High resolution crystal structure of Paracoccus denitrificans cytochrome c oxidase: New insights into the active site and the proton transfer pathways
High resolution crystal structure of Paracoccus denitrificans cytochrome c oxidase: New insights into the active site and the proton transfer pathways
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DOI：
10.1016/j.bbabio.2009.04.003
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发表时间：
2009-06-01
影响因子：
4.3
通讯作者：
Michel, Hartmut
中科院分区：
文献类型：
--
作者：
Koepke, Juergen;Olkhova, Elena;Michel, Hartmut
利用x射线低温数据将反硝化副球菌的双亚基细胞色素c氧化酶的结构细化到2.25埃分辨率，以进一步了解其作用机制。改进的结构模型显示了许多新的特征，包括许多额外的溶剂和洗涤剂分子。活性位点上连接血红素a(3)铁和Cu-B的电子密度用过氧基团或氯离子最合适。两个水或OH-基团不适合，一个水（或OH-）不能提供足够的电子密度。在溴化物而不是氯化物存在下分离的细胞色素c氧化酶晶体的分析似乎排除了氯化物作为桥接配体。在d途径中，由6个水分子组成的氢键链连接Asn131和Glu278，但质子进入该水链被Asn113、Asn131和Asn199阻断。k途径包含两个紧密结合的水分子，一个额外的水链似乎形成了它的入口。血红素上方有一个由13个水分子组成的簇，这些水分子可能为泵送的质子形成多个出口通道。氢键模式排除了以咪唑盐形式存在的Cu-B配体His326。(C) 2009 Elsevier B.V.版权所有
The structure of the two-subunit cytochrome c oxidase from Paracoccus denitrificans has been refined using X-ray cryodata to 2.25 angstrom resolution in order to gain further insights into its mechanism of action. The refined structural model shows a number of new features including many additional solvent and detergent molecules. The electron density bridging the heme a(3) iron and Cu-B of the active site is fitted best by a peroxo-group or a chloride ion. Two waters or OH- groups do not fit, one water (or OH-) does not provide sufficient electron density. The analysis of crystals of cytochrome c oxidase isolated in the presence of bromide instead of chloride appears to exclude chloride as the bridging ligand. In the D-pathway a hydrogen bonded chain of six water molecules connects Asn131 and Glu278, but the access for protons to this water chain is blocked by Asn113, Asn131 and Asn199. The K-pathway contains two firmly bound water molecules, an additional water chain seems to form its entrance. Above the hemes a cluster of 13 water molecules is observed which potentially form multiple exit pathways for pumped protons. The hydrogen bond pattern excludes that the Cu-B ligand His326 is present in the imidazolate form. (C) 2009 Elsevier B.V. All rights reserved.