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Information on EC 1.3.7.4 - phytochromobilin:ferredoxin oxidoreductase and Organism(s) Arabidopsis thaliana and UniProt Accession Q9SR43

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IUBMB Comments
Catalyses the two-electron reduction of biliverdin IXalpha. Can use [2Fe-2S] ferredoxins from a number of sources as acceptor but not the [4Fe-4S] ferredoxin from Clostridium pasteurianum. The isomerization of (3Z)-phytochromobilin to (3E)-phytochromobilin is thought to occur prior to covalent attachment to apophytochrome in the plant cell cytoplasm. Flavodoxins can be used instead of ferredoxin.
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Arabidopsis thaliana
UNIPROT: Q9SR43
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The taxonomic range for the selected organisms is: Arabidopsis thaliana
The expected taxonomic range for this enzyme is: Eukaryota, Bacteria
Synonyms
aurea, phytochromobilin synthase, zmhy2, cshy2, pphib synthase, 3z-phytochromobilin:ferredoxin oxidoreductase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
phytochromobilin synthase
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3Z-phytochromobilin:ferredoxin oxidoreductase
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PFB synthase
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-
-
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phytochromobilin synthase
PphiB synthase
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-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
redox reaction
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-
-
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oxidation
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-
-
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reduction
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-
-
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SYSTEMATIC NAME
IUBMB Comments
(3Z)-phytochromobilin:ferredoxin oxidoreductase
Catalyses the two-electron reduction of biliverdin IXalpha. Can use [2Fe-2S] ferredoxins from a number of sources as acceptor but not the [4Fe-4S] ferredoxin from Clostridium pasteurianum. The isomerization of (3Z)-phytochromobilin to (3E)-phytochromobilin is thought to occur prior to covalent attachment to apophytochrome in the plant cell cytoplasm. Flavodoxins can be used instead of ferredoxin.
CAS REGISTRY NUMBER
COMMENTARY hide
138263-99-7
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SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
(3Z)-phytochromobilin + oxidized ferredoxin
biliverdin IXa + reduced ferredoxin
show the reaction diagram
biliverdin IXalpha + reduced ferredoxin
(3Z)-phytochromobilin + oxidized ferredoxin
show the reaction diagram
(3Z)-phytochromobilin + oxidized ferredoxin
biliverdin IXalpha + reduced ferredoxin
show the reaction diagram
-
-
-
-
?
biliverdin IXalpha + reduced ferredoxin
(3Z)-phytochromobilin + 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
(3Z)-phytochromobilin + oxidized ferredoxin
biliverdin IXa + reduced ferredoxin
show the reaction diagram
biosynthesis of bilin pigments
-
-
?
biliverdin IXalpha + reduced ferredoxin
(3Z)-phytochromobilin + oxidized ferredoxin
show the reaction diagram
-
-
-
?
(3Z)-phytochromobilin + oxidized ferredoxin
biliverdin IXalpha + reduced ferredoxin
show the reaction diagram
-
-
-
-
?
biliverdin IXalpha + reduced ferredoxin
(3Z)-phytochromobilin + oxidized ferredoxin
show the reaction diagram
-
-
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Ferredoxin
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Ferredoxin
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Fe2+
cofactor ferredoxin
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
HY2 synthesizes the open chain tetrapyrrole chromophore for light-sensing phytochromes. It catalyzes the double bond reduction of a heme-derived tetrapyrrole intermediate biliverdin IXalpha at the A-ring diene system
evolution
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synthesis of linear tetrapyrrole chromophores in cyanobacteria, algae, and plants, overview
physiological function
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
PFBS_ARATH
329
0
38130
Swiss-Prot
Chloroplast (Reliability: 2)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
33000
calculated from amino acid sequence, mature protein
38100
calculated from amino acid sequence, precursor protein with putative N-terminal plastid transit peptide
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
E110Q
site-directed mutagenesis, the mutant shows 321.7% of wild-type activity
E187Q
site-directed mutagenesis, the mutant shows 20.3% of wild-type activity
H259Q
site-directed mutagenesis, the mutant shows 123.4% of wild-type activity
K183Q
site-directed mutagenesis, the mutant shows 24.6% of wild-type activity
K255Q
site-directed mutagenesis, the mutant shows 11.7% of wild-type activity
K263Q
site-directed mutagenesis, the mutant shows 25.8% of wild-type activity
R200Q
site-directed mutagenesis, the mutant shows 12.5% of wild-type activity
R200Q/R264Q
site-directed mutagenesis, the mutant shows 11.9% of wild-type activity
R264Q
site-directed mutagenesis, the mutant shows 18.9% of wild-type activity
D116N
-
mutant still retains the ability of substrate binding, but with only 1.5% relative activity of wild type protein
D146N
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mutant completely loses catalytic activity and also the ability of biliverdin binding
D256E
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mutant retains only partial activity
N133
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mutant produces only partial activity
R252Q
-
mutant loses catalytic activity and the ability of substrate binding
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
HPLC Phenomenex Ultracarb reverse phase column chromatography
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Superdex 200 gel filtration
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Pichia pastoris
wild type and mutant allels
expressed in Escherichia coli strain BL21
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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, the cells show a phenotype only slightly less pigmented and blue-green than the wild-type, the strain producing phycobiliproteins carrying phytochromobilin grow much more slowly at low light intensity. Transformant colonies in which pcyA is inactivated in the HY2 overexpression background does not develop a chlorotic appearance, and segregation of the mutant and wild-type alleles is rapidly achieved
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recombinant functional expression of HT-HY2 in Escherichia coli with production of phytochromobilin, 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
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
synthesis
production of full-length plant phytochrome assembled with phytochromobilin in Pichia pastoris by coexpressing apophytochromes and chromophore biosynthetic genes, heme oxygenase (HY1) and phytochromobilin oxidoreductase (HY2) from Arabidopsis thaliana. Mitochondria localization of the phytochromobilin biosynthetic genes increases the efficiency of holophytochrome biosynthesis
biotechnology
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transposon-based directed tagging strategy using maize Ds element generates a wide diversity of tagged and non-tagged alleles that can be used to generate allelic series or deletion of clustered genes
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
Arabidopsis thaliana (Q9SR43)
Manually annotated by BRENDA team
Kohchi, T.; Mukougawa, K.; Frankenberg, N.; Masuda, M.; Yokota, A.; Lagarias, J.C.
The Arabidopsis hy2 gene encodes phytochromobilin synthase, a ferredoxin-dependent biliverdin reductase
Plant Cell
13
425-436
2001
Arabidopsis thaliana (Q9SR43)
Manually annotated by BRENDA team
Tu, S.L.; Rockwell, N.C.; Lagarias, J.C.; Fisher, A.J.
Insight into the radical mechanism of phycocyanobilin-ferredoxin oxidoreductase (PcyA) revealed by X-ray crystallography and biochemical measurements
Biochemistry
46
1484-1494
2007
Arabidopsis thaliana
Manually annotated by BRENDA team
Tu, S.L.; Chen, H.C.; Ku, L.W.
Mechanistic studies of the phytochromobilin synthase HY2 from Arabidopsis
J. Biol. Chem.
283
27555-27564
2008
Arabidopsis thaliana
Manually annotated by BRENDA team
Chiu, F.Y.; Chen, Y.R.; Tu, S.L.
Electrostatic interaction of phytochromobilin synthase and ferredoxin for biosynthesis of phytochrome chromophore
J. Biol. Chem.
285
5056-5065
2010
Arabidopsis thaliana (Q9SR43), Arabidopsis thaliana
Manually annotated by BRENDA team
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
Arabidopsis thaliana
Manually annotated by BRENDA team
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
Arabidopsis thaliana
Manually annotated by BRENDA team
Shin, A.Y.; Han, Y.J.; Song, P.S.; Kim, J.I.
Expression of recombinant full-length plant phytochromes assembled with phytochromobilin in Pichia pastoris
FEBS Lett.
588
2964-2970
2014
Arabidopsis thaliana (Q9SR43)
Manually annotated by BRENDA team
Creff, A.; Lonard, B.; Desnos, T.
Targeted Ds-tagging strategy generates high allelic diversity at the Arabidopsis HY2 locus
Plant Mol. Biol.
61
603-613
2006
Arabidopsis thaliana
Manually annotated by BRENDA team