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(3Z)-phycoerythrobilin + oxidized ferredoxin
biliverdin IXalpha + reduced ferredoxin
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Substrates: 15,16-dihydrobiliverdin is formed as a bound intermediate
Products: -
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15,16-dihydrobiliverdin + oxidized ferredoxin
biliverdin IXalpha + reduced ferredoxin
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Substrates: -
Products: -
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biliverdin IXalpha + 2 reduced ferredoxin
(3Z)-phycoerythrobilin + 2 oxidized ferredoxin
additional information
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Substrates: recombinant metagenomically derived enzymes PcyX-EBQ and PcyX-ECK are functional FDBRs catalysing the reduction of BV via 5,16-dihydrobiliverdin (DHBV) to phycoerythrobilin (PEB). The rate determining step in the PcyX-catalysed reaction is the conversion of the intermediate DHBV to the final product PEB. Enzyme PcyX_ECK forms 3(E/Z)-PPhiB as side products
Products: -
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biliverdin IXalpha + 2 reduced ferredoxin
(3Z)-phycoerythrobilin + 2 oxidized ferredoxin
Substrates: -
Products: -
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biliverdin IXalpha + 2 reduced ferredoxin
(3Z)-phycoerythrobilin + 2 oxidized ferredoxin
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Substrates: -
Products: -
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biliverdin IXalpha + 2 reduced ferredoxin
(3Z)-phycoerythrobilin + 2 oxidized ferredoxin
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Substrates: 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
Products: -
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biliverdin IXalpha + 2 reduced ferredoxin
(3Z)-phycoerythrobilin + 2 oxidized ferredoxin
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Substrates: ferredoxin from Synechococcus sp. PCC 7002 or from cyanophage P-SSM2
Products: -
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biliverdin IXalpha + 2 reduced ferredoxin
(3Z)-phycoerythrobilin + 2 oxidized ferredoxin
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Substrates: -
Products: -
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biliverdin IXalpha + 2 reduced ferredoxin
(3Z)-phycoerythrobilin + 2 oxidized ferredoxin
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Substrates: -
Products: -
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biliverdin IXalpha + 2 reduced ferredoxin
(3Z)-phycoerythrobilin + 2 oxidized ferredoxin
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Substrates: (3Z)-phycoerythrobilin is synthesized from biliverdin IXalpha by the sequential actions of two reductases, PebA and PebB
Products: -
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biliverdin IXalpha + 2 reduced ferredoxin
(3Z)-phycoerythrobilin + 2 oxidized ferredoxin
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Substrates: -
Products: -
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biliverdin IXalpha + 2 reduced ferredoxin
(3Z)-phycoerythrobilin + 2 oxidized ferredoxin
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Substrates: (3Z)-phycoerythrobilin is synthesized from biliverdin IXalpha by the sequential actions of two reductases, PebA and PebB
Products: -
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biliverdin IXalpha + 2 reduced ferredoxin
(3Z)-phycoerythrobilin + 2 oxidized ferredoxin
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Substrates: -
Products: -
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biliverdin IXalpha + 2 reduced ferredoxin
(3Z)-phycoerythrobilin + 2 oxidized ferredoxin
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Substrates: importance of the correct electron donor for the activity of the PcyX-like FDBRs
Products: -
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biliverdin IXalpha + 2 reduced ferredoxin
(3Z)-phycoerythrobilin + 2 oxidized ferredoxin
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Substrates: -
Products: -
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biliverdin IXalpha + 2 reduced ferredoxin
(3Z)-phycoerythrobilin + 2 oxidized ferredoxin
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Substrates: importance of the correct electron donor for the activity of the PcyX-like FDBRs
Products: -
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biliverdin IXalpha + 2 reduced ferredoxin
(3Z)-phycoerythrobilin + 2 oxidized ferredoxin
biliverdin IXalpha + 2 reduced ferredoxin
(3Z)-phycoerythrobilin + 2 oxidized ferredoxin
Substrates: -
Products: -
?
biliverdin IXalpha + 2 reduced ferredoxin
(3Z)-phycoerythrobilin + 2 oxidized ferredoxin
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Substrates: 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
Products: -
?
biliverdin IXalpha + 2 reduced ferredoxin
(3Z)-phycoerythrobilin + 2 oxidized ferredoxin
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Substrates: -
Products: -
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biliverdin IXalpha + 2 reduced ferredoxin
(3Z)-phycoerythrobilin + 2 oxidized ferredoxin
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Substrates: -
Products: -
?
biliverdin IXalpha + 2 reduced ferredoxin
(3Z)-phycoerythrobilin + 2 oxidized ferredoxin
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Substrates: -
Products: -
?
biliverdin IXalpha + 2 reduced ferredoxin
(3Z)-phycoerythrobilin + 2 oxidized ferredoxin
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Substrates: -
Products: -
?
biliverdin IXalpha + 2 reduced ferredoxin
(3Z)-phycoerythrobilin + 2 oxidized ferredoxin
-
Substrates: -
Products: -
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physiological function
the enzyme is involved in the biosynthesis of phycoerythrobilin
evolution
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synthesis of linear tetrapyrrole chromophores in cyanobacteria, algae, and plants, ooverview
evolution
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the enzyme belongs to the ferredoxin-dependent bilin reductase family
evolution
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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 (PEB). But PcyX converts the same substrate to phycoerythrobilin, resembling the reaction catalysed by cyanophage PebS
evolution
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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 (PEB). But PcyX converts the same substrate to phycoerythrobilin, resembling the reaction catalysed by cyanophage PebS. 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
evolution
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synthesis of linear tetrapyrrole chromophores in cyanobacteria, algae, and plants, ooverview
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metabolism
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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
metabolism
phycoerythrobilin (PEB) is an open-chain tetrapyrrole that is derived from heme. The biosynthesis of PEB is, outgoing from heme, mediated by two classes of enzymes: heme oxygenases (HOs) and ferredoxin-dependent bilin reductases (FDBRs). In the first step, HOs (EC: 1.14.99.3) catalyze the ring-opening reaction of the cyclic tetrapyrrole heme at the alpha-mesocarbon bridge, yielding the open-chain tetrapyrrole biliverdin IXalpha (BV), CO and free iron. The sequential reductive cleavage of heme to BV consumes three molecules of O2 and seven electrons. HOs are involved in iron acquisition, oxidative-stress response and pigment biosynthesis. In plants and prokaryotes reduced ferredoxin and ascorbate are able to provide the electrons for the reaction. In the second step, BV is further reduced to PEB by a class of enzymes called ferredoxin-dependent bilin reductases (FDBRs)
additional information
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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
additional information
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PebS-catalysed PEB synthesis proceeds via a radical mechanism and both aspartate residues involved, Asp105 and Asp206, are important for stereospecific substrate protonation and conversion. Both Asp residues are highly conserved throughout the family of ferredoxin-dependent bilin reductases, bilin radical intermediates during PebS reaction, and superposition of the active site of the wild-type enzyme, the D105N and D206N mutant with bound substrate biliverdin
additional information
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a conserved aspartate-histidine pair is critical for activity of PcyX. 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. Modelling of the substrate into the active site. His69 and Asp86 are catalytic important residues, the Asp86/His69 pair of PcyX is critical for catalysis. Also Met67 is crucial for the activity of PcyX, Asn198 is essential for the correct binding of the substrate
additional information
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the X-ray structure of PhiPcyX (EBK42635) shows the typical alpha/beta/alpha-sandwich fold, with a central antiparallel beta-sheet, flanked by alpha-helices, as described before for other FDBRs. Analysis of the substrate binding pocket structure of PcyX, structure comparisons, overview
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structures of substrate complex solved at 1.8- and 2.1 A resolution and of the substrate-free form at 1.55 A resolution. The overall folding reveals an alpha/beta/alpha-sandwich with similarity to the structure of phycocyanobilin:ferredoxin oxidoreductase. The substrate-binding site is located between the central beta-sheet and C-terminal alpha-helices. The substrate binding pocket shows a high flexibility. The substrate is either in a planar porphyrin-like conformation or in a helical conformation and is coordinated by a conserved aspartate/asparagine pair from the beta-sheet side. From the alpha-helix side, a conserved highlyflexible aspartate/proline pair is involved in substrate binding and presumably catalysis
purified recombinant substrate free form of PhiPcyX, sitting drop vapour diffusion method, mixing of 100 nl of 10-16.5 mg/ml protein in 20 mM TES-KOH pH 7.5, and 20 mM KCl, with 100 nl of reservoir solution containing 0.1 M Tris-HCl, pH 8.5, 0.2 M trimethylamine N-oxide (TMAO), and 20% w/v PEG MME 2000, at 4 °C. Final crystals used for structure determination grow at 4 °C via hanging drop vapour diffusion with 0.001 ml of 10 mg/ml protein in 20 mM TES-KOH pH 7.5, and 20 mM KCl mixed with 0.001 ml of 0.1 M Tris-HCl, pH 8.5, 0.05 M, TMAO, and 15% w/v PEG MME 2000 as reservoir solution, X-ray diffraction structure determination and analysis at 2.2 A resolution
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D105N
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site-directed mutagenesis, inactive mutant
C71A
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site-directed mutagenesis, mutant shows reduced activity compared to wild-type
D55N
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site-directed mutagenesis
D86N
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site-directed mutagenesis, inactive mutant
H200Q
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site-directed mutagenesis, the PcyX mutant shows a faster turnover compared with to wild-type enzyme
H69Q
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site-directed mutagenesis, altered substrate biliverdin binding compared to wild-type, the mutant shows highly reduced activity compared to wild-type
M67I
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site-directed mutagenesis, mutant shows highly reduced activity compared to wild-type
N198D
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site-directed mutagenesis, inactive mutant
D105E
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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
D105E
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site-directed mutagenesis, the mutant fully retains the ability to catalyse the first reduction at the 15,16-methine bridge, but cannot catalyse the second reduction at the A-ring 2,3,31,32-diene system, thereby yielding 15,16-DHBV as the final product
D206E
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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
D206E
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site-directed mutagenesis, the mutant fully retains the ability to catalyse the first reduction at the 15,16-methine bridge, but cannot catalyse the second reduction at the A-ring 2,3,31,32-diene system, however, in this mutant the reaction can be pushed further to produce (3Z)-phycoerythrobilin by a 10fold increase in ferredoxin concentration
D206N
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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
D206N
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site-directed mutagenesis, the mutant fully retains the ability to catalyse the first reduction at the 15,16-methine bridge, but cannot catalyse the second reduction at the A-ring 2,3,31,32-diene system, thereby yielding 15,16-DHBV as the final product
additional information
development and evaluation of an improved method for high yield production and purification of phycoerythrobilin (PEB) in Escherichia coli via heterologous expression where the two required enzymes heme oxygenase and PEB synthase subsequently convert the substrate heme provided by the host cell. Experiments in shaking flasks result in the highest product yield of 0.680 mg PEB per g cell dry weight, by induction with 0.1 mM IPTG. Scale-up to batch-operated fermentation in a 2 L bioreactor reached product concentrations up to 5.02 mg PEB/l by adjustment of aeration, induction time, media composition and supplementation of precursors, separation of PEB from developed foam above the culture, detailed overview
additional information
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because PcyA, EC 1.3.7.5, and PebA utilize the same substrate, biliverdin IXalpha, severe overexpression of pebA can limit the availability of phycocyanobilin, which appears to be required for viability when cells are grown in continuous light, phenotype, overview
additional information
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because PcyA, EC 1.3.7.5, and PebA utilize the same substrate, biliverdin IXalpha, severe overexpression of pebA can limit the availability of phycocyanobilin, which appears to be required for viability when cells are grown in continuous light, phenotype, overview
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additional information
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a conserved aspartate-histidine pair is critical for activity. The same residues are part of a catalytic Asp-His-Glu triad in PcyA (EC 1.3.7.2), including an additional Glu. While this Glu residue is replaced by Asp in PcyX, it is not involved in catalysis. Substitution back to a Glu fails to convert PcyX to a PcyA
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gene pcyX, phylogenetic analysis and tree, recombinant overexpression of synthetic construct of GST-tagged enzyme
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gene pcyX, phylogenetic analysis and tree, recombinant overexpression of synthetic constructs with the original sequences of the genes derived from metagenomic data (termed PcyX-EBQ, PcyX-ECK and PcyX-actino) in Escherichia coli. PcyX-EBQ and PcyX-ECK are functional FDBRs catalysing the reduction of BV via DHBV to PEB, recombinant expression of GST-tagged enzymes in Escherichia coli strain BL21(DE3)
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gene pebAB, overexpression in Synechococcus sp. strain PCC 7002, from endogenous plasmid pAQ1 under the control of the Synechocystis sp. strain PCC 6803 cpcBA promoter, leads to overproduction of phytochromobilin. Colonies of Synechococcus sp. strain PCC 7002 transformed with the pebAB overexpression cassette mostly exhibit a reddish-brown phenotype
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gene pebS, production of His-tagged phycocyanin alpha-subunit-(3Z)-phycoerythrobilin using the alternative FDBR, phycoerythrobilin synthase, PebS, overview. Recombinant functional expression of PebS in Escherichia coli, co-expression with phycocyanin alpha-subunit, CpcA, from Synechocystis sp. PCC 6803 or Synechococcus sp. PCC 7002, cyanobacterial heme oxygenase, 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
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gene pebS, recombinant expression in Escherichia coli strain BL21 (DE3) from plasmid pTDho1pebS, Phycoerythrobilin production in batch-operated bioreactors, phycoerythrobilin enrichment in the bioreactor foam
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Dammeyer, T.; Bagby, S.C.; Sullivan, M.B.; Chisholm, S.W.; Frankenberg-Dinkel, N.
Efficient phage-mediated pigment biosynthesis in oceanic cyanobacteria
Curr. Biol.
18
442-448
2008
uncultured cyanophage
brenda
Dammeyer, T.; Hofmann, E.; Frankenberg-Dinkel, N.
Phycoerythrobilin synthase (PebS) of a marine virus. Crystal structures of the biliverdin complex and the substrate-free form
J. Biol. Chem.
283
27547-27554
2008
Prochlorococcus phage P-SSM2 (Q58MU6)
brenda
Busch, A.W.; Reijerse, E.J.; Lubitz, W.; Hofmann, E.; Frankenberg-Dinkel, N.
Radical mechanism of cyanophage phycoerythrobilin synthase (PebS)
Biochem. J.
433
469-476
2011
Prochlorococcus phage P-SSM2
brenda
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
Biochem. J.
439
257-264
2011
Prochlorococcus phage P-SSM2
brenda
Alvey, R.M.; Biswas, A.; Schluchter, W.M.; Bryant, D.A.
Attachment of noncognate chromophores to CpcA of Synechocystis sp. PCC 6803 and Synechococcus sp. PCC 7002 by heterologous expression in Escherichia coli
Biochemistry
50
4890-4902
2011
Prochlorococcus phage P-SSM4
brenda
Alvey, R.M.; Biswas, A.; Schluchter, W.M.; Bryant, D.A.
Effects of modified phycobilin biosynthesis in the cyanobacterium Synechococcus sp. strain PCC 7002
J. Bacteriol.
193
1663-1671
2011
Synechococcus sp., Synechococcus sp. PCC 7335
brenda
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
FEBS J.
285
339-356
2018
uncultured actinobacterium, uncultured marine phage
brenda
Stiefelmaier, J.; Ledermann, B.; Sorg, M.; Banek, A.; Geib, D.; Ulber, R.; Frankenberg-Dinkel, N.
Pink bacteria-Production of the pink chromophore phycoerythrobilin with Escherichia coli
J. Biotechnol.
274
47-53
2018
Prochlorococcus phage P-SSM2 (Q58MU6)
brenda