Literature summary for 1.3.7.4 extracted from

Sugishima, M.; Wada, K.; Fukuyama, K.; Yamamoto, K.
Crystal structure of phytochromobilin synthase in complex with biliverdin IXalpha, a key enzyme in the biosynthesis of phytochrome (2020), J. Biol. Chem., 295, 771-782 .

Cloned(Commentary)

Cloned (Comment)	Organism
recombinant overexpression of His-tagged enzyme in Escherichia coli strain BL21(DE3)	Solanum lycopersicum

Crystallization (Commentary)

Crystallization (Comment)	Organism
purified recombinant wild-type and selenomethionine-labeled phytochromobilin synthase in complex with substrate biliverdin IXalpha, sitting drop vapor diffusion method, mixing of protein in 150 mM KCl, and 20 mM Tris-HCl, pH 7.4, with reservoir solution, at 4°C. Tiny needle-shaped crystals of the BV-PPhiB synthase complex are obtained with a reservoir solution containing 20% w/v PEG 8000, 0.1 M Tris-HCl, pH 8.5, and 0.2 M MgCl2. Isomorphous crystals are also obtained with a reservoir solution containing 30% w/v PEG 4000, 0.1 M Tris-HCl, pH 8.5, and 0.2 M MgCl2, X-ray diffraction structure determination and analysis at 1.95-2.2 A resolution	Solanum lycopersicum

Crystallization (Comment)

Organism

purified recombinant wild-type and selenomethionine-labeled phytochromobilin synthase in complex with substrate biliverdin IXalpha, sitting drop vapor diffusion method, mixing of protein in 150 mM KCl, and 20 mM Tris-HCl, pH 7.4, with reservoir solution, at 4°C. Tiny needle-shaped crystals of the BV-PPhiB synthase complex are obtained with a reservoir solution containing 20% w/v PEG 8000, 0.1 M Tris-HCl, pH 8.5, and 0.2 M MgCl2. Isomorphous crystals are also obtained with a reservoir solution containing 30% w/v PEG 4000, 0.1 M Tris-HCl, pH 8.5, and 0.2 M MgCl2, X-ray diffraction structure determination and analysis at 1.95-2.2 A resolution

Solanum lycopersicum

Protein Variants

Protein Variants	Comment	Organism
D123N	site-directed mutagenesis, the mutated enzyme retains biliverdin IXalpha binding activity and radical formation activity, whereas the PPhiB formation activity is negligible	Solanum lycopersicum
D263N	site-directed mutagenesis, the mutated enzyme retains biliverdin IXalpha binding activity and radical formation activity, whereas the PPhiB formation activity is negligible	Solanum lycopersicum
V121A	site-directed mutagenesis, single-turnover analysis demonstrates that the V121A mutated protein is slightly slower, although it produces 3Z/E-PPhiB on wild-type level, whereas no activity is detected in the V121A mutated protein in the steady-state analysis	Solanum lycopersicum

Metals/Ions

Metals/Ions	Comment	Organism	Structure
Fe2+	in cofactor ferrdoxin	Solanum lycopersicum

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
biliverdin IXalpha + 2 reduced ferredoxin	Solanum lycopersicum	-	(3Z)-phytochromobilin + 2 oxidized ferredoxin	-	?

Organism

Organism	UniProt	Comment	Textmining
Solanum lycopersicum	Q588D6	-	-

Purification (Commentary)

Purification (Comment)	Organism
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography, anion exchange chromatography, and gel filtration. The PPhiB synthase monomer is contained in the major peak of anion-exchange chromatography, and the PPhiB synthase homodimer in the minor peak, for purification, the monomeric major peak fraction is used	Solanum lycopersicum

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
biliverdin IXalpha + 2 reduced ferredoxin	-	Solanum lycopersicum	(3Z)-phytochromobilin + 2 oxidized ferredoxin	-	?
biliverdin IXalpha + 2 reduced ferredoxin	substrate binding structure analysis, overview	Solanum lycopersicum	(3Z)-phytochromobilin + 2 oxidized ferredoxin	-	?
additional information	two aspartic acid residues, Asp123 and Asp263, form hydrogen bonds with water molecules and are essential for the site-specific A-ring reduction of biliverdin. PPhiB synthase catalyzes the reduction of BV to produce 2(R), 3Z/E-PPhiB using reducing equivalents from ferredoxin. The 2,3,31,32-diene system of the A-ring is site-specifically reduced. The ZZZssa configurations of BV and PPhiB are displayed as observed in the present crystal structure	Solanum lycopersicum	?	-	-

Synonyms

Synonyms	Comment	Organism
phytochromobilin synthase	-	Solanum lycopersicum
PphiB synthase	-	Solanum lycopersicum

Temperature Optimum [°C]

Temperature Optimum [°C]	Temperature Optimum Maximum [°C]	Comment	Organism
20	-	assay at	Solanum lycopersicum

pH Optimum

pH Optimum Minimum	pH Optimum Maximum	Comment	Organism
8	-	assay at	Solanum lycopersicum

Cofactor

Cofactor	Comment	Organism	Structure
Ferredoxin	enzyme binding structure and interaction analysis	Solanum lycopersicum

General Information

General Information	Comment	Organism
evolution	enzyme structure analysis and comparison, overview. PPhiB synthase is a member of the ferredoxin-dependent bilin reductase (FDBR) family. The FDBR family comprises several different but closely related proteins including phycocyanobilin: ferredoxin oxidoreductase (PcyA, EC 1.3.7.5), 15,16-dihydrobiliverdin:ferredoxin oxidoreductase (PebA, EC 1.3.7.2), phycoerythrobilin:ferredoxin oxidoreductase (PebB, EC 1.3.7.3), phycoerythrobilin synthase (PebS, EC 1.3.7.6), and PPhiB synthase (EC 1.3.7.4). These enzymes are widely distributed in oxygenic phototrophs	Solanum lycopersicum
additional information	the overall structure of tomato PPhiB synthase is similar to those of other ferredoxin-dependent bilin reductases (FDBRs), except for the addition of a long C-terminal loop and short helices. The C-terminal loop is part of the biliverdin-binding pocket and that two basic residues in the C-terminal loop form salt bridges with the propionate groups of biliverdin. The C-terminal loop is involved in the interaction with ferredoxin and biliverdin. The configuration of biliverdin bound to tomato PPhiB synthase differed from that of biliverdin ound to other FDBRs, and its orientation in PPhiB synthase is inverted relative to its orientation in the other FDBRs. Enzyme structure analysis and comparison, overview. Two aspartic acid residues, Asp123 and Asp263, form hydrogen bonds with water molecules and are essential for the site-specific A-ring reduction of biliverdin. Product release mechanism: PPhiB synthase-catalyzed stereospecific reduction produces 2(R)-PPhiB, which when bound to PPhiB synthase collides with the side chain of Val-121, releasing 2(R)-PPhiB from the synthase	Solanum lycopersicum
physiological function	PPhiB synthase is a ferredoxin-dependent bilin reductase (FDBR) that catalyzes the site-specific reduction of bilins, which are sensory and photosynthesis pigments, and produces phytochromobilin (PPhiB) from biliverdin, a heme-derived linear tetrapyrrole pigment. Phytochromobilin is a red/far-red light sensory pigment in plant phytochrome	Solanum lycopersicum