Literature summary for 1.3.7.2 extracted from

Ledermann, B.; Schwan, M.; Sommerkamp, J.A.; Hofmann, E.; Beja, O.; Frankenberg-Dinkel, N.
Evolution and molecular mechanism of four-electron reducing ferredoxin-dependent bilin reductases from oceanic phages (2018), FEBS J., 285, 339-356 .

Search for more literature for 1.3.7.2

Cloned(Commentary)

Cloned (Comment)	Organism
gene pcyA or BRADO1265, CAL75167, phylogenetic analysis and tree, recombinant expression of GST-tagged enzyme in Escherichia coli strain BL21(DE3), coexpression of the chaperone pair GroES/GroEL	Bradyrhizobium sp. ORS 278

Protein Variants

Protein Variants	Comment	Organism
D105N	site-directed mutagenesis, altered substrate biliverdin binding compared to wild-type, the mutant shows 89% reduced activity compared to wild-type	Bradyrhizobium sp. ORS 278
E76Q	site-directed mutagenesis, the mutant shows 80% reduced activity compared to wild-type	Bradyrhizobium sp. ORS 278
H88Q	site-directed mutagenesis, altered substrate biliverdin binding compared to wild-type, the mutant shows 95% reduced activity compared to wild-type	Bradyrhizobium sp. ORS 278
I86D	site-directed mutagenesis, inactive mutant	Bradyrhizobium sp. ORS 278

Metals/Ions

Metals/Ions	Comment	Organism	Structure
Fe2+	in cofactor ferredoxin	Bradyrhizobium sp. ORS 278

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
biliverdin IXalpha + reduced ferredoxin	Bradyrhizobium sp. ORS 278	-	15,16-dihydrobiliverdin + oxidized ferredoxin	-	?

Organism

Organism	UniProt	Comment	Textmining
Bradyrhizobium sp. ORS 278	-	-	-

Purification (Commentary)

Purification (Comment)	Organism
recombinant GST-tagged enzyme from Escherichia coli strain BL21(DE3) by glutathione affinity chromatography, ultrafiltration, and gel filtration	Bradyrhizobium sp. ORS 278

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
biliverdin IXalpha + reduced ferredoxin	-	Bradyrhizobium sp. ORS 278	15,16-dihydrobiliverdin + oxidized ferredoxin	-	?

Synonyms

Synonyms	Comment	Organism
BRADO1265	-	Bradyrhizobium sp. ORS 278
FDBR	-	Bradyrhizobium sp. ORS 278
ferredoxin-dependent bilin reductase	-	Bradyrhizobium sp. ORS 278
PcyA	-	Bradyrhizobium sp. ORS 278

Cofactor

Cofactor	Comment	Organism	Structure
Ferredoxin	-	Bradyrhizobium sp. ORS 278

General Information

General Information	Comment	Organism
evolution	ferredoxin-dependent bilin reductases (FDBRs) are a class of enzymes reducing the heme metabolite biliverdin IXa (BV) to form open-chain tetrapyrroles used for light-perception and light-harvesting in photosynthetic organisms. Evolution and molecular mechanism of four-electron reducing ferredoxin-dependent bilin reductases from oceanic phages, overview. PcyX is originally identified from metagenomics data derived from phage. PcyA (EC 1.3.7.2) is the closest relative catalysing the reduction of biliverdin (BV) to phycocyanobilin. But PcyX converts the same substrate to phycoerythrobilin, resembling the reaction catalysed by cyanophage PebS. But the change in regiospecificity from PcyA to PcyX is not only caused by individual catalytic amino acid residues. Rather the combination of the architecture of the active site with the positioning of the substrate triggers specific proton transfer yielding the individual phycobilin products. Phylogenetic analysis and tree suggest PcyX sequences forming a distinct clade	Bradyrhizobium sp. ORS 278
additional information	a conserved aspartate-histidine pair is critical for activity of PcyA. PcyA contains the catalytic Asp-His-Glu triad. Strutcure comparisons of FDBRs, PcyA and PcyX, overview. Ile86 in PcyA is replaced by Met67, whereas Val90 is substituted by Cys71 in PcyX. Both are strictly conserved in all PcyX sequences, but small hydrophobic residues in all other FDBR. Due to the disorder on the distal side of the binding pocket, residues corresponding to Asn219 in PcyA or to Asp206 in PebS are not visible in our PcyX structure. Glu76 of PcyA is central for exovinyl-reduction	Bradyrhizobium sp. ORS 278

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Release 2023.1 (January 2023)