Structural and mechanistic insights into the biosynthesis of CDP-archaeol in membranes

• Published in: Cell research 2017-11, Vol.27 (11), p.1378-1391
• Main Authors: Ren, Sixue, Caforio, Antonella, Yang, Qin, Sun, Bo, Yu, Feng, Zhu, Xiaofeng, Wang, Jinjing, Dou, Chao, Fu, Qiuyu, Huang, Niu, Sun, Qiu, Nie, Chunlai, Qi, Shiqian, Gong, Xinqi, He, Jianhua, Wei, Yuquan, Driessen, Arnold JM, Cheng, Wei
• Format: Article
• Language: English
• Subjects: 631/326/26/2523; 631/45/535; 631/57/2272; Aeropyrum - enzymology; Archaea; Archaeal Proteins - chemistry; Archaeal Proteins - metabolism; Bacteria; Binding Sites; Biomedical and Life Sciences; Biosynthesis; CDP-archaeol synthase; Cell Biology; Chains; Chemical bonds; Cytidine Triphosphate - chemistry; Divergence; Enzymes; Eukaryotes; Evolution; Fatty acids; Glycerol; Glycerol-3-phosphate; Grooves; Helices; Hydrophobicity; Life Sciences; Lipids; Lipophilic; Magnesium; Membrane Lipids - biosynthesis; Membranes; Metals - chemistry; Models, Molecular; Original; original-article; Phospholipids; Site-directed mutagenesis; Thermotoga maritima - enzymology; Transferases - chemistry; Transferases - metabolism
• ISSN: 1001-0602; 1748-7838
• DOI: 10.1038/cr.2017.122

The divergence of archaea, bacteria and eukaryotes was a fundamental step in evolution. One marker of this event is a major difference in membrane lipid chemistry between these kingdoms. Whereas the membranes of bac- teria and eukaryotes primarily consist of straight fatty acids ester-bonded to glycerol-3-phosphate, archaeal phos- pholipids consist of isoprenoid chains ether-bonded to glycerol-l-phosphate. Notably, the mechanisms underlying the biosynthesis of these lipids remain elusive. Here, we report the structure of the CDP-archaeol synthase （CarS） of Aeropyrum pernix （ApCarS） in the CTP- and Mg2＋-bound state at a resolution of 2.4 A.. The enzyme comprises a transmembrane domain with five helices and cytoplasmic loops that together form a large charged cavity providing a binding site for CTP. Identification of the binding location of CTP and Mg2＋ enabled modeling of the specific lipophil- ie substrate-binding site, which was supported by site-directed mutagenesis, substrate-binding affinity analyses, and enzyme assays. We propose that archaeol binds within two hydrophobic membrane-embedded grooves formed by the flexible transmembrane helix 5 （TM5）, together with TM1 and TM4. Collectively, structural comparisons and analyses, combined with functional studies, not only elucidated the mechanism governing the biosynthesis of pbospholipids with ether-bonded isoprenoid chains by CTP transferase, but also provided insights into the evolution of this enzyme superfamily from archaea to bacteria and eukaryotes.