著者

中村 春木 栗栖 源嗣

出版者

一般社団法人 日本生物物理学会

雑誌

生物物理 (ISSN:05824052)

巻号頁・発行日

vol.58, no.2, pp.071-077, 2018 (Released:2018-03-31)

参考文献数

31

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These days, “Data Science” becomes a new trend of science by accumulation and analysis of scientific big data. This data science is considered to provide a very useful approach for, in particular, biological science because of its very diversed characters. Here, we point out the essential issues in biological data science, and how they could be solved in the PDB (Protein Data Bank) archive, which the authors manage as PDBj (PDB Japan), one of the wwPDB (world wide PDB) members with the global cooperation.

著者

八木 俊樹 戸田 暁之 市川 宗厳 栗栖 源嗣

出版者

一般社団法人 日本生物物理学会

雑誌

生物物理 (ISSN:05824052)

巻号頁・発行日

vol.61, no.1, pp.020-022, 2021 (Released:2021-01-29)

参考文献数

9

被引用文献数

1

著者

栗栖 源嗣

出版者

日本結晶学会

雑誌

日本結晶学会誌 (ISSN:03694585)

巻号頁・発行日

vol.65, no.1, pp.1, 2023-02-28 (Released:2023-03-08)

著者

宮原 郁子 五十嵐 教之 田中 信忠 栗栖 源嗣

出版者

日本結晶学会

雑誌

日本結晶学会誌 (ISSN:03694585)

巻号頁・発行日

vol.56, no.4, pp.223, 2014-08-31 (Released:2014-09-03)

著者

藤田 祐一 栗栖 源嗣

出版者

一般社団法人 日本生物物理学会

雑誌

生物物理 (ISSN:05824052)

巻号頁・発行日

vol.51, no.2, pp.066-071, 2011 (Released:2011-03-30)

参考文献数

25

被引用文献数

1

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Protochlorophyllide (Pchlide) reduction is the final step to make up the spectroscopic properties of chlorophyll a in biosynthesis of chlorophyll. During evolution, photosynthetic organisms have invented two structurally unrelated Pchlide reductases; light-dependent Pchlide reductase (LPOR) and light-independent (dark-operative) Pchlide reductase (DPOR). LPOR is an NADPH-dependent enzyme operating as a key enzyme for the light-dependent greening in angiosperms, and DPOR is a nitrogenase-like enzyme that allows gymnosperms, algae, cyanobacteria and photosynthetic bacteria to produce (bacterio)chlorophylls even in the dark. We will review recent major research progresses on Pchlide reductases, especially, crystallographic structure and proposed reaction mechanism of DPOR. Differential operation and evolutionary implications of these enzymes are also discussed.

著者

栗栖 源嗣

出版者

日本結晶学会

雑誌

日本結晶学会誌 (ISSN:03694585)

巻号頁・発行日

vol.64, no.1, pp.77-80, 2022-02-28 (Released:2022-03-04)

著者

村木 則文 栗栖 源嗣 野亦 次郎 藤田 祐一

出版者

日本結晶学会

雑誌

日本結晶学会誌 (ISSN:03694585)

巻号頁・発行日

vol.53, no.2, pp.113-118, 2011-04-30 (Released:2011-05-25)

参考文献数

16

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Dark-operative protochlorophyllide reductase (DPOR) catalyses the reduction of protochlorophyllide (Pchlide) to chlorophyllide a, which is a key step in the chlorophyll biosynthesis pathway. DPOR is a nitrogenase-like enzyme consisting of two components, BchL and BchNB, which are structurally related to nitrogenase NifH and NifDK, respectively. We determined the crystal structure of the catalytic component of DPOR, BchNB, in Pchlide-bound and Pchlide-free forms. BchNB has a novel FeS cluster (NB-cluster) coordinated uniquely by one aspartate and three cysteines. NB-cluster is located at the spatial position corresponding to an electron mediating FeS cluster, P-cluster, in nitrogenase NifDK. A Pchlide molecule found in the Pchlide-bound form is accommodated in the cavity surrounded by many hydrophobic residues. We propose a unique trans-specific reduction mechanism by comparison between the Pchlide-bound and the Pchlide-free forms. The spatial arrangement of the NB-cluster and Pchlide is almost identical to that of the P-cluster and FeMo-cofactor in nitrogenase NifDK, suggesting that a common architecture exists to reduce chemically stable multibonds of porphyrin and dinitrogen.