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Electrostatic properties deduced from refined structures of NADH‐cytochrome b 5 reductase and the other flavin‐dependent reductases: Pyridine nucleotide‐binding and interaction with an electron‐transfer partner
Author(s) -
Nishida Hirokazu,
Miki Kunio
Publication year - 1996
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/(sici)1097-0134(199609)26:1<32::aid-prot3>3.0.co;2-i
Subject(s) - flavin group , cytochrome b5 , chemistry , stereochemistry , reductase , electron transfer , biochemistry , enzyme , photochemistry
Electrostatic properties on the protein surface were examined on the basis of the crystal structure of NADH‐cytochrome b 5 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 b 5 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 b 5 reductase was positive over a wide area while that of the surface near the heme‐binding site of cytochrome b 5 was negative. This implied that the flavin‐protruding side of NADH‐cytochrome b 5 reductase is suitable for interacting with its electron‐transfer partner, cytochrome b 5 . 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.