7.4 | - |
assay at | Nicotiana tabacum |
Cofactor
| Cofactor | Comment | Organism | Structure |
|---|---|---|---|
| FAD | enzyme interaction structure, overview | Homo sapiens | |
| FAD | enzyme interaction structure, overview | Nicotiana tabacum | |
General Information
| General Information | Comment | Organism |
|---|---|---|
| malfunction | inhibition or functional loss of PPO results in the accumulation of protogen, which can be spontaneously oxidized to proto by oxygen. As a photosensitizer, in the presence of light, proto can further induce the production of singlet oxygen, causing lipid peroxidation and cell death | Homo sapiens |
| malfunction | inhibition or functional loss of PPO results in the accumulation of protogen, which can be spontaneously oxidized to proto by oxygen. As a photosensitizer, in the presence of light, proto can further induce the production of singlet oxygen, causing lipid peroxidation and cell death | Nicotiana tabacum |
| metabolism | protoporphyrinogen IX oxidase is an essential enzyme catalyzing the last common step in the pathway leading to heme and chlorophyll biosynthesis | Nicotiana tabacum |
| metabolism | protoporphyrinogen IX oxidase is an essential enzyme catalyzing the last common step in the pathway leading to heme biosynthesis | Homo sapiens |
| additional information | substrate binding model, molecular docking studies, overview. The protogen is surrounded by R97, L166, R168, G169, V170, F331, L334, M368, and FAD in hPPO. Ring A of protogen interacts with R168 and is kept in position by hydrophobic interaction with M368. Ring B of protogen is sandwiched between hPPO residue V170 and FAD | Homo sapiens |
| additional information | substrate binding model, molecular docking studies, overview. The protogen is surrounded by R98, F172, A174, G175, T176, F353, L356, F392, and FAD in tobacco mtPPO. Possible role of R98 during the substrate recognition mechanism, | Nicotiana tabacum |
kcat/KM [mM/s]
| kcat/KM Value [1/mMs-1] | kcat/KM Value Maximum [1/mMs-1] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 2.81 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, mutant G169A | Homo sapiens | |
| 4.87 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, mutant R168S | Homo sapiens | |
| 5.94 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, mutant L166N | Homo sapiens | |
| 11.06 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, mutant F331A | Homo sapiens | |
| 11.7 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, mutant M368Q | Homo sapiens | |
| 23.8 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, wild-type enzyme | Homo sapiens | |
| 42.14 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, mutant M368K | Homo sapiens | |
| 42.66 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, mutant V170T | Homo sapiens | |
| 50 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, mutant F331T | Homo sapiens | |
| 64.95 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, mutant R97G | Homo sapiens | |
| 120.1 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, mutant L334V | Homo sapiens | |
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