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Literature summary extracted from

  • Hao, G.F.; Tan, Y.; Yang, S.G.; Wang, Z.F.; Zhan, C.G.; Xi, Z.; Yang, G.F.
    Computational and experimental insights into the mechanism of substrate recognition and feedback inhibition of protoporphyrinogen oxidase (2013), PLoS ONE, 8, e69198 .
    View publication on PubMedView publication on EuropePMC

Protein Variants

EC Number Protein Variants Comment Organism
1.3.3.4 F331A site-directed mutagenesis, calculation of free binding energy shifts Homo sapiens
1.3.3.4 F331T site-directed mutagenesis, calculation of free binding energy shifts Homo sapiens
1.3.3.4 F392E site-directed mutagenesis, calculation of free binding energy shifts Nicotiana tabacum
1.3.3.4 G169A site-directed mutagenesis, calculation of free binding energy shifts Homo sapiens
1.3.3.4 L166N site-directed mutagenesis, calculation of free binding energy shifts Homo sapiens
1.3.3.4 L334V site-directed mutagenesis, calculation of free binding energy shifts Homo sapiens
1.3.3.4 L356N site-directed mutagenesis, calculation of free binding energy shifts Nicotiana tabacum
1.3.3.4 L356V site-directed mutagenesis, calculation of free binding energy shifts Nicotiana tabacum
1.3.3.4 L372N site-directed mutagenesis, calculation of free binding energy shifts Nicotiana tabacum
1.3.3.4 L372V site-directed mutagenesis, calculation of free binding energy shifts Nicotiana tabacum
1.3.3.4 M368K site-directed mutagenesis, calculation of free binding energy shifts Homo sapiens
1.3.3.4 M368Q site-directed mutagenesis, calculation of free binding energy shifts Homo sapiens
1.3.3.4 R168S site-directed mutagenesis, calculation of free binding energy shifts Homo sapiens
1.3.3.4 R97G site-directed mutagenesis, calculation of free binding energy shifts Homo sapiens
1.3.3.4 R98A site-directed mutagenesis, calculation of free binding energy shifts Nicotiana tabacum
1.3.3.4 R98E site-directed mutagenesis, calculation of free binding energy shifts Nicotiana tabacum
1.3.3.4 R98K site-directed mutagenesis, calculation of free binding energy shifts Nicotiana tabacum
1.3.3.4 V170T site-directed mutagenesis, calculation of free binding energy shifts Homo sapiens

Inhibitors

EC Number Inhibitors Comment Organism Structure
1.3.3.4 additional information analysis of the mechanism of substrate recognition and feedback inhibition of protoporphyrinogen oxidase, kinetics, overview Homo sapiens
1.3.3.4 additional information analysis of the mechanism of substrate recognition and feedback inhibition of protoporphyrinogen oxidase, overview Nicotiana tabacum

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
1.3.3.4 additional information
-
 additional information Michaelis-Menten kinetics Homo sapiens
1.3.3.4 0.00208
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, wild-type enzyme Homo sapiens
1.3.3.4 0.00217
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, mutant G169A Homo sapiens
1.3.3.4 0.00298
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, mutant V170T Homo sapiens
1.3.3.4 0.00303
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, mutant F331T Homo sapiens
1.3.3.4 0.00514
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, mutant L166N Homo sapiens
1.3.3.4 0.00564
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, mutant M368K Homo sapiens
1.3.3.4 0.00661
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, mutant F331A Homo sapiens
1.3.3.4 0.00709
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, mutant L334V Homo sapiens
1.3.3.4 0.01134
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, mutant R168S Homo sapiens
1.3.3.4 0.0139
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, mutant M368Q Homo sapiens
1.3.3.4 0.01965
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, mutant R97G Homo sapiens

Localization

EC Number Localization Comment Organism GeneOntology No. Textmining
1.3.3.4 mitochondrion
-
 Nicotiana tabacum 5739
-

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
1.3.3.4 protoporphyrinogen IX + 3 O2 Homo sapiens
-
 protoporphyrin IX + 3 H2O2
-
 ?
1.3.3.4 protoporphyrinogen IX + 3 O2 Nicotiana tabacum
-
 protoporphyrin IX + 3 H2O2
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
1.3.3.4 Homo sapiens P50336
-
-
1.3.3.4 Nicotiana tabacum O24164
-
-

Reaction

EC Number Reaction Comment Organism Reaction ID
1.3.3.4 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
a
1.3.3.4 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
a

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
1.3.3.4 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 ?
-
 ?
1.3.3.4 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 ?
-
 ?
1.3.3.4 protoporphyrinogen IX + 3 O2
-
 Homo sapiens protoporphyrin IX + 3 H2O2
-
 ?
1.3.3.4 protoporphyrinogen IX + 3 O2
-
 Nicotiana tabacum protoporphyrin IX + 3 H2O2
-
 ?

Synonyms

EC Number Synonyms Comment Organism
1.3.3.4 hPPO
-
 Homo sapiens
1.3.3.4 mtPPO
-
 Nicotiana tabacum
1.3.3.4 PPO
-
 Homo sapiens
1.3.3.4 PPO
-
 Nicotiana tabacum
1.3.3.4 protoporphyrinogen IX oxidase
-
 Homo sapiens
1.3.3.4 protoporphyrinogen IX oxidase
-
 Nicotiana tabacum

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
1.3.3.4 0.0062
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, mutant G169A Homo sapiens
1.3.3.4 0.0303
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, mutant L166N Homo sapiens
1.3.3.4 0.0495
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, wild-type enzyme Homo sapiens
1.3.3.4 0.0553
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, mutant R168S Homo sapiens
1.3.3.4 0.0727
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, mutant F331A Homo sapiens
1.3.3.4 0.1283
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, mutant V170T Homo sapiens
1.3.3.4 0.1513
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, mutant F331T Homo sapiens
1.3.3.4 0.1548
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, mutant M368Q Homo sapiens
1.3.3.4 0.2362
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, mutant M368K Homo sapiens
1.3.3.4 0.8532
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, mutant L334V Homo sapiens
1.3.3.4 1.273
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, mutant R97G Homo sapiens

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
1.3.3.4 7.4
-
 assay at Homo sapiens

Cofactor

EC Number Cofactor Comment Organism Structure
1.3.3.4 FAD binding structure analysis through molecular docking using the crystal structure of Nicotiana tabacum mitochondrial PPO enzyme, overview Homo sapiens
1.3.3.4 FAD binding structure analysis through molecular docking using the crystal structure of Nicotiana tabacum mitochondrial PPO enzyme, overview Nicotiana tabacum

General Information

EC Number General Information Comment Organism
1.3.3.4 metabolism protoporphyrinogen IX oxidase is an essential enzyme catalyzing the last common step in the pathway leading to heme and chlorophyll biosynthesis Homo sapiens
1.3.3.4 metabolism protoporphyrinogen IX oxidase is an essential enzyme catalyzing the last common step in the pathway leading to heme and chlorophyll biosynthesis Nicotiana tabacum