6VW8

Formate Dehydrogenase FdsABG subcomplex FdsBG from C. necator

Summary for 6VW8

• Entry DOI: 10.2210/pdb6vw8/pdb
• Descriptor: NAD-dependent formate dehydrogenase gamma subunit, NAD-dependent formate dehydrogenase beta subunit, FE2/S2 (INORGANIC) CLUSTER, ... (8 entities in total)
• Functional Keywords: rossmann fold, thioredoxin-like, oxidoreductase
• Biological source: Cupriavidus necator; More
• Total number of polymer chains: 4
• Total formula weight: 159559.91

Authors

Young, T. (deposition date: 2020-02-18, release date: 2020-04-08, Last modification date: 2024-03-06)

Primary citation

Young, T.,Niks, D.,Hakopian, S.,Tam, T.K.,Yu, X.,Hille, R.,Blaha, G.M.
Crystallographic and kinetic analyses of the FdsBG subcomplex of the cytosolic formate dehydrogenase FdsABG fromCupriavidus necator.
J.Biol.Chem., 295:6570-6585, 2020

PubMed Abstract: Formate oxidation to carbon dioxide is a key reaction in one-carbon compound metabolism, and its reverse reaction represents the first step in carbon assimilation in the acetogenic and methanogenic branches of many anaerobic organisms. The molybdenum-containing dehydrogenase FdsABG is a soluble NAD-dependent formate dehydrogenase and a member of the NADH dehydrogenase superfamily. Here, we present the first structure of the FdsBG subcomplex of the cytosolic FdsABG formate dehydrogenase from the hydrogen-oxidizing bacterium H16 both with and without bound NADH. The structures revealed that the two iron-sulfur clusters, FeS in FdsB and FeS in FdsG, are closer to the FMN than they are in other NADH dehydrogenases. Rapid kinetic studies and EPR measurements of rapid freeze-quenched samples of the NADH reduction of FdsBG identified a neutral flavin semiquinone, FMNH, not previously observed to participate in NADH-mediated reduction of the FdsABG holoenzyme. We found that this semiquinone forms through the transfer of one electron from the fully reduced FMNH, initially formed via NADH-mediated reduction, to the FeS cluster. This FeS cluster is not part of the on-path chain of iron-sulfur clusters connecting the FMN of FdsB with the active-site molybdenum center of FdsA. According to the NADH-bound structure, the nicotinamide ring stacks onto the -face of the FMN. However, NADH binding significantly reduced the electron density for the isoalloxazine ring of FMN and induced a conformational change in residues of the FMN-binding pocket that display peptide-bond flipping upon NAD binding in proper NADH dehydrogenases.

PubMed: 32249211
DOI: 10.1074/jbc.RA120.013264

Experimental method

X-RAY DIFFRACTION (2.3 Å)