Atomic-resolution structure of the phycocyanobilin:ferredoxin oxidoreductase I86D mutant in complex with fully protonated biliverdin.
Phycocyanobilin:ferredoxin oxidoreductase (PcyA) catalyzes the reduction of biliverdin (BV) to produce phycocyanobilin, a linear tetrapyrrole pigment used for light harvesting and light sensing. Spectroscopic and HPLC analyses inidicate that BV bound to the I86D mutant of PcyA is fully protonated (BVH+) and can accept an electron, but I86D is unable to donate protons for the reduction; therefore, compared to the wild-type PcyA, the I86D mutant stabilizes BVH+. To elucidate the structural basis of the I86D mutation, we determined the atomic-resolution structure of the I86D-BVH+complex and the protonation states of the essential residues Asp105 and Glu76 in PcyA. Our study revealed that Asp105 adopted a fixed conformation in the I86D mutant, although it had dual conformations in wild-type PcyA which reflected the protonation states of BV. Taken together with biochemical/spectroscopic results, our analysis of the I86D-BVH+structure supports the hypothesis that flexibility of Asp105 is essential for the catalytic activity of PcyA.
Department of Biochemistry and Applied Chemistry, National Institute of Technology, Kurume College, Kurume, Japan.
Yoshinori
Y
Hagiwara
Organization for Promotion of Tenure Track, University of Miyazaki, Kiyotake, Japan.
Kei
K
Wada
Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan.
Teppei
T
Irikawa
Department of Medical Biochemistry, Kurume University School of Medicine, Kurume, Japan.
Hideaki
H
Sato
Graduate School of Science and Engineering, Ibaraki University, Hitachi, Japan.|Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Naka, Japan.
Masaki
M
Unno
Department of Medical Biochemistry, Kurume University School of Medicine, Kurume, Japan.
Ken
K
Yamamoto
Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Japan. fukuyama@chem.eng.osaka-u.ac.jp.|Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Japan. fukuyama@chem.eng.osaka-u.ac.jp.
Keiichi
K
Fukuyama
Department of Medical Biochemistry, Kurume University School of Medicine, Kurume, Japan. sugishima_masakazu@med.kurume-u.ac.jp.
Masakazu
http://orcid.org/0000-0002-0840-4929
M
Sugishima
D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D001664:Biliverdine / Q000737:chemistry* / Q000378:metabolism; D001665:Binding Sites; D062105:Molecular Docking Simulation; D009154:Mutation; D010088:Oxidoreductases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D011485:Protein Binding; D046939:Synechocystis / Q000201:enzymology
D001426:Bacterial Proteins; D010088:Oxidoreductases; C442236:phycocyanobilin ferredoxin oxidoreductase, Synechocystis; D001664:Biliverdine
atomic-resolution structure; photosynthesis; protonation state