XVIth International Workshop on
Quantum Systems in
Chemistry and Physics
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Computational study of electronic structures of a characteristic [4Fe-4S] cluster, [Fe4S4(SCH3)3(CH3COO)], in dark-operative protochlorophyllide oxidoreductase
Yu Takano,1 Yasushige Yonezawa,1 Yuichi Fujita,2 Genji Kurisu,1 and Haruki Nakamura1
1Institute for Protein Research, Osaka University, Japan

2Graduate School of Bioagricultural Sciences, Nagoya University, Japan
The [4Fe-4S] clusters play important roles in electron transfer and catalysis in ferredoxins and nitrogenases. Recently, a X-ray structure of the dark-operative protochlorophyllide oxidoreductase (DPOR) has been determined at 2.3 ┼ resolution [1]. The [4Fe-4S] cluster in DPOR (NB cluster) has such a characteristic structural feature that one of the iron ions is chelated by the carboxylate group of Asp36, unlike conventional [4Fe-4S] clusters coordinated with four Cys residues. To examine the effect of the Asp ligation on the enzymatic activities, three NB-protein mutants, D36C, D36S, and D36A, were prepared. Although the D36C and D36S substitutions almost nullified the activity, the D36A mutant exhibited 13 % of the wild-type level. The crystal structures of the D36C mutant was found to have the conventional [4Feľ4S] cluster coordinated with four Cys residues, while that of the D36A mutant had a [4Feľ4S] cluster chelated by three Cys residues and an unknown fourth non-protein ligand, which was likely to be the hydroxide or chloride ion. These findings indicate that Asp ligation is important for the enzymatic activity.
In this study, we have investigated the electronic structure of the NB cluster to understand the role of the Asp ligation to the [4Feľ4S] cluster in the catalysis of DPOR using the density functional theory [2]. The electronic structure of the NB cluster is compared with those of the conventional [4Feľ4S] clusters in the D36C variant and the putative [4Feľ4S] clusters in the D36A mutant. Although the electronic structures are similar to each other, our computation shows that the redox potential of the NB cluster is lower than that of the D36C model in the 2ľ/3ľ reduction reaction, in an environment with the dielectric constant higher than 10, showing that the NB cluster can transfer an electron more easily than the conventional [4Feľ4S] cluster. This redox character demonstrates the important role of Asp36 in DPOR. It is also found that the electron-donating character of the [4Feľ4S] clusters in the 2ľ/3ľ reduction in an environment with high dielectric constant is in the same order as the experimental enzymatic activities of the wild type DPOR and its mutant, indicating that the fourth ligand of the [4Feľ4S] cluster in the D36A mutant is likely to be a chloride ion.

[1] N. Muraki, J. Nomata, K. Ebata, T. Mizoguchi, T. Shiba, H. Tamiaki, G. Kurisu, Y. Fujita, Nature 465 (2010) 110ľ114.
[2] Y. Takano, Y. Yonezawa, Y. Fujita, G. Kurisu, H. Nakamura, Chem. Phys. Lett. 503 (2011) 296ľ300.

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