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Journal Articles

Insights into the proton transfer mechanism of a bilin reductase PcyA following neutron crystallography

Unno, Masayoshi*; Ishikawa, Kumiko*; Kusaka, Katsuhiro*; Tamada, Taro; Hagiwara, Yoshinori*; Sugishima, Masakazu*; Wada, Kei*; Yamada, Taro*; Tomoyori, Katsuaki; Hosoya, Takaaki*; et al.

Journal of the American Chemical Society, 137(16), p.5452 - 5460, 2015/04

 Times Cited Count:28 Percentile:64.6(Chemistry, Multidisciplinary)

Phycocyanobilin, a light-harvesting and photoreceptor pigment in higher plants, algae, and cyanobacteria, is synthesized from biliverdin IX$$alpha$$ (BV) by phycocyanobilin:ferredoxin oxidoreductase (PcyA) via two steps of two-proton-coupled two-electron reduction. We determined the neutron structure of PcyA from cyanobacteria complexed with BV, revealing the exact location of the hydrogen atoms involved in catalysis. Notably, approximately half of the BV bound to PcyA was BVH$$^{+}$$, a state in which all four pyrrole nitrogen atoms were protonated. The protonation states of BV complemented the protonation of adjacent Asp105. The "axial "water molecule that interacts with the neutral pyrrole nitrogen of the A-ring was identified. His88 N$$delta$$ was protonated to form a hydrogen bond with the lactam O atom of the BV A-ring. His88 and His74 were linked by hydrogen bonds via H$$_{3}$$O$$^{+}$$. These results imply that Asp105, His88, and the axial water molecule contribute to proton transfer during PcyA catalysis.

Journal Articles

${it Klavier}$ (${it klv}$), a novel hypernodulation mutant of ${it Lotus japonicus}$ affected in vascular tissue organization and floral induction

Kira, Erika*; Tateno, Kumiko*; Miura, Kinichiro*; Haga, Tatsuya*; Hayashi, Masaki*; Harada, Kyuya*; Sato, Shusei*; Tabata, Satoshi*; Shikazono, Naoya; Tanaka, Atsushi; et al.

Plant Journal, 44(3), p.505 - 515, 2005/11

 Times Cited Count:89 Percentile:86.56(Plant Sciences)

no abstracts in English

Journal Articles

Theoretical analysis of electronic structure for the chemical bonding of Pu and Am in MgO

Tanaka, Kumiko; Hirata, Masaru; Sekine, Rika*

Journal of Nuclear and Radiochemical Sciences, 5(2), p.27 - 31, 2004/12

The relativistic discrete-variational Dirac-Fock-Slater (DV-DFS) method was performed to investigate the electronic structure of MgO doped with Pu or Am atoms. The differences between these systems, in particular, the participation of d-electrons and f-electrons in chemical bonding, were clarified by calculating their electronic structures. Substitution of actinide atoms was found to result in the effective charges of MgO becoming smaller, with a large charge transfer occurring as far as the second layer. It was also found that the bonding feature between the center atom and the surrounding oxygen atoms was extended to lower energy in the case of actinide (An) substituted systems. Moreover, the bonding characteristics were assigned; a bonding interaction for An6d-O2p and an anti-bonding for An5f-O2p near the HOMO level. These complex effects were found to dominate the strength of the covalent bonding between MgO and actinide atoms.

Oral presentation

Hydration and electronic structures of nobelium ion

Hirata, Masaru; Tanaka, Kumiko*; Nagame, Yuichiro; Anton, J.*; Fricke, B.*

no journal, , 

no abstracts in English

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