The 1.25 Å resolution structure of the diheme NapB subunit of soluble nitrate reductase reveals a novel cytochrome c fold with a stacked heme arrangement
The 1.25 Å resolution structure of the diheme NapB subunit of soluble nitrate reductase reveals a novel cytochrome c fold with a stacked heme arrangement
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DOI：
10.1021/bi012144b
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发表时间：
2002-04-16
期刊：
影响因子：
2.9
通讯作者：
Van Beeumen, JJ
中科院分区：
文献类型：
--
作者：
Brigé, A;Leys, D;Van Beeumen, JJ
二血红素细胞色素NapB构成了广泛存在于多种细菌物种（包括病原体）中的质周硝酸盐还原酶的小亚基。NapB蛋白在将电子转移到大催化亚基NapA中至关重要，NapA随后将硝酸盐还原为亚硝酸盐。在这里，我们展示了来自流感嗜血杆菌的蛋白水解形式的重组NapB的晶体结构，它是通过多波长异常色散（MAD）方法在1.25埃分辨率下确定的。这种结构显示出前所未有的折叠，证实了NapB蛋白属于一类新的细胞色素。这两个血红素基团具有几乎平行的血红素平面，并以范德华距离堆叠，铁与铁之间的距离仅为9.9埃，这两个结构特征也存在于来自Desulfovibrio脱硫菌ATCC 27774的分裂- soret二血红素细胞色素c中，否则与肽链折叠模式无关。两个血红素基团上的两个丙酸侧链是相互氢键的，这是迄今为止在任何其他血红素蛋白中也没有报道过的结构特征。由于盐桥和丙酸酯与保守残基之间的一些氢键，其中一个血红素基团的丙酸酯被拉向分子内部。我们提出了一个假设但合理的NapAB复合物模型，其中四个氧化还原中心位于一个几乎线性的结构中，跨越近40埃的距离，这表明NapB的生理电子供体NapC将电子转移到NapA催化位点的硝酸盐分子上是一个有效的途径。
The diheme cytochrome NapB constitutes the small subunit of a periplasmic nitrate reductase found in a wide variety of bacterial species, including pathogens. The NapB protein is essential in transferring electrons to the large catalytic subunit NapA, which subsequently reduces nitrate to nitrite. Here we present the crystal structure of a proteolyzed form of recombinant NapB from Haemophilus influenzae, which was determined by the multiple-wavelength anomalous dispersion (MAD) method at 1.25 Angstrom resolution. This structure shows an unprecedented fold, confirming that NapB proteins belong to a new class of cytochromes. The two heme groups have nearly parallel heme planes and are stacked at van der Waals distances with an iron-to-iron distance of only 9.9 Angstrom, two structural features that are also present in the split-Soret diheme cytochrome c from Desulfovibrio desulfuricans ATCC 27774, which is otherwise unrelated in the peptide chain folding pattern. The two propionate side chains on both heme groups are hydrogen-bonded to each other, a structural characteristic that to date also has not been reported in any other heme protein. The propionates of one of the heme groups are pulled toward the interior of the molecule due to a salt bridge and a number of hydrogen bonds between the propionates and conserved residues. We propose a hypothetical but plausible model of the NapAB complex in which the four redox centers are positioned in a virtually linear configuration which spans a distance of nearly 40 Angstrom, suggesting an efficient pathway for the transfer of electrons from NapC, the physiological electron donor of NapB, to a nitrate molecule at the catalytic site of NapA.