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Information on EC 1.3.7.2 - 15,16-dihydrobiliverdin:ferredoxin oxidoreductase
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1.3.7.2 15,16-dihydrobiliverdin:ferredoxin oxidoreductaseIUBMB Comments
Catalyses the two-electron reduction of biliverdin IXalpha at the C15 methine bridge. It has been proposed that this enzyme and EC 1.3.7.3, phycoerythrobilin:ferredoxin oxidoreductase, function as a dual enzyme complex in the conversion of biliverdin IXalpha into phycoerythrobilin.
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Word Map
- 1.3.7.2
-
bilins
- tetrapyrrole
-
light-harvesting
- ixalpha
- cyanobacteria
-
a-ring
- phycoerythrobilin
- phycocyanobilin
- reductases
- chromophore
-
fdbrs
-
phycobiliproteins
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phycocyanobilin:ferredoxin
- chlorophyll
-
phytochrome
-
open-chain
-
proton-donating
-
substrate-bound
-
phycobilisomes
-
phycobilin
- synechococcus
-
substrate-free
-
four-electron
-
two-electron
- prochlorococcus
- pheophorbide
- cryptomonads
- nostoc
- cryptophytes
-
apophytochromes
- phytochromobilin
-
antenna
-
cyanophage
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota
Reaction Schemes
Synonyms
ferredoxin-dependent bilin reductase, 15,16-dihydrobiliverdin:ferredoxin oxidoreductase, dhbv:ferredoxin oxidoreductase, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
15,16-DHBV:ferredoxin oxidoreductase
ferredoxin-dependent bilin reductase
ferredoxin:15,16-dihydrobiliverdin oxidoreductase
-
-
-
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oxidoreductase, ferredoxin:15,16-dihydrobiliverdin
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-
-
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PebA
PebA
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-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
15,16-dihydrobiliverdin + oxidized ferredoxin = biliverdin IXalpha + reduced ferredoxin + 2 H+
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-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
oxidation
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-
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redox reaction
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-
-
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reduction
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-
-
-
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PATHWAY SOURCE
PATHWAYS
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SYSTEMATIC NAME
IUBMB Comments
15,16-dihydrobiliverdin:ferredoxin oxidoreductase
Catalyses the two-electron reduction of biliverdin IXalpha at the C15 methine bridge. It has been proposed that this enzyme and EC 1.3.7.3, phycoerythrobilin:ferredoxin oxidoreductase, function as a dual enzyme complex in the conversion of biliverdin IXalpha into phycoerythrobilin.
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CAS REGISTRY NUMBER
COMMENTARY
347401-20-1
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
15,16-dihydrobiliverdin + oxidized ferrdoxin
biliverdin IXalpha + reduced ferrdoxin
the 15,16-DHBV:ferredoxin oxidoreductase PebA reduces biliverdin IXalpha at the C15C16 double bond to produce 15,16-dihydrobiliverdin
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-
r
15,16-dihydrobiliverdin + oxidized ferrdoxin
biliverdin IXalpha + reduced ferrdoxin
the 15,16-DHBV:ferredoxin oxidoreductase PebA reduces biliverdin IXalpha at the C15C16 double bond to produce 15,16-dihydrobiliverdin, assay under anaerobic conditions
-
-
r
15,16-dihydrobiliverdin + oxidized ferrdoxin
biliverdin IXalpha + reduced ferrdoxin
the 15,16-DHBV:ferredoxin oxidoreductase PebA reduces biliverdin IXalpha at the C15C16 double bond to produce 15,16-dihydrobiliverdin
-
-
r
15,16-dihydrobiliverdin + oxidized ferrdoxin
biliverdin IXalpha + reduced ferrdoxin
the 15,16-DHBV:ferredoxin oxidoreductase PebA reduces biliverdin IXalpha at the C15C16 double bond to produce 15,16-dihydrobiliverdin, assay under anaerobic conditions
-
-
r
15,16-dihydrobiliverdin + oxidized ferredoxin
biliverdin IXa + reduced ferredoxin
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-
?
15,16-dihydrobiliverdin + oxidized ferredoxin
biliverdin IXa + reduced ferredoxin
-
-
-
?
15,16-dihydrobiliverdin + oxidized ferredoxin
biliverdin IXa + reduced ferredoxin
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biosynthesis of bilin pigments, functions with EC1.3.7.3. as a dual enzyme complex in the conversion of biliverdin IXa into phycoerythrobilin
-
-
?
15,16-dihydrobiliverdin + oxidized ferredoxin
biliverdin IXa + reduced ferredoxin
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-
-
?
15,16-dihydrobiliverdin + oxidized ferredoxin
biliverdin IXa + reduced ferredoxin
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biosynthesis of bilin pigments, functions with EC1.3.7.3. as a dual enzyme complex in the conversion of biliverdin IXa into phycoerythrobilin
-
-
?
15,16-dihydrobiliverdin + reduced ferredoxin
phycoerythrobilin + oxidized ferredoxin
-
-
-
r
15,16-dihydrobiliverdin + reduced ferredoxin
phycoerythrobilin + oxidized ferredoxin
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-
-
r
biliverdin IXa + reduced ferredoxin
15,16-dihydrobiliverdin + oxidized ferredoxin
-
-
-
r
biliverdin IXa + reduced ferredoxin
15,16-dihydrobiliverdin + oxidized ferredoxin
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-
-
r
biliverdin IXa + reduced ferredoxin
15,16-dihydrobiliverdin + oxidized ferredoxin
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-
-
-
r
biliverdin IXa + reduced ferredoxin
15,16-dihydrobiliverdin + oxidized ferredoxin
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-
-
-
r
biliverdin IXalpha + reduced ferredoxin
15,16-dihydrobiliverdin + oxidized ferredoxin
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-
-
-
?
biliverdin IXalpha + reduced ferredoxin
15,16-dihydrobiliverdin + oxidized ferredoxin
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-
-
-
?
biliverdin IXalpha + reduced ferredoxin
15,16-dihydrobiliverdin + oxidized ferredoxin
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-
-
-
?
biliverdin IXalpha + reduced ferredoxin
15,16-dihydrobiliverdin + oxidized ferredoxin
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-
-
?
biliverdin IXalpha + reduced ferredoxin
15,16-dihydrobiliverdin + oxidized ferredoxin
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-
-
?
biliverdin IXalpha + reduced ferredoxin
15,16-dihydrobiliverdin + oxidized ferredoxin
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-
-
?
phytochromobilin + biliverdin IXa + reduced ferredoxin
phycoerythrobilin
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r
phytochromobilin + biliverdin IXa + reduced ferredoxin
phycoerythrobilin
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r
additional information
?
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does not convert 3E-phycocyanobilin
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?
additional information
?
-
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does not convert 3E-phycocyanobilin
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-
?
additional information
?
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does not convert 3E-phycocyanobilin
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-
?
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
15,16-dihydrobiliverdin + oxidized ferrdoxin
biliverdin IXalpha + reduced ferrdoxin
the 15,16-DHBV:ferredoxin oxidoreductase PebA reduces biliverdin IXalpha at the C15C16 double bond to produce 15,16-dihydrobiliverdin
-
-
r
15,16-dihydrobiliverdin + oxidized ferrdoxin
biliverdin IXalpha + reduced ferrdoxin
the 15,16-DHBV:ferredoxin oxidoreductase PebA reduces biliverdin IXalpha at the C15C16 double bond to produce 15,16-dihydrobiliverdin
-
-
r
15,16-dihydrobiliverdin + oxidized ferredoxin
biliverdin IXa + reduced ferredoxin
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biosynthesis of bilin pigments, functions with EC1.3.7.3. as a dual enzyme complex in the conversion of biliverdin IXa into phycoerythrobilin
-
-
?
15,16-dihydrobiliverdin + oxidized ferredoxin
biliverdin IXa + reduced ferredoxin
-
biosynthesis of bilin pigments, functions with EC1.3.7.3. as a dual enzyme complex in the conversion of biliverdin IXa into phycoerythrobilin
-
-
?
biliverdin IXalpha + reduced ferredoxin
15,16-dihydrobiliverdin + oxidized ferredoxin
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-
-
-
?
biliverdin IXalpha + reduced ferredoxin
15,16-dihydrobiliverdin + oxidized ferredoxin
-
-
-
-
?
biliverdin IXalpha + reduced ferredoxin
15,16-dihydrobiliverdin + oxidized ferredoxin
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-
-
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
Ferredoxin
ferredoxin from Synechococcus sp. PCC7002 is used in the enzyme assay
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additional information
insensitivity toward metal chelators like 0.01 mM EDTA, 0.005 mM o-phenanthroline, or 0.005 mM 2,2'-dipyridyl
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additional information
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insensitivity toward metal chelators like 0.01 mM EDTA, 0.005 mM o-phenanthroline, or 0.005 mM 2,2'-dipyridyl
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Fe2+
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
metabolism
physiological function
phycobilins are light-harvesting pigments of cyanobacteria, red algae, and cryptophytes. The biosynthesis of phycoerythrobilin (PEB) is catalyzed by the subsequent action of two ferredoxin-dependent bilin reductases (FDBRs). 15,16-Dihydrobiliverdin (DHBV):ferredoxin oxidoreductase (PebA) catalyzes the two-electron reduction of biliverdin IXalpha to 15,16-DHBV, and PEB:ferredoxin oxidoreductase (PebB) reduces this intermediate further to PEB
additional information
evolution
the enzyme belongs to the ferredoxin-dependent bilin reductase family. All members of the FDBR family are radical enzymes
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
evolution
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the enzyme belongs to the ferredoxin-dependent bilin reductase family. All members of the FDBR family are radical enzymes
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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
metabolism
during the biosynthesis of light-harvesting phycobilins in cyanobacteria, two members of the ferredoxin-dependent bilin reductases are involved in the reduction of the open-chain tetrapyrrole biliverdin IXa to the pink pigment phycoerythrobilin. The first reaction is catalyzed by 15,16-dihydrobiliverdin:ferredoxin oxidoreductase (PebA) and produces the unstable intermediate 15,16-dihydrobiliverdin (DHBV). This intermediate is subsequently channeled to and converted by phycoerythrobilin:ferredoxin oxidoreductase to the final product phycoerythrobilin. An on-column assay employing immobilized enzyme in combination with UV-Vis and fluorescence spectroscopy reveals that both enzymes transiently interact and that transfer of the intermediate is facilitated by a significantly higher binding affinity of DHBV toward phycoerythrobilin:ferredoxin oxidoreductase (PebB, EC 1.3.7.3). The intermediate DHBV is transferred via proximity channeling
metabolism
phycobilins are light-harvesting pigments of cyanobacteria, red algae, and cryptophytes. The biosynthesis of phycoerythrobilin (PEB) is catalyzed by the subsequent action of two ferredoxin-dependent bilin reductases (FDBRs). 15,16-Dihydrobiliverdin (DHBV):ferredoxin oxidoreductase (PebA) catalyzes the two-electron reduction of biliverdin IXalpha to 15,16-DHBV, and PEB:ferredoxin oxidoreductase (PebB) reduces this intermediate further to PEB. The biosynthetic intermediate DHBV is transferred via proximity channeling to PEB:ferredoxin oxidoreductase (PebB)
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
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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
additional information
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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
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
additional information
structure comparisons of Synechococcus WH8020 PebA and Guillardia theta PebB, overview. The Asp-99/Asp-219 pair is structurally conserved in most FDBRs, while the corresponding residues are relevant for PebB, for PebA only the homologue of Asp99 (Asp84) is essential for catalytic activity. The homologue of Asp219 (Asp205) is not essential and is rotated out of the active site. PebB binds DHBV analogous to the binding of BV in PebA/PebS
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
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Show AA Sequence and Transmembrane Helices (240 entries)
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PDB
SCOP
CATH
UNIPROT
ORGANISM
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
D105N
-
site-directed mutagenesis, altered substrate biliverdin binding compared to wild-type, the mutant shows 89% reduced activity compared to wild-type
E76Q
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site-directed mutagenesis, the mutant shows 80% reduced activity compared to wild-type
H88Q
-
site-directed mutagenesis, altered substrate biliverdin binding compared to wild-type, the mutant shows 95% reduced activity compared to wild-type
additional information
analysis wether addition of PebB to the immobilized PebA-DHBV complex will result in the interaction of PebA and PebB and, therefore, cause retention of PebB on the column. Retention of PebB on the immobilized PebA column is not observed, but a transfer of almost all PebA-bound DHBV to PebB is seen, DHBV is washed off the column with regular washing buffer. in Synechococcus sp. WH8020, the genes encoding for pebA and pebB share an overlapping region. The pebA stop codon TGA is part of the pebB start codon ATG. In order to generate a translational fusion between pebA and pebB, a guanine base is inserted into the start-stop region of the pebAB-operon generating an artificial fusion of both enzymes, termed PebAgB. The newly generated codon GTG encodes for a valine residue, which then serves as a diminutive linker between PebA and PebB. This fusion protein is significantly different to the phage encoded PebS (EC 1.3.7.6), which is a homologue to PebA. But the fusion protein PebAgB shows PebS-like activity. Comparison of the PebAgB-catalyzed conversion of BV with an assay containing both PebA and PebB reveals no significant changes in velocity
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
by two affinity chromatography steps to 90% purity and a third gel filtration step
GST-tagged PebA forms inactive aggregates
recombinant GST-tagged enzyme from Escherichia coli by ultrafiltration, glutathione affinity chromatography, and gel filtration
recombinant GST-tagged enzyme from Escherichia coli strain BL21(DE3) by glutathione affinity chromatography, ultrafiltration, and gel filtration
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recombinant GST-tagged PebA from Escherichia coli strain BL21(DE3) by glutathione affinity chromatography, gel filtration, and ultrafiltration, recombinant tagged PebAgB by affinity chromatography
by two affinity chromatography steps to 90% purity and a third gel filtration step
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by two affinity chromatography steps to 90% purity and a third gel filtration step
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli
expression in Escherichia coli
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
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gene pebA, in Synechococcus sp. WH8020, the genes encoding for pebA and pebB share an overlapping region. The pebA stop codon TGA is part of the pebB start codon ATG, recombinant expression of a translational fusion between pebA and pebB, N-terminally Strep-tagged and C-terminally His-tagged PebAgB, recombinant expression of GST-tagged PebA in Escherichia coli BL21(DE3)
gene pebA, recombinant expression of GST-tagged enzyme in Escherichia coli
gene pebA, recombinant expression of wild-type and mutant enzymes, native and selenomethionine-labeled PebA
into pGEX-6P-3 vector for N-terminal fusion with glutathione S-transferase and transformed in Escherichia coli BL21(lambdaDE3) cells
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Frankenberg, N.; Mukougawa, K.; Kohchi, T.; Lagarias, J.C.
Functional genomic analysis of the HY2 family of ferredoxin-dependent bilin reductases from oxygenic photosynthetic organisms
Plant Cell
13
965-978
2001
Prochlorococcus sp., Synechococcus sp., Nostoc punctiforme (Q93TL6)
brenda
Alvey, R.M.; Karty, J.A.; Roos, E.; Reilly, J.P.; Kehoe, D.M.
Lesions in phycoerythrin chromophore biosynthesis in Fremyella diplosiphon reveal coordinated light regulation of apoprotein and pigment biosynthetic enzyme gene expression
Plant Cell
15
2448-2463
2003
Microchaete diplosiphon
brenda
Dammeyer, T.; Frankenberg-Dinkel, N.
Insights into phycoerythrobilin biosynthesis point toward metabolic channeling
J. Biol. Chem.
281
27081-27089
2006
Synechococcus sp., Microchaete diplosiphon (Q6UR88), Microchaete diplosiphon, Synechococcus sp. WH8020, Microchaete diplosiphon Fd33 (Q6UR88)
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
Synechococcus sp. (Q02189), Synechococcus sp., Synechococcus sp. WH8020 (Q02189)
brenda
Overkamp, K.; Gasper, R.; Kock, K.; Herrmann, C.; Hofmann, E.; Frankenberg-Dinkel, N.
Insights into the biosynthesis and assembly of cryptophycean phycobiliproteins
J. Biol. Chem.
289
26691-26707
2014
Guillardia theta, Synechococcus sp. (Q02189), Synechococcus sp. WH8020 (Q02189)
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
Bradyrhizobium sp. ORS 278
brenda
Aras, M.; Hartmann, V.; Hartmann, J.; Nowaczyk, M.M.; Frankenberg-Dinkel, N.
Proximity channeling during cyanobacterial phycoerythrobilin synthesis
FEBS J.
287
284-294
2020
Synechococcus sp. WH 8020 (Q02189)
brenda
Sommerkamp, J.; Frankenberg-Dinkel, N.; Hofmann, E.
Crystal structure of the first eukaryotic bilin reductase GtPEBB reveals a flipped binding mode of dihydrobiliverdin
J. Biol. Chem.
294
13889-13901
2019
Synechococcus sp. WH 8020 (Q02189)
brenda
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