title: Structure and specificity of the bacterial cysteine methyltransferase effector NleE suggests a novel substrate in human DNA repair pathway.
abstract: 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.
authors.affiliation: National Institute of Biological Sciences, Beijing, China.
authors.forename: Qing
authors.initials: Q
authors.lastname: Yao
authors.affiliation: National Institute of Biological Sciences, Beijing, China.
authors.forename: Li
authors.initials: L
authors.lastname: Zhang
authors.affiliation: National Institute of Biological Sciences, Beijing, China.
authors.forename: Xiaobo
authors.initials: X
authors.lastname: Wan
authors.affiliation: National Institute of Biological Sciences, Beijing, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Chen
authors.affiliation: National Institute of Biological Sciences, Beijing, China.
authors.forename: Liyan
authors.initials: L
authors.lastname: Hu
authors.affiliation: National Institute of Biological Sciences, Beijing, China.
authors.forename: Xiaojun
authors.initials: X
authors.lastname: Ding
authors.affiliation: National Institute of Biological Sciences, Beijing, China.
authors.forename: Lin
authors.initials: L
authors.lastname: Li
authors.affiliation: The Wistar Institute, Philadelphia, Pennsylvania, United States of America.
authors.forename: Jayashree
authors.initials: J
authors.lastname: Karar
authors.affiliation: The Wistar Institute, Philadelphia, Pennsylvania, United States of America.
authors.forename: Hongzhuang
authors.initials: H
authors.lastname: Peng
authors.affiliation: National Institute of Biological Sciences, Beijing, China.
authors.forename: She
authors.initials: S
authors.lastname: Chen
authors.affiliation: National Institute of Biological Sciences, Beijing, China.
authors.forename: Niu
authors.initials: N
authors.lastname: Huang
authors.affiliation: The Wistar Institute, Philadelphia, Pennsylvania, United States of America.
authors.forename: Frank J
authors.initials: FJ
authors.lastname: Rauscher
authors.affiliation: National Institute of Biological Sciences, Beijing, China; National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; National Institute of Biological Sciences, Beijing, Collaborative Innovation Center for Cancer Medicine, Beijing, China.
authors.forename: Feng
authors.initials: F
authors.lastname: Shao
mesh_terms: D002460:Cell Line; D018360:Crystallography, X-Ray; D004265:DNA Helicases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D004260:DNA Repair; D054308:Enteropathogenic Escherichia coli / Q000201:enzymology / Q000235:genetics; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D006801:Humans; D056004:Molecular Dynamics Simulation; D011496:Protein Methyltransferases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D017434:Protein Structure, Tertiary; D012436:S-Adenosylmethionine / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D037521:Virulence Factors / Q000737:chemistry / Q000235:genetics / Q000378:metabolism
chemical_list: D029968:Escherichia coli Proteins; C526043:NleE protein, E coli; D037521:Virulence Factors; D012436:S-Adenosylmethionine; D011496:Protein Methyltransferases; D004265:DNA Helicases; C555409:ZRANB3 protein, human