Structure and Specificity of the Bacterial Cysteine Methyltransferase Effector NleE Suggests a Novel Substrate in Human DNA Repair Pathway

PLoS Pathogens

Jing Chen¹  Qing Yao¹  Lin Li¹  Feng Shao¹  Xiaobo Wan¹  Li Zhang¹  Liyan Hu¹  Niu Huang¹  Xiaojun Ding¹  She Chen¹  Hongzhuang Peng²  Frank J. Rauscher III²  Jayashree Karar² 

[1] National Institute of Biological Sciences, Beijing, China;The Wistar Institute, Philadelphia, Pennsylvania, United States of America

关键词: Methylation;    Cysteine;    Methyltransferases;    Crystal structure;    293T cells;    Transcription factors;    Biochemical simulations;    DNA damage;   

DOI  :  10.1371/journal.ppat.1004522

学科分类：生物科学（综合）

来源: Public Library of Science

【 摘 要 】

Enteropathogenic E. coli (EPEC) and related enterobacteria rely on a type III secretion system (T3SS) effector NleE to block host NF-κB signaling. NleE is a first in class, novel S-adenosyl-L-methionine (SAM)-dependent methyltransferase that methylates a zinc-coordinating cysteine in the Npl4-like Zinc Finger (NZF) domains in TAB2/3 adaptors in the NF-κB pathway, but its mechanism of action and other human substrates are unknown. Here we solve crystal structure of NleE-SAM complex, which reveals a methyltransferase fold different from those of known ones. The SAM, cradled snugly at the bottom of a deep and narrow cavity, adopts a unique conformation ready for nucleophilic attack by the methyl acceptor. The substrate NZF domain can be well docked into the cavity, and molecular dynamic simulation indicates that Cys673 in TAB2-NZF is spatially and energetically favorable for attacking the SAM. We further identify a new NleE substrate, ZRANB3, that functions in PCNA binding and remodeling of stalled replication forks at the DNA damage sites. Specific inactivation of the NZF domain in ZRANB3 by NleE offers a unique opportunity to suggest that ZRANB3-NZF domain functions in DNA repair processes other than ZRANB3 recruitment to DNA damage sites. Our analyses suggest a novel and unexpected link between EPEC infection, virulence proteins and genome integrity.

【 授权许可】

CC BY