5FB3

Structure of glycerophosphate dehydrogenase in complex with NADPH

Summary for 5FB3

• Entry DOI: 10.2210/pdb5fb3/pdb
• Descriptor: Glycerol-1-phosphate dehydrogenase [NAD(P)+], ZINC ION, SULFATE ION, ... (6 entities in total)
• Functional Keywords: rossmann fold, oxidoreductase
• Biological source: Pyrobaculum calidifontis JCM 11548
• Total number of polymer chains: 6
• Total formula weight: 226217.17

Authors

Sakuraba, H.,Hayashi, J.,Yamamoto, K.,Yoneda, K.,Ohshima, T. (deposition date: 2015-12-14, release date: 2016-10-12, Last modification date: 2024-03-20)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (2.45 Å)