Structure of a new crystal modification of the bacterial NAD-dependent formate dehydrogenase with a resolution of 2.1 Å

Formate dehydrogenase (FDG) from methylotrophic bacteria Pseudomonas sp. 101 catalyzes the reaction of oxidation of the formate ion to carbon dioxide, which is accompanied by the reduction of nicotinamid adenine dinucleotide (NAD⁺). The structures of the apo and holo (enzyme-NAD-azide triple complex) forms of the enzyme were determined earlier. In an attempt to prepare a complex of FDG with the product of the enzymatic reaction (NADH), a new crystal modification of FDG is obtained (space group P4₂2₁2, a = b = 93.3 Å, c = 103.05 Å). The FDG structure is solved by the molecular replacement method and refined to R = 20.7%. The asymmetric part of the unit cell contains one FDG molecule. In contrast to the previously studied FDG structures, the biologically active dimer is formed by the crystallographic rotation axis. A comparative structural analysis of the studied form with the apo and holo forms of the enzyme is performed. The influence of the molecular structure on the environment in the crystal is investigated.