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Literature summary extracted from

  • Busch, A.W.; Reijerse, E.J.; Lubitz, W.; Frankenberg-Dinkel, N.; Hofmann, E.
    Structural and mechanistic insight into the ferredoxin-mediated two-electron reduction of bilins (2011), Biochem. J., 439, 257-264.
    View publication on PubMed

Cloned(Commentary)

EC Number Cloned (Comment) Organism
1.3.7.2 gene pebA, recombinant expression of wild-type and mutant enzymes, native and selenomethionine-labeled PebA Synechococcus sp.
1.3.7.3 gene pebB, recombinant expression of wild-type and mutant enzymes Synechococcus sp.

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
1.3.7.2 PebA in complex with substrate biliverdin IXalpha, hanging drop vapour diffusion method, 12-20 mg/ml protein in 0.1 M HEPE, pH 7.0, and 28% PEG 4000, 18°C, X-ray diffraction structure determination and analysis at 1.55 A resolution Synechococcus sp.

Protein Variants

EC Number Protein Variants Comment Organism
1.3.7.2 D205N site-directed mutagenesis, the mutant retains activity Synechococcus sp.
1.3.7.2 D84E site-directed mutagenesis, the mutant retains activity Synechococcus sp.
1.3.7.2 D84N site-directed mutagenesis, inactive mutant Synechococcus sp.
1.3.7.3 D107E site-directed mutagenesis, the mutant retains activity Synechococcus sp.
1.3.7.3 D107N site-directed mutagenesis, inactive mutant Synechococcus sp.
1.3.7.3 D231E site-directed mutagenesis, the mutant retains activity Synechococcus sp.
1.3.7.3 D231N site-directed mutagenesis, inactive mutant Synechococcus sp.
1.3.7.6 D105E site-directed mutagenesis, the mutant catalyzes only the first reaction step, i.e. the formation of 15,16-dihydrobiliverdin, reaction of EC 1.3.7.2 Prochlorococcus phage P-SSM2
1.3.7.6 D105N site-directed mutagenesis, inactive mutant Prochlorococcus phage P-SSM2
1.3.7.6 D206E site-directed mutagenesis, the mutant catalyzes only the second reaction step, i.e. the formation of (3Z)-phycoerythrobilin from 15,16-dihydrobiliverdin, reaction of EC 1.3.7.3 Prochlorococcus phage P-SSM2
1.3.7.6 D206N site-directed mutagenesis, the mutant catalyzes only the first reaction step, i.e. the formation of 15,16-dihydrobiliverdin, reaction of EC 1.3.7.2 Prochlorococcus phage P-SSM2

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
1.3.7.2 15,16-dihydrobiliverdin + oxidized ferrdoxin Synechococcus sp. the 15,16-DHBV:ferredoxin oxidoreductase PebA reduces biliverdin IXalpha at the C15–C16 double bond to produce 15,16-dihydrobiliverdin biliverdin IXalpha + reduced ferrdoxin
-
 r
1.3.7.2 15,16-dihydrobiliverdin + oxidized ferrdoxin Synechococcus sp. WH8020 the 15,16-DHBV:ferredoxin oxidoreductase PebA reduces biliverdin IXalpha at the C15–C16 double bond to produce 15,16-dihydrobiliverdin biliverdin IXalpha + reduced ferrdoxin
-
 r
1.3.7.3 (3Z)-phycoerythrobilin + oxidized ferredoxin Synechococcus sp.
-
 15,16-dihydrobiliverdin + reduced ferredoxin
-
 ?
1.3.7.3 (3Z)-phycoerythrobilin + oxidized ferredoxin Synechococcus sp. WH8020
-
 15,16-dihydrobiliverdin + reduced ferredoxin
-
 ?
1.3.7.6 biliverdin IXalpha + 2 reduced ferredoxin Prochlorococcus phage P-SSM2 a two-step reaction via intermediate 15,16-dihydrobiliverdin, the single steps form the reactions of EC 1.3.7.2 and 1.3.7.3, overview (3Z)-phycoerythrobilin + 2 oxidized ferredoxin
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
1.3.7.2 Synechococcus sp. Q02189 gene pebA
-
1.3.7.2 Synechococcus sp. WH8020 Q02189 gene pebA
-
1.3.7.3 Synechococcus sp.
-
 gene pebB
-
1.3.7.3 Synechococcus sp. WH8020
-
 gene pebB
-
1.3.7.6 Prochlorococcus phage P-SSM2
-
-
-

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
1.3.7.2 15,16-dihydrobiliverdin + oxidized ferrdoxin the 15,16-DHBV:ferredoxin oxidoreductase PebA reduces biliverdin IXalpha at the C15–C16 double bond to produce 15,16-dihydrobiliverdin Synechococcus sp. biliverdin IXalpha + reduced ferrdoxin
-
 r
1.3.7.2 15,16-dihydrobiliverdin + oxidized ferrdoxin the 15,16-DHBV:ferredoxin oxidoreductase PebA reduces biliverdin IXalpha at the C15–C16 double bond to produce 15,16-dihydrobiliverdin, assay under anaerobic conditions Synechococcus sp. biliverdin IXalpha + reduced ferrdoxin
-
 r
1.3.7.2 15,16-dihydrobiliverdin + oxidized ferrdoxin the 15,16-DHBV:ferredoxin oxidoreductase PebA reduces biliverdin IXalpha at the C15–C16 double bond to produce 15,16-dihydrobiliverdin Synechococcus sp. WH8020 biliverdin IXalpha + reduced ferrdoxin
-
 r
1.3.7.2 15,16-dihydrobiliverdin + oxidized ferrdoxin the 15,16-DHBV:ferredoxin oxidoreductase PebA reduces biliverdin IXalpha at the C15–C16 double bond to produce 15,16-dihydrobiliverdin, assay under anaerobic conditions Synechococcus sp. WH8020 biliverdin IXalpha + reduced ferrdoxin
-
 r
1.3.7.3 (3Z)-phycoerythrobilin + oxidized ferredoxin
-
 Synechococcus sp. 15,16-dihydrobiliverdin + reduced ferredoxin
-
 ?
1.3.7.3 (3Z)-phycoerythrobilin + oxidized ferredoxin
-
 Synechococcus sp. WH8020 15,16-dihydrobiliverdin + reduced ferredoxin
-
 ?
1.3.7.6 biliverdin IXalpha + 2 reduced ferredoxin
-
 Prochlorococcus phage P-SSM2 (3Z)-phycoerythrobilin + 2 oxidized ferredoxin
-
 ?
1.3.7.6 biliverdin IXalpha + 2 reduced ferredoxin a two-step reaction via intermediate 15,16-dihydrobiliverdin, the single steps form the reactions of EC 1.3.7.2 and 1.3.7.3, overview Prochlorococcus phage P-SSM2 (3Z)-phycoerythrobilin + 2 oxidized ferredoxin
-
 ?

Synonyms

EC Number Synonyms Comment Organism
1.3.7.2 15,16-DHBV:ferredoxin oxidoreductase
-
 Synechococcus sp.
1.3.7.2 ferredoxin-dependent bilin reductase
-
 Synechococcus sp.
1.3.7.2 PebA
-
 Synechococcus sp.
1.3.7.3 PEB:ferredoxin oxidoreductase
-
 Synechococcus sp.
1.3.7.3 PebB
-
 Synechococcus sp.
1.3.7.6 PEB synthase
-
 Prochlorococcus phage P-SSM2
1.3.7.6 PebS
-
 Prochlorococcus phage P-SSM2
1.3.7.6 phycoerythrobilin synthase
-
 Prochlorococcus phage P-SSM2

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
1.3.7.3 20
-
 assay at Synechococcus sp.

Cofactor

EC Number Cofactor Comment Organism Structure
1.3.7.2 Ferredoxin
-
 Synechococcus sp.
1.3.7.3 Ferredoxin
-
 Synechococcus sp.
1.3.7.6 Ferredoxin
-
 Prochlorococcus phage P-SSM2

General Information

EC Number General Information Comment Organism
1.3.7.2 evolution the enzyme belongs to the ferredoxin-dependent bilin reductase family. All members of the FDBR family are radical enzymes Synechococcus sp.
1.3.7.2 metabolism PebB, phycoerythrobilinPEB:ferredoxin oxidoreductase, EC 1.3.7.3, acts in tandem with PebA, 15,16-DHBV:ferredoxin oxidoreductase, which reduces biliverdin IXalpha at the C15-C16 double bond to produce 15,16-dihydrobiliverdin. Both enzymes function in close contact for metabolic channeling of 15,16-dihydrobiliverdin Synechococcus sp.
1.3.7.2 additional information the highly conserved aspartate residue Asp105 is critical for the reduction. In addition to the importance of certain catalytic residues, the shape of the active site and consequently the binding of the substrate highly determines the catalytic properties Synechococcus sp.
1.3.7.3 evolution the enzyme belongs to the the ferredoxin-dependent bilin reductase family. All members of the FDBR family are radical enzymes Synechococcus sp.
1.3.7.3 metabolism PebB, i.e. phycoerythrobilinPEB:ferredoxin oxidoreductase, acts in tandem with PebA, i.e. 15,16-DHBV:ferredoxin oxidoreductase, EC 1.3.7.2, which reduces biliverdin IXalpha at the C15-C16 double bond to produce 15,16-dihydrobiliverdin. Both enzymes function in close contact for metabolic channeling of 15,16-dihydrobiliverdin Synechococcus sp.
1.3.7.3 additional information the highly conserved aspartate residues Asp107 and Asp231 are critical for the reduction. In addition to the importance of certain catalytic residues, the shape of the active site and consequently the binding of the substrate highly determines the catalytic properties Synechococcus sp.
1.3.7.6 evolution the enzyme belongs to the ferredoxin-dependent bilin reductase family Prochlorococcus phage P-SSM2
1.3.7.6 metabolism a two-step reaction via intermediate 15,16-dihydrobiliverdin, the single steps form the reactions of EC 1.3.7.2 and 1.3.7.3, overview Prochlorococcus phage P-SSM2
1.3.7.6 additional information aspartate residues Asp105 and Asp206 are both involved in interactions with the pyrrole nitrogens upon substrate binding. Both are essential for the complete reduction of biliverdin IXalpha to (3Z)-phycoerythrobilin by PebS and are highly conserved throughout the family of ferredoxin-dependent bilin reductases Prochlorococcus phage P-SSM2