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Structural Basis for Hydration Dynamics in Radical Stabilization of Bilin Reductase Mutants

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§ Department of Chemistry
∥ Department of Molecular and Cellular Biology
⊥ Biophysics Graduate Program
University of California, One Shields Avenue, Davis, California 95616
# Stanford Synchrotron Radiation Lightsource, Menlo Park, California 94025
*To whom correspondence should be addressed. E-mail: [email protected]. Phone: 530-754-6180. Fax: 530-752-8995.
▽Current Address: Laboratory of Structural Microbiology, Rockefeller University, New York, NY 10065
Cite this: Biochemistry 2010, 49, 29, 6206–6218
Publication Date (Web):June 17, 2010
https://doi.org/10.1021/bi100728q
Copyright © 2010 American Chemical Society
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    Abstract

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    Heme-derived linear tetrapyrroles (phytobilins) in phycobiliproteins and phytochromes perform critical light-harvesting and light-sensing roles in oxygenic photosynthetic organisms. A key enzyme in their biogenesis, phycocyanobilin:ferredoxin oxidoreductase (PcyA), catalyzes the overall four-electron reduction of biliverdin IXα to phycocyanobilin—the common chromophore precursor for both classes of biliproteins. This interconversion occurs via semireduced bilin radical intermediates that are profoundly stabilized by selected mutations of two critical catalytic residues, Asp105 and His88. To understand the structural basis for this stabilization and to gain insight into the overall catalytic mechanism, we report the high-resolution crystal structures of substrate-loaded Asp105Asn and His88Gln mutants of Synechocystis sp. PCC 6803 PcyA in the initial oxidized and one-electron reduced radical states. Unlike wild-type PcyA, both mutants possess a bilin-interacting axial water molecule that is ejected from the active site upon formation of the enzyme-bound neutral radical complex. Structural studies of both mutants also show that the side chain of Glu76 is unfavorably located for D-ring vinyl reduction. On the basis of these structures and companion 15N−1H long-range HMQC NMR analyses to assess the protonation state of histidine residues, we propose a new mechanistic scheme for PcyA-mediated reduction of both vinyl groups of biliverdin wherein an axial water molecule, which prematurely binds and ejects from both mutants upon one electron reduction, is required for catalytic turnover of the semireduced state.

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    Picture of crystal of PcyA D105N at start of addition of 100 mM sodium dithionite, picture of same crystal 10 min after dithionite addition; 130 GHz pulsed EPR spectrum of radical intermediate of H88Q crystal at 45 K; microspectrometry of PcyA D105N mutant crystal in the X-ray beam at beamline 7-1 at SSRL, picture of crystal after a 6 min exposure to synchrotron radiation; resonance assignments for 15N−1H LR-HMQC spectrum of BV-free PcyA at pH 7.0; NMR chemical shifts of histidine imidazole side chain resonance. This material is available free of charge via the Internet at http://pubs.acs.org.

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    2. Nathan C Rockwell, J Clark Lagarias, . GUN4 appeared early in cyanobacterial evolution. PNAS Nexus 2023, 2 (5) https://doi.org/10.1093/pnasnexus/pgad131
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    5. Masakazu Sugishima, Kei Wada, Masaki Unno, Keiichi Fukuyama. Bilin-metabolizing enzymes: site-specific reductions catalyzed by two different type of enzymes. Current Opinion in Structural Biology 2019, 59 , 73-80. https://doi.org/10.1016/j.sbi.2019.03.005
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    9. Yoshinori Hagiwara, Kei Wada, Teppei Irikawa, Hideaki Sato, Masaki Unno, Ken Yamamoto, Keiichi Fukuyama, Masakazu Sugishima. Atomic-resolution structure of the phycocyanobilin:ferredoxin oxidoreductase I86D mutant in complex with fully protonated biliverdin. FEBS Letters 2016, 590 (19) , 3425-3434. https://doi.org/10.1002/1873-3468.12387
    10. Masaki Unno, Katsuhiro Kusaka, Taro Tamada, Masakazu Sugishima, Kei Wada, Yoshinori Hagiwara, Keiichi Fukuyama. Findings in the Neutron Crystal Structure Analysis of a Bilin Reductase PcyA Complexed with its Substrate Biliverdin. hamon 2016, 26 (3) , 130-134. https://doi.org/10.5611/hamon.26.3_130
    11. Masaki UNNO, Masakazu SUGISHIMA, Kei WADA, Yoshinori HAGIWARA, Katsuhiro KUSAKA, Taro TAMADA, Keiichi FUKUYAMA. Two Protonation States and Structural Features of a Bilin Reductase PcyA Revealed by Neutron Crystallography. Nihon Kessho Gakkaishi 2015, 57 (5) , 297-303. https://doi.org/10.5940/jcrsj.57.297
    12. Burak V. Kabasakal, David D. Gae, Jie Li, J. Clark Lagarias, Patrice Koehl, Andrew J. Fisher. His74 conservation in the bilin reductase PcyA family reflects an important role in protein-substrate structure and dynamics. Archives of Biochemistry and Biophysics 2013, 537 (2) , 233-242. https://doi.org/10.1016/j.abb.2013.07.021
    13. GUY HANKE, PAULA MULO. Plant type ferredoxins and ferredoxin-dependent metabolism. Plant, Cell & Environment 2013, 36 (6) , 1071-1084. https://doi.org/10.1111/pce.12046
    14. Kei Wada, Yoshinori Hagiwara, Yuko Yutani, Keiichi Fukuyama. One residue substitution in PcyA leads to unexpected changes in tetrapyrrole substrate binding. Biochemical and Biophysical Research Communications 2010, 402 (2) , 373-377. https://doi.org/10.1016/j.bbrc.2010.10.037
    15. Masakazu Sugishima, Yukihiro Okamoto, Masato Noguchi, Takayuki Kohchi, Hitoshi Tamiaki, Keiichi Fukuyama. Crystal Structures of the Substrate-Bound Forms of Red Chlorophyll Catabolite Reductase: Implications for Site-Specific and Stereospecific Reaction. Journal of Molecular Biology 2010, 402 (5) , 879-891. https://doi.org/10.1016/j.jmb.2010.08.021
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