Crystallographic studies of Xe and Kr binding within the large internal cavity of cytochrome ba3 from Thermus thermophilus:: Structural analysis and role of oxygen transport channels in the heme-Cu oxidases
Crystallographic studies of Xe and Kr binding within the large internal cavity of cytochrome ba3 from Thermus thermophilus:: Structural analysis and role of oxygen transport channels in the heme-Cu oxidases
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DOI：
10.1021/bi800045y
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发表时间：
2008-04-22
期刊：
影响因子：
2.9
通讯作者：
Stout, C. David
中科院分区：
文献类型：
--
作者：
Luna, V. Mitch;Chen, Ying;Stout, C. David
细胞色素ba（3）是嗜热栖热菌质膜上的一种细胞色素c氧化酶，在低分子氧张力下是细胞呼吸的首选末端酶。利用细胞色素ba（3）晶体在不同条件下加压的氘或氪气体，和六个晶体的X射线数据，我们确定了多达七个不同的结合位点的氘和氪原子的相对亲和力。这些位点沿着一个连续的Y形通道，长度为18-20埃，由疏水残基排列，从蛋白质表面引出，其中两个入口孔代表Y的顶部，将双层连接到Y底部的a（3）-Cu-B中心。考虑到增加的亲和力的O-2的疏水环境中，疏水性的通道，其在双层内的方向，其连接到活性位点，其均匀的直径，其几乎完全占领的natural酶，和其同晶存在的天然酶，我们推断，该通道是一个扩散途径O-2到双核中心的细胞色素ba 3。这些观察提供了一个基础，用于分析类似的通道在其他氧化酶的已知结构，这些结构进行了讨论，在生物系统中的O-2运输的机制，CO结合到双核中心和出口的细节，氧的分叉和水的途径，和氧通道在有氧嗜热性的可能作用。
Cytochrome ba(3) is a cytochrome c oxidase from the plasma membrane of Thermus thermophilus and is the preferred terminal enzyme of cellular respiration at low dioxygen tensions. Using cytochrome ba(3) crystals pressurized at varying conditions under Xe or Kr gas, and X-ray data for six crystals, we identify the relative affinities of Xe and Kr atoms for as many as seven distinct binding sites. These sites track a continuous, Y-shaped channel, 18-20 angstrom in length, lined by hydrophobic residues, which leads from the surface of the protein where two entrance holes, representing the top of the Y, connect the bilayer to the a(3)-Cu-B center at the base of the Y. Considering the increased affinity of O-2 for hydrophobic environments, the hydrophobic nature of the channel, its orientation within the bilayer, its connection to the active site, its uniform diameter, its virtually complete occupation by Xe, and its isomorphous presence in the native enzyme, we infer that the channel is a diffusion pathway for O-2 into the dinuclear center of cytochrome ba3. These observations provide a basis for analyzing similar channels in other oxidases of known structure, and these structures are discussed in terms of mechanisms of O-2 transport in biological systems, details of CO binding to and egress from the dinuclear center, the bifurcation of the oxygen-in and water-out pathways, and the possible role of the oxygen channel in aerobic thermophily.