Structural and Biochemical Characterization Reveals LysGH15 as an Unprecedented “EF-Hand-Like” Calcium-Binding Phage Lysin

PLoS Pathogens

Wei Ding¹  Ziyin Cui²  Yue Li²  Dong Han²  Chongtao Du²  Liancheng Lei²  Wenyu Han²  Xin Feng²  Changjiang Sun²  Yongjun Yang²  Mei Yang²  Xiaohe Liu²  Jingmin Gu²  Jun Song²  Songying Ouyang³  Fengfeng Niu³  Zhi-Jie Liu³  Lianying Jiao³  Yingang Feng⁴ 

[1] Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China;Key Laboratory of Zoonosis, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, China;National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China;Shandong Provincial Key Laboratory of Energy Genetics, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China

关键词: Protein domains;    Protein structure;    Zinc;    Bacteriophages;    Crystal structure;    Peptidoglycans;    Protein structure comparison;    Sequence alignment;   

DOI  :  10.1371/journal.ppat.1004109

学科分类：生物科学（综合）

来源: Public Library of Science

【 摘 要 】

The lysin LysGH15, which is derived from the staphylococcal phage GH15, demonstrates a wide lytic spectrum and strong lytic activity against methicillin-resistant Staphylococcus aureus (MRSA). Here, we find that the lytic activity of the full-length LysGH15 and its CHAP domain is dependent on calcium ions. To elucidate the molecular mechanism, the structures of three individual domains of LysGH15 were determined. Unexpectedly, the crystal structure of the LysGH15 CHAP domain reveals an “EF-hand-like” calcium-binding site near the Cys-His-Glu-Asn quartet active site groove. To date, the calcium-binding site in the LysGH15 CHAP domain is unique among homologous proteins, and it represents the first reported calcium-binding site in the CHAP family. More importantly, the calcium ion plays an important role as a switch that modulates the CHAP domain between the active and inactive states. Structure-guided mutagenesis of the amidase-2 domain reveals that both the zinc ion and E282 are required in catalysis and enable us to propose a catalytic mechanism. Nuclear magnetic resonance (NMR) spectroscopy and titration-guided mutagenesis identify residues (e.g., N404, Y406, G407, and T408) in the SH3b domain that are involved in the interactions with the substrate. To the best of our knowledge, our results constitute the first structural information on the biochemical features of a staphylococcal phage lysin and represent a pivotal step forward in understanding this type of lysin.

【 授权许可】

CC BY