Crystal structure of phycocyanobilin:ferredoxin oxidoreductase in complex with biliverdin IXα, a key enzyme in the biosynthesis of phycocyanobilin

Hagiwara, Yoko; Sugishima, Masakazu; Takahashi, Yasuhiro; Fukuyama, Keiichi

doi:10.1073/pnas.0507266103

Cited by 65 publications

(163 citation statements)

References 30 publications

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“…Two organic radical intermediates have also been detected in the two double bond reduction steps, strongly supporting the proposed mechanism for sequential electron-coupled proton transfer in the PcyA-catalyzed BV reduction (11). Mutagenesis studies have shown a histidine/aspartate ion pair playing the essential role in the active site, which is further confirmed by the crystal structure of PcyA (12)(13)(14). Combining the structural information and biochemical data, a more detailed mechanism for PcyA reaction has been proposed (12).…”

Section: Phytochromobilin (P⌽b)supporting

confidence: 52%

Mechanistic Studies of the Phytochromobilin Synthase HY2 from Arabidopsis

Chen

2008

Journal of Biological Chemistry

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1 ,3 2 -diene system to produce an ethylidene group for assembly with apophytochromes. In this study, we sought to determine the catalytic mechanism of HY2. Data from UV-visible and EPR spectroscopy showed that the HY2-catalyzed BV reaction proceeds via a transient radical intermediate. Site-directed mutagenesis showed several ionizable residues that are involved in the catalytic steps. Detailed analysis of these sitedirected mutants highlighted a pair of aspartate residues central to proton donation and substrate positioning. A mechanistic prediction for the HY2 reaction is proposed. These results support the hypothesis that ferredoxin-dependent bilin reductases reduce BV through a radical mechanism, but their double bond specificity is decided by strategic placement of different protondonating residues surrounding the bilin substrate in the active sites. Phytochromobilin (P⌽B)2 is an open chain tetrapyrrole chromophore critical for light-sensing phytochromes to regulate growth and development of plants. The phytochromebound P⌽B absorbs light energy and proceeds with reversible structural rearrangement to alter the biochemical activities of phytochrome. P⌽B is covalently linked to apophytochrome through a thioether bond between a conserved cysteine residue on the apoprotein and the ethylidene group on the A-ring of P⌽B (1). The biosynthesis of P⌽B has been shown to reside in the plastids, where heme is first linearized by a heme oxygenase into the reaction intermediate biliverdin IX␣ (BV) and then subsequently reduced by a P⌽B synthase (2-5).In Arabidopsis, the HY2 (LONG HYPOCOTYL 2) gene encodes the P⌽B synthase (EC 1.3.7.4), which catalyzes the ferredoxin-dependent reaction of double bond reduction at the A-ring 2,3,3 1 ,3 2 -diene system of BV to yield 3Z/3E-P⌽B (Fig. 1A) (2). Mutations in HY2 have been shown to severely affect photomorphogenetic processes due to the loss of all functional phytochromes (6, 7). Many HY2-related proteins have been identified from various oxygenic photosynthetic organisms and collectively named ferredoxin-dependent bilin reductases (FDBRs) (8). FDBRs utilize reduced ferredoxin as the electron donor to reduce BV into different biliprotein chromophores with different double bond specificities. Phycocyanobilin:ferredoxin oxidoreductase (PcyA; EC 1.3.7.5) catalyzes two double bond reductions of BV on A-and D-rings to yield phycocyanobilin. 15,16-Dihydrobiliverdin:ferredoxin oxidoreductase (PebA; EC 1.3.7.2) and phycoerythrobilin (PEB):ferredoxin oxidoreductase (PebB; EC 1.3.7.3) work together to reduce the C-15-C-16 and A-ring double bond to produce PEB (8). A recently identified PEB synthase (PebS) can itself catalyze the two double bond reductions to yield PEB (9).PcyA is the most extensively studied FDBR enzyme. Previous biochemical analysis has identified a two-electron reduced intermediate, 181 ,18 2 -dihydrobiliverdin IX␣, present in the PcyA reaction, indicating that D-ring reduction precedes A-ring reduction (Fig. 1B) (10). Two organic radical intermediates have also been ...

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Section: Phytochromobilin (P⌽b)supporting

confidence: 52%

Mechanistic Studies of the Phytochromobilin Synthase HY2 from Arabidopsis

Chen

2008

Journal of Biological Chemistry

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“…The massive changes in the max2 / max1 ratio that occur during binding of DHBV to PebA or PebB suggest a more linearly stretched conformation of the DHBV bound to the enzyme compared with free DHBV (22). This fact is interesting in regard to the conformation of BV in the PcyA crystal structure, which is cyclic (7). The spectroscopic differences between PebA⅐DHBV and PebB⅐DHBV indicate that the protein environment, possibly the conformation or orientation of the tetrapyrrole, is different in both complexes.…”

Section: Peba and Pebb Belong To The Fdbr Family Of Radicalmentioning

confidence: 90%

“…Structural information to this new family of enzymes has recently been added through the solved crystal structure of the Synechocystis sp. PCC 6803 PcyA (7).…”

Section: 18mentioning

confidence: 99%

Insights into Phycoerythrobilin Biosynthesis Point toward Metabolic Channeling

Dammeyer¹,

Frankenberg‐Dinkel

2006

Journal of Biological Chemistry

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“…Interestingly, the TeCpcS-R151G variant still bound enough PCB to confer transfer to the apoprotein CpcB in E. coli (68). For Glu-136, the carboxylic function might be involved in positioning of the substrate by interaction with the tetrapyrrole nitrogens, as found for bilin-binding in FDBRs (51,73,74).…”

Section: Peb Biosynthesis In G Theta Adopted From Cyanobacteria-mentioning

confidence: 94%

Insights into the Biosynthesis and Assembly of Cryptophycean Phycobiliproteins

Overkamp

Gasper

Kock

et al. 2014

Journal of Biological Chemistry

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Background: Cryptophytes like Guillardia theta utilize soluble phycobiliproteins for light-harvesting. Results: Guillardia theta adopted phycoerythrobilin biosynthesis from cyanobacteria, and the phycobiliprotein lyase GtCPES provides structural requirements for transfer of this chromophore to a specific cysteine residue of the apophycobiliprotein. Conclusion: Phycobiliprotein synthesis in Guillardia theta combines proven and novel components. Significance: Results provide a better understanding of the evolution and function of unusual phycobiliproteins in cryptophytes.

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Crystal structure of phycocyanobilin:ferredoxin oxidoreductase in complex with biliverdin IXα, a key enzyme in the biosynthesis of phycocyanobilin

Cited by 65 publications

References 30 publications

Mechanistic Studies of the Phytochromobilin Synthase HY2 from Arabidopsis

Mechanistic Studies of the Phytochromobilin Synthase HY2 from Arabidopsis

Insights into Phycoerythrobilin Biosynthesis Point toward Metabolic Channeling

Insights into the Biosynthesis and Assembly of Cryptophycean Phycobiliproteins

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