2DKE

Crystal structure of substrate-free form of PcyA

Summary for 2DKE

• Entry DOI: 10.2210/pdb2dke/pdb
• Related: 2D1E
• Descriptor: Phycocyanobilin:ferredoxin oxidoreductase, CHLORIDE ION (3 entities in total)
• Functional Keywords: alpha-beta-alpha sandwich, substrate free form, oxidoreductase
• Biological source: Synechocystis sp.
• Total number of polymer chains: 1
• Total formula weight: 28191.61

Authors

Hagiwara, Y.,Sugishima, M.,Takahashi, Y.,Fukuyama, K. (deposition date: 2006-04-10, release date: 2006-07-25, Last modification date: 2023-10-25)

Primary citation

Hagiwara, Y.,Sugishima, M.,Takahashi, Y.,Fukuyama, K.
Induced-fitting and electrostatic potential change of PcyA upon substrate binding demonstrated by the crystal structure of the substrate-free form
Febs Lett., 580:3823-3828, 2006

PubMed Abstract: Phycocyanobilin:ferredoxin oxidoreductase (PcyA) catalyzes the sequential reduction of the vinyl group of the D-ring and the A-ring of biliverdin IXalpha (BV) using ferredoxin to produce phycocyanobilin, a pigment used for light-harvesting and light-sensing in red algae and cyanobacteria. We have determined the crystal structure of the substrate-free form of PcyA from Synechocystis sp. PCC 6803 at 2.5 A resolution. Structural comparison of the substrate-free form and the PcyA-BV complex shows major changes around the entrance of the BV binding pocket; upon BV binding, two alpha-helices and nearby side-chains move to produce tight BV binding. Unexpectedly, these movements localize the positive charges around the BV binding site, which may contribute to the proper binding of ferredoxin to PcyA. In the substrate-free form, the side-chain of Asp105 was located at a site that would be underneath the BV A-ring in the PcyA-BV complex and hydrogen-bonded with His88. We propose that BV is protonated by a mechanism involving conformational changes of these two residues before reduction.

PubMed: 16782089
DOI: 10.1016/j.febslet.2006.05.075

Experimental method

X-RAY DIFFRACTION (2.5 Å)