5B4H

Crystal structure of I86D mutant of phycocyanobilin:ferredoxin oxidoreductase in complex with biliverdin (data 1)

Summary for 5B4H

• Entry DOI: 10.2210/pdb5b4h/pdb
• Related: 5B4I 5B4J
• Descriptor: Phycocyanobilin:ferredoxin oxidoreductase, BILIVERDINE IX ALPHA (3 entities in total)
• Functional Keywords: oxidoreductase, photosynthesis pigment, heme metabolism
• Biological source: Synechocystis sp. PCC 6803
• Total number of polymer chains: 1
• Total formula weight: 28740.73

Authors

Hagiwara, Y.,Wada, K.,Irikawa, T.,Unno, M.,Fukuyama, K.,Sugishima, M. (deposition date: 2016-04-04, release date: 2017-03-15, Last modification date: 2023-11-08)

Primary citation

Hagiwara, Y.,Wada, K.,Irikawa, T.,Sato, H.,Unno, M.,Yamamoto, K.,Fukuyama, K.,Sugishima, M.
Atomic-resolution structure of the phycocyanobilin:ferredoxin oxidoreductase I86D mutant in complex with fully protonated biliverdin
FEBS Lett., 590:3425-3434, 2016

PubMed Abstract: 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.

PubMed: 27596987
DOI: 10.1002/1873-3468.12387

Experimental method

X-RAY DIFFRACTION (1.11 Å)