5GV8

Structure of NADH-cytochrome b5 reductase refined with the multipolar atomic model at 0.78A

5GV8 の概要

• エントリーDOI: 10.2210/pdb5gv8/pdb
• 関連するPDBエントリー: 5GV7
• 分子名称: NADH-cytochrome b5 reductase 3, FLAVIN-ADENINE DINUCLEOTIDE, GLYCEROL, ... (4 entities in total)
• 機能のキーワード: oxidoreductase, electron transfer, flavoprotein
• 由来する生物種: Sus scrofa (Pig)
• 細胞内の位置: Endoplasmic reticulum membrane ; Lipid-anchor ; Cytoplasmic side : P83686
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 32027.60

構造登録者

Takaba, K.,Takeda, K.,Miki, K. (登録日: 2016-09-03, 公開日: 2017-04-05, 最終更新日: 2023-11-08)

主引用文献

Takaba, K.,Takeda, K.,Kosugi, M.,Tamada, T.,Miki, K.
Distribution of valence electrons of the flavin cofactor in NADH-cytochrome b5 reductase.
Sci Rep, 7:43162-43162, 2017

PubMed Abstract: Flavin compounds such as flavin adenine dinucleotide (FAD), flavin mononucleotide and riboflavin make up the active centers in flavoproteins that facilitate various oxidoreductive processes. The fine structural features of the hydrogens and valence electrons of the flavin molecules in the protein environment are critical to the functions of the flavoproteins. However, information on these features cannot be obtained from conventional protein X-ray analyses at ordinary resolution. Here we report the charge density analysis of a flavoenzyme, NADH-cytochrome b reductase (b5R), at an ultra-high resolution of 0.78 Å. Valence electrons on the FAD cofactor as well as the peptide portion, which are clearly visualized even after the conventional refinement, are analyzed by the multipolar atomic model refinement. The topological analysis for the determined electron density reveals the valence electronic structure of the isoalloxazine ring of FAD and hydrogen-bonding interactions with the protein environment. The tetrahedral electronic distribution around the N5 atom of FAD in b5R is stabilized by hydrogen bonding with CH of Tyr65 and amide-H of Thr66. The hydrogen bonding network leads to His49 composing the cytochrome b-binding site via non-classical hydrogen bonds between N5 of FAD and CH of Tyr65 and O of Tyr65 and CH of His49.

PubMed: 28225078
DOI: 10.1038/srep43162

実験手法

X-RAY DIFFRACTION (0.78 Å)