Electrostatic properties deduced from refined structures of NADH-cytochrome b5 reductase and the other flavin-dependent reductases: Pyridine nucleotide-binding and interaction with an electron-transfer partner

Electrostatic properties on the protein surface were examined on the basis of the crystal structure of NADH-cytochrome b₅ reductase refined to a crystallographic R factor of 0.223 at 2.1 Å resolution and of the other three flavin-dependent reductases. A structural comparison of NADH-cytochrome b₅ reductase with the other flavin-dependent reductases, ferredoxin-NADP⁺ reductase, phthalate dioxygenase reductase, and nitrate reductase, showed that the α/β structure is the common motif for binding pyridine nucleotide. Although the amino acid residues associated with pyridine nucleotide-binding are not conserved, the electrostatic properties and the location of the pyridine nucleotide-binding pockets of NADH-requiring reductases were similar to each other. The electrostatic potential of the surface near the flavin-protruding side (dimethylbenzene end of the flavin ring) of NADH-cytochrome b₅ reductase was positive over a wide area while that of the surface near the heme-binding site of cytochrome b₅ was negative. This implied that the flavin-protruding side of NADH-cytochrome b₅ reductase is suitable for interacting with its electron-transfer partner, cytochrome b₅. This positive potential area is conserved among four flavin-dependent reductases. A comparison of the electron-transfer partners of four flavin-dependent reductases showed that there are significant differences in the distribution of electrostatic potential between inter-molecular and inter-domain electron-transfer reactions. © 1996 Wiley-Liss, Inc.