Volume 34, No 8, Aug 2024

ISSN: 1001-0602 
EISSN: 1748-7838 2018 
impact factor 17.848* 
(Clarivate Analytics, 2019)

Volume 34 Issue 8, August 2024: 545-555   |  Open Access

ORIGINAL ARTICLES

Molecular and structural basis of an ATPase-nuclease dual-enzyme anti-phage defense complex

Qiyin An^1,2,† , Yong Wang^1,2,† , Zhenhua Tian^1,2,† , Jie Han^3,† , Jinyue Li¹ , Fumeng Liao⁴ , Feiyang Yu⁵ , Haiyan Zhao⁵ , Yancheng Wen⁶ , Heng Zhang⁴ , Zengqin Deng^1,7,*

¹Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
²University of Chinese Academy of Sciences, Beijing, China
³Department of Human Anatomy, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
⁴Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
⁵State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, Hubei, China
⁶Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, Fuzhou, Fujian, China
⁷Hubei Jiangxia Laboratory, Wuhan, Hubei, China
^†These authors contributed equally: Qiyin An, Yong Wang, Zhenhua Tian, Jie Han
Correspondence: Zengqin Deng(dengzengqin@wh.iov.cn)

Coupling distinct enzymatic effectors emerges as an efficient strategy for defense against phage infection in bacterial immune responses, such as the widely studied nuclease and cyclase activities in the type III CRISPR-Cas system. However, concerted enzymatic activities in other bacterial defense systems are poorly understood. Here, we biochemically and structurally characterize a two-component defense system DUF4297–HerA, demonstrating that DUF4297–HerA confers resistance against phage infection by cooperatively cleaving dsDNA and hydrolyzing ATP. DUF4297 alone forms a dimer, and HerA alone exists as a nonplanar split spiral hexamer, both of which exhibit extremely low enzymatic activity. Interestingly, DUF4297 and HerA assemble into an approximately 1 MDa supramolecular complex, where two layers of DUF4297 (6 DUF4297 molecules per layer) linked via inter-layer dimerization of neighboring DUF4297 molecules are stacked on top of the HerA hexamer. Importantly, the complex assembly promotes dimerization of DUF4297 molecules in the upper layer and enables a transition of HerA from a nonplanar hexamer to a planar hexamer, thus activating their respective enzymatic activities to abrogate phage infection. Together, our findings not only characterize a novel dual-enzyme anti-phage defense system, but also reveal a unique activation mechanism by cooperative complex assembly in bacterial immunity.

https://doi.org/10.1038/s41422-024-00981-w

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