5FB3

Structure of glycerophosphate dehydrogenase in complex with NADPH

5FB3 の概要

• エントリーDOI: 10.2210/pdb5fb3/pdb
• 分子名称: Glycerol-1-phosphate dehydrogenase [NAD(P)+], ZINC ION, SULFATE ION, ... (6 entities in total)
• 機能のキーワード: rossmann fold, oxidoreductase
• 由来する生物種: Pyrobaculum calidifontis JCM 11548
• タンパク質・核酸の鎖数: 6
• 化学式量合計: 226217.17

構造登録者

Sakuraba, H.,Hayashi, J.,Yamamoto, K.,Yoneda, K.,Ohshima, T. (登録日: 2015-12-14, 公開日: 2016-10-12, 最終更新日: 2024-03-20)

主引用文献

Hayashi, J.,Yamamoto, K.,Yoneda, K.,Ohshima, T.,Sakuraba, H.
Unique coenzyme binding mode of hyperthermophilic archaeal sn-glycerol-1-phosphate dehydrogenase from Pyrobaculum calidifontis
Proteins, 84:1786-1796, 2016

PubMed Abstract: A gene encoding an sn-glycerol-1-phosphate dehydrogenase (G1PDH) was identified in the hyperthermophilic archaeon Pyrobaculum calidifontis. The gene was overexpressed in Escherichia coli, and its product was purified and characterized. In contrast to conventional G1PDHs, the expressed enzyme showed strong preference for NADH: the reaction rate (V ) with NADPH was only 2.4% of that with NADH. The crystal structure of the enzyme was determined at a resolution of 2.45 Å. The asymmetric unit consisted of one homohexamer. Refinement of the structure and HPLC analysis showed the presence of the bound cofactor NADPH in subunits D, E, and F, even though it was not added in the crystallization procedure. The phosphate group at C2' of the adenine ribose of NADPH is tightly held through the five biased hydrogen bonds with Ser40 and Thr42. In comparison with the known G1PDH structure, the NADPH molecule was observed to be pushed away from the normal coenzyme binding site. Interestingly, the S40A/T42A double mutant enzyme acquired much higher reactivity than the wild-type enzyme with NADPH, which suggests that the biased interactions around the C2'-phosphate group make NADPH binding insufficient for catalysis. Our results provide a unique structural basis for coenzyme preference in NAD(P)-dependent dehydrogenases. Proteins 2016; 84:1786-1796. © 2016 Wiley Periodicals, Inc.

PubMed: 27616573
DOI: 10.1002/prot.25161

実験手法

X-RAY DIFFRACTION (2.45 Å)