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Information on EC 1.3.7.6 - phycoerythrobilin synthase and Organism(s) Prochlorococcus phage P-SSM2 and UniProt Accession Q58MU6

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IUBMB Comments
This enzyme, from a cyanophage infecting oceanic cyanobacteria of the Prochlorococcus genus, uses a four-electron reduction to carry out the reactions catalysed by EC 1.3.7.2 (15,16-dihydrobiliverdin:ferredoxin oxidoreductase) and EC 1.3.7.3 (phycoerythrobilin:ferredoxin oxidoreductase). 15,16-Dihydrobiliverdin is formed as a bound intermediate. Free 15,16-dihydrobiliverdin can also act as a substrate to form phycoerythrobilin.
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Prochlorococcus phage P-SSM2
UNIPROT: Q58MU6
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The taxonomic range for the selected organisms is: Prochlorococcus phage P-SSM2
The enzyme appears in selected viruses and cellular organisms
Synonyms
phycoerythrobilin synthase, peb synthase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ferredoxin-dependent bilin reductase
-
phycoerythrobilin synthase
-
phycoerythrobilin synthase
-
-
SYSTEMATIC NAME
IUBMB Comments
(3Z)-phycoerythrobilin:ferredoxin oxidoreductase (from biliverdin IXalpha)
This enzyme, from a cyanophage infecting oceanic cyanobacteria of the Prochlorococcus genus, uses a four-electron reduction to carry out the reactions catalysed by EC 1.3.7.2 (15,16-dihydrobiliverdin:ferredoxin oxidoreductase) and EC 1.3.7.3 (phycoerythrobilin:ferredoxin oxidoreductase). 15,16-Dihydrobiliverdin is formed as a bound intermediate. Free 15,16-dihydrobiliverdin can also act as a substrate to form phycoerythrobilin.
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
biliverdin IXalpha + 2 reduced ferredoxin
(3Z)-phycoerythrobilin + 2 oxidized ferredoxin
show the reaction diagram
-
-
-
?
biliverdin IXalpha + 2 reduced ferredoxin
(3Z)-phycoerythrobilin + 2 oxidized ferredoxin
show the reaction diagram
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
biliverdin IXalpha + 2 reduced ferredoxin
(3Z)-phycoerythrobilin + 2 oxidized ferredoxin
show the reaction diagram
-
-
-
?
biliverdin IXalpha + 2 reduced ferredoxin
(3Z)-phycoerythrobilin + 2 oxidized ferredoxin
show the reaction diagram
-
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
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-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Fe2+
in cofactor ferredoxin
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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)
physiological function
the enzyme is involved in the biosynthesis of phycoerythrobilin
evolution
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the enzyme belongs to the ferredoxin-dependent bilin reductase family
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
evolution
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the enzyme belongs to the ferredoxin-dependent bilin reductase family
additional information
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
PEBS_BPPRM
233
0
27256
Swiss-Prot
other Location (Reliability: 2)
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
D105N
-
site-directed mutagenesis, inactive mutant
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
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
D105E
-
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
-
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
-
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
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
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
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
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)
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
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)
Manually annotated by BRENDA team