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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 .
Protein Variants
| Protein Variants | Comment | Organism |
|---|---|---|
| F331A | site-directed mutagenesis, calculation of free binding energy shifts | Homo sapiens |
| F331T | site-directed mutagenesis, calculation of free binding energy shifts | Homo sapiens |
| F392E | site-directed mutagenesis, calculation of free binding energy shifts | Nicotiana tabacum |
| G169A | site-directed mutagenesis, calculation of free binding energy shifts | Homo sapiens |
| L166N | site-directed mutagenesis, calculation of free binding energy shifts | Homo sapiens |
| L334V | site-directed mutagenesis, calculation of free binding energy shifts | Homo sapiens |
| L356N | site-directed mutagenesis, calculation of free binding energy shifts | Nicotiana tabacum |
| L356V | site-directed mutagenesis, calculation of free binding energy shifts | Nicotiana tabacum |
| L372N | site-directed mutagenesis, calculation of free binding energy shifts | Nicotiana tabacum |
| L372V | site-directed mutagenesis, calculation of free binding energy shifts | Nicotiana tabacum |
| M368K | site-directed mutagenesis, calculation of free binding energy shifts | Homo sapiens |
| M368Q | site-directed mutagenesis, calculation of free binding energy shifts | Homo sapiens |
| R168S | site-directed mutagenesis, calculation of free binding energy shifts | Homo sapiens |
| R97G | site-directed mutagenesis, calculation of free binding energy shifts | Homo sapiens |
| R98A | site-directed mutagenesis, calculation of free binding energy shifts | Nicotiana tabacum |
| R98E | site-directed mutagenesis, calculation of free binding energy shifts | Nicotiana tabacum |
| R98K | site-directed mutagenesis, calculation of free binding energy shifts | Nicotiana tabacum |
| V170T | site-directed mutagenesis, calculation of free binding energy shifts | Homo sapiens |
Inhibitors
| Inhibitors | Comment | Organism | Structure |
|---|---|---|---|
| additional information | analysis of the mechanism of substrate recognition and feedback inhibition of protoporphyrinogen oxidase, kinetics, overview | Homo sapiens | |
| additional information | analysis of the 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 | |
| 0.00208 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, wild-type enzyme | Homo sapiens |  |
| 0.00217 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, mutant G169A | Homo sapiens | |
| 0.00298 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, mutant V170T | Homo sapiens | |
| 0.00303 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, mutant F331T | Homo sapiens | |
| 0.00514 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, mutant L166N | Homo sapiens | |
| 0.00564 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, mutant M368K | Homo sapiens | |
| 0.00661 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, mutant F331A | Homo sapiens | |
| 0.00709 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, mutant L334V | Homo sapiens | |
| 0.01134 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, mutant R168S | Homo sapiens | |
| 0.0139 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, mutant M368Q | Homo sapiens | |
| 0.01965 | - |
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 | P50336 | - |
- |
| Nicotiana tabacum | O24164 | - |
- |
Reaction
| Reaction | Comment | Organism | Reaction ID |
|---|---|---|---|
| protoporphyrinogen IX + 3 O2 = protoporphyrin IX + 3 H2O2 | reaction and substrate recognition mechanisms, conformational analysis based on molecular docking, molecular dynamics (MD) simulation, molecular mechanic/Poisson-Boltzmann surface area (MM/PBSA) calculations, umbrella sampling MD simulations, and potential of mean force (PMF) calculations, overview | Homo sapiens | |
| protoporphyrinogen IX + 3 O2 = protoporphyrin IX + 3 H2O2 | reaction and substrate recognition mechanisms, conformational analysis based on molecular docking, molecular dynamics (MD) simulation, molecular mechanic/Poisson-Boltzmann surface area (MM/PBSA) calculations, umbrella sampling MD simulations, and potential of mean force (PMF) calculations, overview | Nicotiana tabacum |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| additional information | development of a binding model for the protogen substrate protoporphyrinogen IX through extensive computational simulations, analysis of essential active site residues (protogen surrounded by R97, L166, R168, G169, V170, F331, L334, M368, and FAD in hPPO) and mechanism of substrate recognition, docking uses the crystal structure of Nicotiana tabacum mitochondrial PPO enzyme and of the human PPO enzyme, overview | Homo sapiens | ? | - |
? | |
| additional information | development of a binding model for the protogen substrate protoporphyrinogen IX through extensive computational simulations, analysis of essential active site residues (protogen surrounded by R98, F172, A174, G175, T176, F353, L356, F392, and FAD in tobacco mtPPO) and mechanism of substrate recognition, docking uses the crystal structure of Nicotiana tabacum mitochondrial PPO enzyme and of the human PPO enzyme, overview | Nicotiana tabacum | ? | - |
? | |
| protoporphyrinogen IX + 3 O2 | - |
Homo sapiens | protoporphyrin IX + 3 H2O2 | - |
? | |
| protoporphyrinogen IX + 3 O2 | - |
Nicotiana tabacum | protoporphyrin IX + 3 H2O2 | - |
? | |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| hPPO | - |
Homo sapiens |
| mtPPO | - |
Nicotiana tabacum |
| 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 | |
| 0.0495 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, wild-type enzyme | Homo sapiens | |
| 0.0553 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, mutant R168S | Homo sapiens | |
| 0.0727 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, mutant F331A | Homo sapiens | |
| 0.1283 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, mutant V170T | Homo sapiens | |
| 0.1513 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, mutant F331T | Homo sapiens | |
| 0.1548 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, mutant M368Q | Homo sapiens | |
| 0.2362 | - |
protoporphyrinogen IX | pH 7.4, temperature not specified in the publication, mutant M368K | Homo sapiens | |
| 0.8532 | - |
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 | |
pH Optimum
| pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
|---|---|---|---|
| 7.4 | - |
assay at | Homo sapiens |
Cofactor
| Cofactor | Comment | Organism | Structure |
|---|---|---|---|
| FAD | binding structure analysis through molecular docking using the crystal structure of Nicotiana tabacum mitochondrial PPO enzyme, overview | Homo sapiens | |
| FAD | binding structure analysis through molecular docking using the crystal structure of Nicotiana tabacum mitochondrial PPO enzyme, overview | Nicotiana tabacum | |
General Information
| General Information | Comment | Organism |
|---|---|---|
| metabolism | protoporphyrinogen IX oxidase is an essential enzyme catalyzing the last common step in the pathway leading to heme and chlorophyll biosynthesis | Homo sapiens |
| metabolism | protoporphyrinogen IX oxidase is an essential enzyme catalyzing the last common step in the pathway leading to heme and chlorophyll biosynthesis | Nicotiana tabacum |
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