7YK9

Neutron Structure of PcyA I86D Mutant Complexed with Biliverdin at Room Temperature

Summary for 7YK9

• Entry DOI: 10.2210/pdb7yk9/pdb
• Related: 4qcd 5B4H 5B4I 5B4J
• Descriptor: Phycocyanobilin:ferredoxin oxidoreductase, 3-[5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-2-[[5-[(Z)-(3-ethenyl-4-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1H-pyrrol-2-yl]methyl]-4-methyl-1H-pyrrol-3-yl]propanoic acid (3 entities in total)
• Functional Keywords: phycocyanobilin, biliverdin, neutron, joint-refinement, room temperature, pigment, substrate, inactive, absorption spectrum, hydrogen atom, proton, mutant, oxidoreductase
• Biological source: Synechocystis sp. PCC 6803
• Total number of polymer chains: 1
• Total formula weight: 28742.75

Authors

Unno, M.,Igarashi, K. (deposition date: 2022-07-22, release date: 2023-01-25, Last modification date: 2024-04-03)

Primary citation

Joutsuka, T.,Nanasawa, R.,Igarashi, K.,Horie, K.,Sugishima, M.,Hagiwara, Y.,Wada, K.,Fukuyama, K.,Yano, N.,Mori, S.,Ostermann, A.,Kusaka, K.,Unno, M.
Neutron crystallography and quantum chemical analysis of bilin reductase PcyA mutants reveal substrate and catalytic residue protonation states.
J.Biol.Chem., 299:102763-102763, 2022

PubMed Abstract: PcyA, a ferredoxin-dependent bilin pigment reductase, catalyzes the site-specific reduction of the two vinyl groups of biliverdin (BV), producing phycocyanobilin. Previous neutron crystallography detected both the neutral BV and its protonated form (BVH) in the wildtype (WT) PcyA-BV complex, and a nearby catalytic residue Asp105 was found to have two conformations (protonated and deprotonated). Semiempirical calculations have suggested that the protonation states of BV are reflected in the absorption spectrum of the WT PcyA-BV complex. In the previously determined absorption spectra of the PcyA D105N and I86D mutants, complexed with BV, a peak at 730 nm, observed in the WT, disappeared and increased, respectively. Here, we performed neutron crystallography and quantum chemical analysis of the D105N-BV and I86D-BV complexes to determine the protonation states of BV and the surrounding residues and study the correlation between the absorption spectra and protonation states around BV. Neutron structures elucidated that BV in the D105N mutant is in a neutral state, whereas that in the I86D mutant is dominantly in a protonated state. Glu76 and His88 showed different hydrogen bonding with surrounding residues compared with WT PcyA, further explaining why D105N and I86D have much lower activities for phycocyanobilin synthesis than the WT PcyA. Our quantum mechanics/molecular mechanics calculations of the absorption spectra showed that the spectral change in D105N arises from Glu76 deprotonation, consistent with the neutron structure. Collectively, our findings reveal more mechanistic details of bilin pigment biosynthesis.

PubMed: 36463961
DOI: 10.1016/j.jbc.2022.102763

Experimental method

NEUTRON DIFFRACTION (2 Å)
X-RAY DIFFRACTION (1.9 Å)