Fukuyama K, Matsubara H, Tsukihara T, Katsube Y
Department of Biology, Faculty of Science, Osaka University, Japan.
J Mol Biol. 1989 Nov 20;210(2):383-98. doi: 10.1016/0022-2836(89)90338-0.
The structure of a low-potential ferredoxin isolated from Bacillus thermoproteolyticus has been refined by a restrained least-squares method. The final crystallographic R factor is 0.204 for 2906 reflections with F greater than 3 sigma F in the 6.0 to 2.3 A resolution range. The model contains 81 amino acid residues, one [4Fe-4S] cluster, and 59 water molecules. The root-mean-square deviation from ideal values for bond lengths is 0.018 A, and the mean coordinate error is estimated to be 0.25 A. The present ferredoxin is similar in the topology of the polypeptide backbone to the dicluster-type ferredoxins from Peptococcus aerogenes and Azotobacter vinelandii, but has considerable insertions and deletions of the peptide segments as well as different secondary structures. Although all but the C-terminal C zeta atoms of P. aerogenes ferredoxin superpose on the C alpha atoms of A. vinelandii ferredoxin, only 60% superpose on the C alpha atoms of B. thermoproteolyticus ferredoxin, with a root-mean-square distance of 0.82 A for each pair. The conformations of the peptide segments surrounding the [4Fe-4S] clusters in these three ferredoxins are all conserved. Moreover, the schemes for the NH...S hydrogen bonds in these ferredoxins are nearly identical. The site of the aromatic ring of Tyr27 in B. thermoproteolyticus ferredoxin is close spatially to that of Tyr28 in P. aerogenes ferredoxin with reference to the cluster, but these residues do not correspond in the spatial alignment of their polypeptide backbones. We infer that in monocluster-type ferredoxins, the side-chain at the 27th residue has a crucial effect on the stability of the cluster. Of the four cysteine residues that bind to the second Fe-S cluster in the dicluster-type ferredoxins, two are conserved in the monocluster-type ferredoxins from Desulfovibrio gigas. D. desulfuricans Norway, and Clostridium thermoaceticum. The tertiary structure of B. thermoproteolyticus ferredoxin suggests that in such monocluster-type ferredoxins these two cysteine residues, which in it correspond to Ala21 and Asp53, form a disulfide bridge.
通过约束最小二乘法对从嗜热解蛋白酶芽孢杆菌中分离出的低电位铁氧化还原蛋白的结构进行了优化。在6.0至2.3埃分辨率范围内，对于2906个F大于3σF的反射，最终晶体学R因子为0.204。该模型包含81个氨基酸残基、一个[4Fe-4S]簇和59个水分子。键长与理想值的均方根偏差为0.018埃，平均坐标误差估计为0.25埃。目前的铁氧化还原蛋白在多肽主链拓扑结构上与产气消化球菌和棕色固氮菌的双簇型铁氧化还原蛋白相似，但在肽段上有相当多的插入和缺失以及不同的二级结构。尽管除产气消化球菌铁氧化还原蛋白的C末端Cζ原子外，其余所有原子都与棕色固氮菌铁氧化还原蛋白的Cα原子重叠，但只有60%与嗜热解蛋白酶芽孢杆菌铁氧化还原蛋白的Cα原子重叠，每对原子的均方根距离为0.82埃。这三种铁氧化还原蛋白中围绕[4Fe-4S]簇的肽段构象都是保守的。此外，这些铁氧化还原蛋白中NH...S氢键的模式几乎相同。嗜热解蛋白酶芽孢杆菌铁氧化还原蛋白中Tyr27芳香环的位置相对于簇在空间上与产气消化球菌铁氧化还原蛋白中Tyr28的位置接近，但这些残基在其多肽主链的空间排列中并不对应。我们推断在单簇型铁氧化还原蛋白中，第27位残基的侧链对簇的稳定性有至关重要的影响。在双簇型铁氧化还原蛋白中与第二个Fe-S簇结合的四个半胱氨酸残基中，有两个在巨大脱硫弧菌、挪威脱硫弧菌和热醋酸梭菌的单簇型铁氧化还原蛋白中是保守的。嗜热解蛋白酶芽孢杆菌铁氧化还原蛋白的三级结构表明，在这种单簇型铁氧化还原蛋白中，这两个半胱氨酸残基（在其中对应于Ala21和Asp53）形成了一个二硫键。
