Literature summary for 1.3.3.4 extracted from

Qin, X.; Sun, L.; Wen, X.; Yang, X.; Tan, Y.; Jin, H.; Cao, Q.; Zhou, W.; Xi, Z.; Shen, Y.
Structural insight into unique properties of protoporphyrinogen oxidase from Bacillus subtilis (2010), J. Struct. Biol., 170, 76-82.

Crystallization (Commentary)

Crystallization (Comment)	Organism
purified native and SeMet-labeled enzyme in complex with inhibitor acifluorfen, sitting-drop, vapor-diffusion method, 10 mg/ml wild-type bsPPO protein in 50 mM TrisHCl, pH 7.5, 200 mM sodium chloride, 5 mM DTT, 1 mM EDTA, and acifluorfen in a 1:5 ratio, equilibrating against a reservoir solution of 2.4 M ammonium phosphate dibasic, 0.1 M Tris-HCl, pH 7.5, 1 week, 20°C, X-ray diffraction structure determination and analysis at 2.8-3.5 A resolution	Bacillus subtilis

Crystallization (Comment)

Organism

purified native and SeMet-labeled enzyme in complex with inhibitor acifluorfen, sitting-drop, vapor-diffusion method, 10 mg/ml wild-type bsPPO protein in 50 mM TrisHCl, pH 7.5, 200 mM sodium chloride, 5 mM DTT, 1 mM EDTA, and acifluorfen in a 1:5 ratio, equilibrating against a reservoir solution of 2.4 M ammonium phosphate dibasic, 0.1 M Tris-HCl, pH 7.5, 1 week, 20°C, X-ray diffraction structure determination and analysis at 2.8-3.5 A resolution

Bacillus subtilis

Protein Variants

Protein Variants	Comment	Organism
F227R	the mutant shows reduced activity compared to the wild-type enzyme	Bacillus subtilis
I176A	the mutant shows reduced activity compared to the wild-type enzyme	Bacillus subtilis
K71A	the mutant shows reduced activity compared to the wild-type enzyme	Bacillus subtilis
P64A	the mutant shows reduced activity compared to the wild-type enzyme	Bacillus subtilis

Inhibitors

Inhibitors	Comment	Organism	Structure
acifluorfen	a herbicide, binding structure, overview	Bacillus subtilis

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism
0.001	-	protoporphyrinogen IX	mutant F227R, pH 7.5, temperature not specified in the publication	Bacillus subtilis
0.001	-	protoporphyrinogen IX	mutant I176A, pH 7.5, temperature not specified in the publication	Bacillus subtilis
0.001	-	protoporphyrinogen IX	mutant K71A, pH 7.5, temperature not specified in the publication	Bacillus subtilis
0.001	-	protoporphyrinogen IX	mutant P64A, pH 7.5, temperature not specified in the publication	Bacillus subtilis
0.001	-	protoporphyrinogen IX	wild-type enzyme, pH 7.5, temperature not specified in the publication	Bacillus subtilis

Localization

Localization	Comment	Organism	GeneOntology No.	Textmining
soluble	Bacillus subtilis PPO is unique among PPO family members in that it is a soluble monomer	Bacillus subtilis	-	-

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
protoporphyrinogen IX + 3 O2	Bacillus subtilis	-	protoporphyrin IX + 3 H2O2	-	?
protoporphyrinogen IX + 3 O2	Bacillus subtilis 168	-	protoporphyrin IX + 3 H2O2	-	?

Organism

Organism	UniProt	Comment	Textmining
Bacillus subtilis	P32397	-	-

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
additional information	bsPPO has a broader substrate specificity compared to other PPOs, substrate binding structure comparison of wild-type and mutant enzymes, overview	Bacillus subtilis	?	-	?
additional information	bsPPO has a broader substrate specificity compared to other PPOs, substrate binding structure comparison of wild-type and mutant enzymes, overview	Bacillus subtilis 168	?	-	?
protoporphyrinogen IX + 3 O2	-	Bacillus subtilis	protoporphyrin IX + 3 H2O2	-	?
protoporphyrinogen IX + 3 O2	-	Bacillus subtilis 168	protoporphyrin IX + 3 H2O2	-	?

Subunits

Subunits	Comment	Organism
monomer	Bacillus subtilis PPO is unique among PPO family members in that it is a soluble monomer	Bacillus subtilis
More	prototypical PPO enzyme structure consists of three domains: a FAD-binding domain, a substrate binding domain and a membrane-binding domain, structure analysis and comparison, overview	Bacillus subtilis

Synonyms

Synonyms	Comment	Organism
PPO	-	Bacillus subtilis
protoporphyrinogen IX oxidase	-	Bacillus subtilis

Turnover Number [1/s]

Turnover Number Minimum [1/s]	Turnover Number Maximum [1/s]	Substrate	Comment	Organism
0.0004	-	protoporphyrinogen IX	mutant K71A, pH 7.5, temperature not specified in the publication	Bacillus subtilis
0.001	-	protoporphyrinogen IX	mutant I176A, pH 7.5, temperature not specified in the publication	Bacillus subtilis
0.0027	-	protoporphyrinogen IX	mutant P64A, pH 7.5, temperature not specified in the publication	Bacillus subtilis
0.0131	-	protoporphyrinogen IX	wild-type enzyme, pH 7.5, temperature not specified in the publication	Bacillus subtilis
0.0181	-	protoporphyrinogen IX	mutant F227R, pH 7.5, temperature not specified in the publication	Bacillus subtilis

pH Optimum

pH Optimum Minimum	pH Optimum Maximum	Comment	Organism
7.5	-	assay at	Bacillus subtilis

Cofactor

Cofactor	Comment	Organism	Structure
FAD	a FAD molecule is non-covalently bound to domain I, binding structure, overview	Bacillus subtilis

General Information

General Information	Comment	Organism
metabolism	PPO plays an important part in the heme/chlorophyll biosynthetic pathway	Bacillus subtilis

kcat/KM [mM/s]

kcat/KM Value [1/mMs^-1]	kcat/KM Value Maximum [1/mMs^-1]	Substrate	Comment	Organism
0.016	-	protoporphyrinogen IX	mutant K71A, pH 7.5, temperature not specified in the publication	Bacillus subtilis
0.027	-	protoporphyrinogen IX	mutant I176A, pH 7.5, temperature not specified in the publication	Bacillus subtilis
0.057	-	protoporphyrinogen IX	mutant P64A, pH 7.5, temperature not specified in the publication	Bacillus subtilis
0.464	-	protoporphyrinogen IX	mutant F227R, pH 7.5, temperature not specified in the publication	Bacillus subtilis
0.784	-	protoporphyrinogen IX	wild-type enzyme, pH 7.5, temperature not specified in the publication	Bacillus subtilis