title: 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.
abstract: 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 A 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 alpha/beta 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.
authors.affiliation: Research Laboratory of Resources Utilization, Tokyo Institute of Technology, Yokohama, Japan.
authors.forename: H
authors.initials: H
authors.lastname: Nishida
authors.forename: K
authors.initials: K
authors.lastname: Miki
mesh_terms: D001665:Binding Sites; D055598:Chemical Phenomena; D002621:Chemistry; D018360:Crystallography, X-Ray; D003579:Cytochrome Reductases / Q000737:chemistry*; D042966:Cytochrome-B(5) Reductase; D015786:Cytochromes b5 / Q000378:metabolism; D004579:Electron Transport; D005287:Ferredoxin-NADP Reductase / Q000737:chemistry; D005415:Flavins / Q000378:metabolism*; D006860:Hydrogen Bonding; D008958:Models, Molecular; D050901:Nitrate Reductase; D009565:Nitrate Reductases / Q000737:chemistry; D009711:Nucleotides / Q000378:metabolism*; D010088:Oxidoreductases / Q000737:chemistry*; D011487:Protein Conformation; D017433:Protein Structure, Secondary
chemical_list: D005415:Flavins; D009711:Nucleotides; D015786:Cytochromes b5; D010088:Oxidoreductases; C049135:phthalate oxygenase reductase; D005287:Ferredoxin-NADP Reductase; D003579:Cytochrome Reductases; D042966:Cytochrome-B(5) Reductase; D009565:Nitrate Reductases; D050901:Nitrate Reductase