BRENDA - Information on EC 1.3.7.5 - phycocyanobilin:ferredoxin oxidoreductase

3Z-phycocyanobilin:ferredoxin oxidoreductase

2 entries

ferredoxin:3Z-phycocyanobilin oxidoreductase

-

oxidoreductase, ferredoxin:3Z-phycocyanobilin

-

Pcb:Fd oxidoreductase

Thermosynechococcus elongatus

-

712008

PCB:ferredoxin oxidoreductase

2 entries

PcyA

13 entries

phycocyanobilin synthase

2 entries

phycocyanobilin-ferredoxin oxidoreductase

Nostoc sp. PCC 7120

Q93TN0

-

685125

phycocyanobilin:ferredoxin oxidoreductase

3 entries

(3Z)-phycocyanobilin + 4 oxidized ferredoxin = biliverdin IXalpha + 4 reduced ferredoxin

-

oxidation

-

redox reaction

-

reduction

-

KEGG

Biosynthesis of secondary metabolites, Porphyrin and chlorophyll metabolism

MetaCyc

phycocyanobilin biosynthesis, phycoviolobilin biosynthesis

(3Z)-phycocyanobilin:ferredoxin oxidoreductase

Catalyses the four-electron reduction of biliverdin IXalpha (2-electron reduction at both the A and D rings). Reaction proceeds via an isolatable 2-electron intermediate, 181,182-dihydrobiliverdin. Flavodoxins can be used instead of ferredoxin. The direct conversion of biliverdin IXalpha (BV) to (3Z)-phycocyanolbilin (PCB) in the cyanobacteria Synechocystis sp. PCC 6803, Anabaena sp. PCC7120 and Nostoc punctiforme is in contrast to the proposed pathways of PCB biosynthesis in the red alga Cyanidium caldarium, which involves (3Z)-phycoerythrobilin (PEB) as an intermediate [2] and in the green alga Mesotaenium caldariorum, in which PCB is an isolable intermediate.

347401-12-1

-

(3Z)-phycocyanobilin + oxidized ferredoxin

biliverdin IXa + reduced ferredoxin

10 entries

biliverdin IXa + reduced ferredoxin

(3Z)-phycocyanobilin + oxidized ferredoxin

5 entries

biliverdin IXa diamide + reduced ferredoxin

? + oxidized ferredoxin

2 entries

biliverdin IXalpha + reduced ferredoxin

(3E)-phycocyanobilin + oxidized ferredoxin

Anabaena sp.

-

Synechococcus ferredoxin

655796

-

?

biliverdin Ixalpha + reduced ferredoxin

(3Z)-phycocyanobilin + oxidized ferredoxin

15 entries

biliverdin IXalpha + reduced ferredoxin

phycocyanobilin + oxidized ferredoxin

5 entries

biliverdin IXalpha 12-monoamide + reduced ferredoxin

phycocyanobilin 12-monoamide + oxidized ferredoxin

2 entries

biliverdin IXalpha 8-monoamide + reduced ferredoxin

phycocyanobilin 8-monoamide + oxidized ferredoxin

Anabaena sp.

-

724287

products are corresponding phycocyanobilin monoamides with a mix of the 3E and 3Z forms

-

?

biliverdin XIII + reduced ferredoxin

phycocyanobilin + oxidized ferredoxin

Anabaena sp.

-

724287

biliverdin XIII contains two endovinyl groups, so PcyA can convert either (or both) to an ethylidene

-

?

biliverdin XIIIalpha + reduced ferredoxin

(3E)-isophytochromobilin + oxidized ferredoxin

2 entries

biliverdin XIIIalpha + reduced ferredoxin

(3Z)-isophytochromobilin + oxidized ferredoxin

2 entries

biliverdin XIIIalpha + reduced ferredoxin

? + oxidized ferredoxin

2 entries

biliverdin XIIIalpha monoamide + reduced ferredoxin

? + oxidized ferredoxin

Anabaena sp.

-

724287

mixture of products

-

?

additional information

?

-

2 entries

biliverdin Ixalpha + reduced ferredoxin

(3Z)-phycocyanobilin + oxidized ferredoxin

9 entries

biliverdin IXalpha + reduced ferredoxin

phycocyanobilin + oxidized ferredoxin

2 entries

Ferredoxin

4 entries

-

Diethylpyrocarbonate

Nostoc sp.

-

reduces PcyA activity to less than 20% of mock-treated enzyme within 10 min, diethylpyrocarbonate-inactivation can be prevented by the presence of biliverdin IXa substrate

674669

6

Anabaena sp.

-

assay with substrate biliverdin diamide

724287

7.5

Thermosynechococcus elongatus

-

assay at

712008

8.5

2 entries

16

Synechocystis sp.

-

assay at

724131

25

Thermosynechococcus elongatus

-

assay at

712008

Anabaena sp.

3 entries

Anabaena sp. PCC 7120

-

674771, 724287

-

Mesotaenium caldariorum

green alga

-

-

Uniprot

-

-

-

-

Prochlorococcus sp. CCMP1378 / MED4

-

437673

-

Synechococcus sp.

-

437673, 673636, 724317, 725252

-

Synechococcus sp. 7002

-

724317

-

Synechococcus sp. W8020

-

673636

-

Synechococcus sp. WH8102

-

437673

-

Synechocystis sp.

9 entries

Synechocystis sp. PCC 6803

-

742318, 742524

Q55891

UniProt

Thermosynechococcus elongatus

-

712008

-

chloroplast

Mesotaenium caldariorum

-

soluble

evolution

malfunction

metabolism

physiological function

4 entries

additional information

6 entries

2g18, download, 3D-view

SCOPe (2g18)

CATH (2g18)

Q93TN0

Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)

18 entries

Synechocystis sp. (strain PCC 6803 / Kazusa)

27000

Thermosynechococcus elongatus

-

x * 27000, recombinant enzyme, SDS-PAGE

712008

28700

Anabaena sp.

-

SDS-PAGE

437673

28726

Anabaena sp.

-

1 * 28726, deduced from nucleotide sequence

28900

SDS-PAGE

30400

-

gel filtration, glycerol gradient sedimentation

656197

?

Thermosynechococcus elongatus

-

x * 27000, recombinant enzyme, SDS-PAGE

712008

monomer

Anabaena sp.

-

1 * 28726, deduced from nucleotide sequence

656197

additional information

2 entries

hanging drop vapour diffusion method with 18% PEG-8000, 0.025 M MES-NaOH at pH 6.5, 0.05 M Ca(OAc)2 at pH 6.5, and 5% dioxane (or 5% ethanol)

Nostoc sp. PCC 7120

Q93TN0

685125

high-field electron paramagnetic resonance spectroscopy of frozen solutions and single crystals of the one-electron reduced protein-substrate complex of mutant D102N. Spectra reveal a biliverdin radical with a very narrow g tensor. This g tensor is consistent with a biliverdin radical where the carbonyl oxygen atoms on both the A and the D pyrrole rings are protonated

Nostoc sp. PCC 7120

Q93TN0

698489

high-field electron paramagnetic resonance spectroscopy of frozen solutions and single crystals of the one-electron reduced protein-substrate complex of mutant D105N. Spectra reveal a biliverdin radical with a very narrow g tensor with principal values 2.00359(5), 2.00341(5), and 2.00218(5). This g tensor is consistent with a biliverdin radical where the carbonyl oxygen atoms on both the A and the D pyrrole rings are protonated

Synechocystis sp.

-

698489

PcyA–biliverdin IXalpha complex by the hanging-drop vapor-diffusion method, PcyA is folded in a three-layer alpha/beta/alpha sandwich structure, in which biliverdin IXalpha in a cyclic conformation is positioned between the beta-sheet and C-terminal alpha-helices

Synechocystis sp.

Q55891

676847

purified recombinant enzyme mutant V225D in complex with substrates biliverdin IXalpha or biliverdin XIIIalpha, mixing of 0.0009 ml of protein solution, containing 11.5 mg/ml protein and biliverdin, with 0.0009 ml of reservoir solution containing 0.8-1.0 M NaH2PO4, 1.0-1.2 M K2HPO4, and 100 mM sodium acetate, pH 4.0, 20°C, a few days, X-ray diffraction structure determination and analysis at 1.9 A resolution

Synechocystis sp.

-

711117

purified recombinant mutant enzymes, hanging drop vapour diffusion method, dithionite-treated reduced D105N PcyA crystals from 1.45-1.8 M ammonium sulfate, 0.15-0.4 M NaCl, and 0.1 M HEPES, pH 7.0, dithionite-treated reduced H88Q PcyA crystals from 1.7-2.2 M ammonium sulfate, 0.26-0.32 M NaCl, and 0.1 M sodium cacodylate, pH 7.0, 20°C in the dark, cryoprotectant solution is consisting of 30% v/v ethylene glycol in mother liquor, X-ray diffraction structure determination and analysis at 1.5 A resolution

Synechocystis sp.

-

724288

purified recombinant wild-type and mutant enzymes, hanging drop vapor diffusion method, mixing of 0.002 ml of protein solution containing 15 mg/mL protein and 0.67 mM biliverdin IXalpha, with 0.002 ml of reservoir solution containing 1-1.25 M sodium citrate, 0.1-0.4 M NaCl, and 0.1 M Tris HCl, pH 7.0, 21°C, 1-2 weeks. Crystal trials are set up under green safelight and stored in the dark, X-ray diffraction structure determination and analysis at 1.18-1.49 A resolution

Synechocystis sp.

-

724131

purified recombinant wild-type PcyA and PcyA-E76Q mutant in complex with 18EtBV or biloverdin IXalpha and biliverdin XIIIalpha, hanging drop vapor diffusion method, 20°C, method optimization, protein solution containing wild-type PcyA or mutant E76Q and bilin is mixed with reservoir solutions containing 0.85 M sodium citrate, 0.1 M sodium cacodylate, pH 7.0, for the PcyA-18EtBV complex and 2.0 M ammonium sulfate, 0.2 M NaCl, and 0.1M sodium cacodylate, pH7.0, for the PcyA-BV13 complex, for the mutant a reservoir solution containing 1.7 M ammonium sulfate, 2% PEG 400, and 0.1 M HEPES, pH 7.0, is used, X-ray diffraction structure determination and analysis at 1.04-1.48 A resolution

Synechocystis sp.

-

712411

substrate-free form of PcyA by the hanging-drop vapor-diffusion method, at 2.5 A resolution, the side-chain of Asp105 is located at a site that would be underneath the biliverdin IXa A-ring in the PcyA-biliverdin IXa complex and hydrogen-bonded with His88, biliverdin IXa may be protonated by a mechanism involving conformational changes of these two residues before reduction

Synechocystis sp.

-

673657

quantum mechanical approaches show that the propensity of biliverdin to bind PcyA is dominated by electrostatic interactions, especially related to residues Arg149 and Lys221, while H-bonds are formed with His88 and Ser114. The antioxidant activity is dependent on the intramolecular noncovalent bond interactions. The surrounding residues increase the antioxidant character of biliverdin by 2 eV

Synechocystis sp. PCC 6803

-

742318

structure of the I86D-BVH+ complex and the protonation states of residues Asp105 and Glu76 in PcyA. Asp105 adopts a fixed conformation in the I86D mutant, but has dual conformations in wild-type PcyA which reflects the protonation states of biliverdin

Synechocystis sp. PCC 6803

-

742524

C210A

Nostoc sp.

-

retains 90% relative to wild type

674669

C86A

Nostoc sp.

-

retains 90% activity relative to wild type

674669

D102N

Nostoc sp.

-

retains 11% activity relative to wild type

674669

D116N

Nostoc sp.

-

retains 11% activity relative to wild type

674669

D217N

Nostoc sp.

-

retains 87% relative to wild type

674669

H71A

Nostoc sp.

-

retains less than 1% activity relative to wild type

674669

H71D

Nostoc sp.

-

retains 28% activity relative to wild type

674669

H71E

Nostoc sp.

-

retains 50% activity relative to wild type

674669

H71N

Nostoc sp.

-

retains 46% activity relative to wild type

674669

H71Q

Nostoc sp.

-

retains 65% activity relative to wild type

674669

H85A

Nostoc sp.

-

retains less than 1% activity relative to wild type

674669

H85D

Nostoc sp.

-

retains less than 1% activity relative to wild type

674669

H85E

Nostoc sp.

-

retains 5% activity relative to wild type

674669

H85N

Nostoc sp.

-

retains less than 1% activity relative to wild type

674669

H85Q

Nostoc sp.

-

retains 5% activity relative to wild type

674669

K218E

Nostoc sp.

-

retains 20% activity relative to wild type

D102N

E73Q

exhibits 20% of wild type activity

685125

H71Q

Nostoc sp. PCC 7120

Q93TN0

exhibits 65% of wild type activity

685125

H85Q

Nostoc sp. PCC 7120

Q93TN0

exhibits 5% of wild type activity

685125

K218E

Nostoc sp. PCC 7120

Q93TN0

exhibits 20% of wild type activity

685125

D105N

2 entries

E76Q

Synechocystis sp.

-

site-directed mutagenesis, substrate-binding structure compared to the wild-type enzyme. Overall folds and the binding sites of the U-shaped substrates of all three complexes are similar with wild-type PcyABV, the orientation of the Glu76 side chain, which is in close contact with the exo-vinyl group in PcyA-biliverdin IXalpha, is rotated away from the bilin D-ring. The local structures around the A-rings in the three complexes, which all retain the ability to reduce the A-ring of their bound pigments, are nearly identical with that of wild-type PcyA-biliverdin IXalpha

712411

H74A

Synechocystis sp.

-

site-directed mutagenesis, inactive mutant

724131

H74E

Synechocystis sp.

-

site-directed mutagenesis, the mutant retains reasonable activity

724131

H74Q

Synechocystis sp.

-

site-directed mutagenesis, the mutant retains reasonable activity

724131

H88Q

2 entries

V225D

Synechocystis sp.

-

site-directed mutagenesis,substrate binding structure, overview

711117

I86D

Synechocystis sp. PCC 6803

-

biliverdin bound to the I86D mutant is fully protonated (BVH+) and can accept an electron, but I86D is unable to donate protons for the reduction. Compared to the wild-type PcyA, the I86D mutant stabilizes BVH+

742524

additional information

3 entries

-30°C, purified recombinant enzyme, 50 mM HEPES-NaOH, pH 7.5, containing 100 mM NaCl, 6 months, full activity is maintained

Thermosynechococcus elongatus

-

-80°C

-

-

by gel filtration

recombinant enzyme from Escherichia coli strain BL21(DE3) by anion-exchange chromatography, hydrophobic interaction chromatography, hydroxyapatite chromatography, and gel filtration

Thermosynechococcus elongatus

-

712008

recombinant GST-tagged PcyA from Escherichia coli by glutathione affinity chromatography

Anabaena sp.

-

724287

recombinant mutant enzymes from Escherichia coli strain BL21(DE3) by cyanide affinity chromatography

-

recombinant PcyA

-

recombinant wild-type and mutant enzymes from Escherichia coli strain Bl21(DE3)

Synechocystis sp.

-

724131

Superdex G-200 gel filtration

Nostoc sp. PCC 7120

Q93TN0

685125

wild-type and mutants, histidine mutants purified to homogeneity

Nostoc sp.

-

674669

-

6 entries

cloned into plasmid containing the sequence coding for HO1 protein

Synechocystis sp.

-

437764

coexpression in Escherichia coli BL21(DE3) with cpcB(C155I) or pecB(C155I) and with cpeS, ho1 and pcyA, resulting in biosynthesis of the respective beta-subunits singly chromophorylated at cysteine-beta84

Anabaena sp.

-

674771

expression in Arabidopsis thaliana

Synechocystis sp.

-

657164

expression in Escherichia coli

2 entries

expression of mutant enzymes in Escherichia coli strain BL21(DE3)

Synechocystis sp.

-

724288

gene pycA, expression of wild-type and mutant enzymes in Escherichia coli strain BL21(DE3)

Synechocystis sp.

-

724131

into vector pET-21a and expressed in Escherichia coli C41(DE3)

Synechocystis sp.

Q55891

676847

PcyA expression in Escherichia coli strain BL21(DE3)

Thermosynechococcus elongatus

-

712008

recombinant expression of GST-tagged PcyA in Escherichia coli

Anabaena sp.

-

724287

recombinant functional expression of PcyA in Escherichia coli with production of phycocyanobilin, functional co-expression with cyanobacterial heme oxygenase, and the phycocyanin alpha-subunit, CpcA, from Synechocystis sp. PCC 6803 or Synechococcus sp. PCC 7002, and with the phycocyanin alpha-subunit phycocyanobilin lyase, CpcE/CpcF, or the phycoerythrocyanin alpha-subunit phycocyanobilin isomerizing lyase, PecE/PecF, from Noctoc sp. PCC 7120. Production levels of fluorescent pigments and chromophore analysis, overview

Synechococcus sp.

-

724317

subcloned into pKT210, co-expression with heme oxygenase in Escherichia coli cells

Synechococcus sp.

-

673636

wild-type and mutants, mutant plasmid constructs expressed in Escherichia coli strain DH5alpha

Nostoc sp.

-

674669

analysis

Synechocystis sp.

-

construction of a plasmid containing genes of apo-allophycocyanin alpha-subunit without chromophore and chromophore synthetases HO1, i.e. ferredoxin-dependent heme oxygenase, and PcyA, i.e. phycocyanobilin:ferredoxin oxidoreductase, and expression in Escherichia coli. Holo-allophycocyanin, i.e. allophycocyanin alpha-subunit with chromophore, can be synthesized by autocatalysis in Escherichia coli. Recombinant holo-allophycocyanin alpha-subunit shows the same spectral and fluorescent properties as phycocyanin and serves as a good substitute for native phycocyanin for fluorescent tagging. Recombinant allophycocyanin alpha-subunit can inhibit hydroxyl and peroxyl radicals more strongly than holo-allophycocyanin alpha-subunit and native allophycocyanin

696870

additional information

5 entries