5YJX

Structure of the Ndi1 protein from Saccharomyces cerevisiae in complex with myxothiazol.

5YJX の概要

• エントリーDOI: 10.2210/pdb5yjx/pdb
• 分子名称: Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial, FLAVIN-ADENINE DINUCLEOTIDE, MAGNESIUM ION, ... (5 entities in total)
• 機能のキーワード: monotopic membrane protein, nucleotide-binding domain, oxidoreductase
• 由来する生物種: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
• 細胞内の位置: Mitochondrion inner membrane ; Peripheral membrane protein ; Matrix side : P32340
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 111603.52

構造登録者

Yamasita, T.,Inaoka, D.K.,Shiba, T.,Oohashi, T.,Iwata, S.,Yagi, T.,Kosaka, H.,Harada, S.,Kita, K.,Hirano, K. (登録日: 2017-10-11, 公開日: 2018-02-14, 最終更新日: 2023-11-22)

主引用文献

Yamashita, T.,Inaoka, D.K.,Shiba, T.,Oohashi, T.,Iwata, S.,Yagi, T.,Kosaka, H.,Miyoshi, H.,Harada, S.,Kita, K.,Hirano, K.
Ubiquinone binding site of yeast NADH dehydrogenase revealed by structures binding novel competitive- and mixed-type inhibitors
Sci Rep, 8:2427-2427, 2018

PubMed Abstract: Yeast Ndi1 is a monotopic alternative NADH dehydrogenase. Its crystal structure in complex with the electron acceptor, ubiquinone, has been determined. However, there has been controversy regarding the ubiquinone binding site. To address these points, we identified the first competitive inhibitor of Ndi1, stigmatellin, along with new mixed-type inhibitors, AC0-12 and myxothiazol, and thereby determined the crystal structures of Ndi1 in complexes with the inhibitors. Two separate binding sites of stigmatellin, STG-1 and STG-2, were observed. The electron density at STG-1, located at the vicinity of the FAD cofactor, further demonstrated two binding modes: STG-1a and STG-1b. AC0-12 and myxothiazol are also located at the vicinity of FAD. The comparison of the binding modes among stigmatellin at STG-1, AC0-12, and myxothiazol revealed a unique position for the aliphatic tail of stigmatellin at STG-1a. Mutations of amino acid residues that interact with this aliphatic tail at STG-1a reduced the affinity of Ndi1 for ubiquinone. In conclusion, the position of the aliphatic tail of stigmatellin at STG-1a provides a structural basis for its competitive inhibition of Ndi1. The inherent binding site of ubiquinone is suggested to overlap with STG-1a that is distinct from the binding site for NADH.

PubMed: 29402945
DOI: 10.1038/s41598-018-20775-6

実験手法

X-RAY DIFFRACTION (3.21 Å)