Nishida H, Miki K
Research Laboratory of Resources Utilization, Tokyo Institute of Technology, Yokohama, Japan.
Proteins. 1996 Sep;26(1):32-41. doi: 10.1002/(SICI)1097-0134(199609)26:1<32::AID-PROT3>3.0.CO;2-I.
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.
基于在2.1埃分辨率下晶体学R因子为0.223的NADH - 细胞色素b5还原酶的晶体结构以及其他三种黄素依赖性还原酶，对蛋白质表面的静电性质进行了研究。NADH - 细胞色素b5还原酶与其他黄素依赖性还原酶（铁氧化还原蛋白 - NADP + 还原酶、邻苯二甲酸双加氧酶还原酶和硝酸还原酶）的结构比较表明，α/β结构是结合吡啶核苷酸的共同基序。尽管与吡啶核苷酸结合相关的氨基酸残基并不保守，但需要NADH的还原酶的静电性质和吡啶核苷酸结合口袋的位置彼此相似。NADH - 细胞色素b5还原酶黄素突出侧（黄素环的二甲苯端）附近表面的静电势在很大区域内为正，而细胞色素b5血红素结合位点附近表面的静电势为负。这表明NADH - 细胞色素b5还原酶的黄素突出侧适合与其电子传递伙伴细胞色素b5相互作用。这个正电势区域在四种黄素依赖性还原酶中是保守的。对四种黄素依赖性还原酶的电子传递伙伴的比较表明，分子间和结构域间电子传递反应之间的静电势分布存在显著差异。
