5WED

Structure of bacterial type II NADH dehydrogenase from Caldalkalibacillus thermarum at 2.15A resolution

Summary for 5WED

• Entry DOI: 10.2210/pdb5wed/pdb
• Related: 4NWZ
• Descriptor: FAD-dependent pyridine nucleotide-disulfide oxidoreductase, FLAVIN-ADENINE DINUCLEOTIDE (3 entities in total)
• Functional Keywords: rossmann fold, dehydrogenase, nucleotide binding, membrane/cytoplasm, oxidoreductase
• Biological source: Caldalkalibacillus thermarum TA2.A1
• Total number of polymer chains: 4
• Total formula weight: 181430.15

Authors

Nakatani, Y.,Aragao, D.,Cook, G.M. (deposition date: 2017-07-09, release date: 2017-10-18, Last modification date: 2024-05-22)

Primary citation

Nakatani, Y.,Jiao, W.,Aragao, D.,Shimaki, Y.,Petri, J.,Parker, E.J.,Cook, G.M.
Crystal structure of type II NADH:quinone oxidoreductase from Caldalkalibacillus thermarum with an improved resolution of 2.15 angstrom.
Acta Crystallogr F Struct Biol Commun, 73:541-549, 2017

PubMed Abstract: Type II NADH:quinone oxidoreductase (NDH-2) is a respiratory enzyme found in the electron-transport chain of many species, with the exception of mammals. It is a 40-70 kDa single-subunit monotopic membrane protein that catalyses the oxidation of NADH and the reduction of quinone molecules via the cofactor FAD. NDH-2 is a promising new target for drug development given its essential role in many bacterial species and intracellular parasites. Only two bacterial NDH-2 structures have been reported and these structures are at moderate resolution (2.3-2.5 Å). In this communication, a new crystallization platform is reported that produced high-quality NDH-2 crystals that diffracted to high resolution (2.15 Å). The high-resolution NDH-2 structure was used for in silico quinone substrate-docking studies to investigate the binding poses of menadione and ubiquinone molecules. These studies revealed that a very limited number of molecular interactions occur at the quinone-binding site of NDH-2. Given that the conformation of the active site is well defined, this high-resolution structure is potentially suitable for in silico inhibitor-compound screening and ligand-docking applications.

PubMed: 28994401
DOI: 10.1107/S2053230X17013073

Experimental method

X-RAY DIFFRACTION (2.15 Å)