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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

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
1.3.3.4 crystal structure analysis Homo sapiens

Protein Variants

EC Number Protein Variants Comment Organism
1.3.3.4 F331A site-directed mutagenesis of ring A, the mutant shows decreased activity compared to the wild-type enzyme Homo sapiens
1.3.3.4 F331T site-directed mutagenesis of ring A, the mutant shows increased activity compared to the wild-type enzyme Homo sapiens
1.3.3.4 F392E site-directed mutagenesis Nicotiana tabacum
1.3.3.4 G169A site-directed mutagenesis of ring C, the mutant shows decreased activity compared to the wild-type enzyme Homo sapiens
1.3.3.4 L166N site-directed mutagenesis of ring C, the mutant shows decreased activity compared to the wild-type enzyme Homo sapiens
1.3.3.4 L334V site-directed mutagenesis of ring A, the mutant shows highly increased activity compared to the wild-type enzyme Homo sapiens
1.3.3.4 L356N site-directed mutagenesis Nicotiana tabacum
1.3.3.4 L356V site-directed mutagenesis Nicotiana tabacum
1.3.3.4 L372N site-directed mutagenesis Nicotiana tabacum
1.3.3.4 L372V site-directed mutagenesis Nicotiana tabacum
1.3.3.4 M368K site-directed mutagenesis of ring A, the mutant shows increased activity compared to the wild-type enzyme Homo sapiens
1.3.3.4 M368Q site-directed mutagenesis of ring A, the mutant shows decreased activity compared to the wild-type enzyme Homo sapiens
1.3.3.4 R168S site-directed mutagenesis of ring A, the mutant shows decreased activity compared to the wild-type enzyme Homo sapiens
1.3.3.4 R97G site-directed mutagenesis of ring A, the mutant shows increased activity compared to the wild-type enzyme Homo sapiens
1.3.3.4 R98A site-directed mutagenesis, the mutant has a 60fold increased catalytic activity compared to the wild-type enzyme Nicotiana tabacum
1.3.3.4 R98E site-directed mutagenesis Nicotiana tabacum
1.3.3.4 R98K site-directed mutagenesis Nicotiana tabacum
1.3.3.4 V170T site-directed mutagenesis of ring B, the mutant shows increased activity compared to the wild-type enzyme Homo sapiens

Inhibitors

EC Number Inhibitors Comment Organism Structure
1.3.3.4 additional information mechanism of substrate recognition and feedback inhibition of protoporphyrinogen oxidase, overview Homo sapiens
1.3.3.4 additional information 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 additional information
-
 additional information Michaelis-Menten kinetics Nicotiana tabacum
1.3.3.4 0.00117
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, wild-type enzyme Nicotiana tabacum
1.3.3.4 0.0021
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, wild-type enzyme Homo sapiens
1.3.3.4 0.0022
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, mutant G169A Homo sapiens
1.3.3.4 0.003
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, mutant V170T Homo sapiens
1.3.3.4 0.00302
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, mutant F331T Homo sapiens
1.3.3.4 0.0051
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, mutant L166N Homo sapiens
1.3.3.4 0.0056
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, mutant M368K Homo sapiens
1.3.3.4 0.0066
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, mutant F331A Homo sapiens
1.3.3.4 0.0071
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, mutant L334V Homo sapiens
1.3.3.4 0.0083
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, mutant R98A Nicotiana tabacum
1.3.3.4 0.0113
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, mutant R168S Homo sapiens
1.3.3.4 0.014
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, mutant M368Q Homo sapiens
1.3.3.4 0.0196
-
 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
-
-
-
1.3.3.4 Nicotiana tabacum
-
-
-

Source Tissue

EC Number Source Tissue Comment Organism Textmining
1.3.3.4 leaf
-
 Nicotiana tabacum
-

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) 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
-
 ?

Synonyms

EC Number Synonyms Comment Organism
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 0.05
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, wild-type enzyme Homo sapiens
1.3.3.4 0.055
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, mutant R168S Homo sapiens
1.3.3.4 0.073
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, mutant F331A Homo sapiens
1.3.3.4 0.128
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, mutant V170T Homo sapiens
1.3.3.4 0.151
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, mutant F331T Homo sapiens
1.3.3.4 0.155
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, mutant M368Q Homo sapiens
1.3.3.4 0.236
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, mutant M368K Homo sapiens
1.3.3.4 0.853
-
 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
1.3.3.4 6
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, wild-type enzyme Nicotiana tabacum
1.3.3.4 365
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, mutant R98A Nicotiana tabacum

pH Optimum

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

Cofactor

EC Number Cofactor Comment Organism Structure
1.3.3.4 FAD enzyme interaction structure, overview Homo sapiens
1.3.3.4 FAD enzyme interaction structure, overview Nicotiana tabacum

General Information

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

EC Number kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
1.3.3.4 2.81
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, mutant G169A Homo sapiens
1.3.3.4 4.87
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, mutant R168S Homo sapiens
1.3.3.4 5.94
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, mutant L166N Homo sapiens
1.3.3.4 11.06
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, mutant F331A Homo sapiens
1.3.3.4 11.7
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, mutant M368Q Homo sapiens
1.3.3.4 23.8
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, wild-type enzyme Homo sapiens
1.3.3.4 42.14
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, mutant M368K Homo sapiens
1.3.3.4 42.66
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, mutant V170T Homo sapiens
1.3.3.4 50
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, mutant F331T Homo sapiens
1.3.3.4 64.95
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, mutant R97G Homo sapiens
1.3.3.4 120.1
-
 protoporphyrinogen IX pH 7.4, temperature not specified in the publication, mutant L334V Homo sapiens