Grund Tamara N, Kabashima Yoshiki, Kusumoto Tomoichirou, Wu Di, Welsch Sonja, Sakamoto Junshi, Michel Hartmut, Safarian Schara
Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt, Germany.
Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Fukuoka, Japan.
Front Chem. 2023 Jan 4;10:1085463. doi: 10.3389/fchem.2022.1085463. eCollection 2022.
Cytochromes are essential for microaerobic respiration of many prokaryotes including a number of human pathogens. These enzymes catalyze the reduction of molecular oxygen to water using quinols as electron donors. Their importance for prokaryotic survival and the absence of eukaryotic homologs make these enzyme ideal targets for antimicrobial drugs. Here, we determined the cryoEM structure of the menaquinol-oxidizing cytochrome -type oxygen reductase of the facultative anaerobic Actinobacterium at a resolution of 2.7 Å. The obtained structure adopts the signature pseudosymmetrical heterodimeric architecture of canonical cytochrome oxidases formed by the core subunits CydA and CydB. No accessory subunits were identified for this cytochrome homolog. The two -type hemes and the oxygen binding heme are organized in a triangular geometry with a protein environment around these redox cofactors similar to that of the closely related cytochrome from . We identified oxygen and a proton conducting channels emerging from the membrane space and the cytoplasm, respectively. Compared to the prototypical enzyme homolog from the , the most apparent difference is found in the location and size of the proton channel entry site. In canonical cytochrome oxidases quinol oxidation occurs at the highly flexible periplasmic Q-loop located in the loop region between TMHs six and seven. An alternative quinol-binding site near heme was previously identified for cytochrome from . We discuss the relevance of the two quinol oxidation sites in actinobacterial -type oxidases and highlight important differences that may explain functional and electrochemical differences between and . This study expands our current understanding of the structural diversity of actinobacterial and proteobacterial cytochrome oxygen reductases and provides deeper insights into the unique structural and functional properties of various cytochrome variants from different phylae.
细胞色素对于包括许多人类病原体在内的许多原核生物的微需氧呼吸至关重要。这些酶以醌醇作为电子供体,催化分子氧还原为水。它们对原核生物生存的重要性以及真核生物同源物的缺失,使这些酶成为抗菌药物的理想靶点。在此,我们以2.7 Å的分辨率确定了兼性厌氧放线菌的甲萘醌氧化细胞色素c型氧还原酶的冷冻电镜结构。所获得的结构采用了由核心亚基CydA和CydB形成的典型细胞色素c氧化酶的标志性假对称异二聚体结构。未鉴定出该细胞色素c同源物的辅助亚基。两种类型的血红素和氧结合血红素c以三角形几何结构排列,这些氧化还原辅因子周围的蛋白质环境与来自[具体物种]的密切相关的细胞色素c相似。我们分别鉴定出了从膜间隙和细胞质中出现的氧和质子传导通道。与来自[具体物种]的原型酶同源物相比,最明显的差异在于质子通道入口位点的位置和大小。在典型的细胞色素c氧化酶中,醌醇氧化发生在位于跨膜螺旋6和7之间环区域的高度灵活的周质Q环处。先前已为来自[具体物种]的细胞色素c鉴定出一个靠近血红素b的替代醌醇结合位点。我们讨论了放线菌c型氧化酶中两个醌醇氧化位点的相关性,并强调了可能解释[具体物种1]和[具体物种2]之间功能和电化学差异的重要差异。这项研究扩展了我们目前对放线菌和变形菌细胞色素c氧还原酶结构多样性的理解,并为来自不同菌系的各种细胞色素c变体的独特结构和功能特性提供了更深入的见解。