Mechanistic insight into how multidrug resistant Acinetobacter baumannii response regulator AdeR recognizes an intercistronic region

• Published in: Nucleic acids research Vol. 45; no. 16; pp. 9773 - 9787
• Main Authors: Wen, Yurong, Ouyang, Zhenlin, Yu, Yue, Zhou, Xiaorong, Pei, Yingmei, Devreese, Bart, Higgins, Paul G, Zheng, Fang
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 19.09.2017
• Subjects: Acinetobacter baumannii - drug effects; Bacterial Proteins - chemistry; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Crystallography, X-Ray; DNA, Intergenic - metabolism; Drug Resistance, Multiple, Bacterial; Models, Molecular; Phosphorylation; Protein Domains; Scattering, Small Angle; Structural Biology; Thermodynamics; X-Ray Diffraction
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkx624

AdeR-AdeS is a two-component regulatory system, which controls expression of the adeABC efflux pump involved in Acinetobacter baumannii multidrug resistance. AdeR is a response regulator consisting of an N-terminal receiver domain and a C-terminal DNA-binding-domain. AdeR binds to a direct-repeat DNA in the intercistronic region between adeR and adeABC. We demonstrate a markedly high affinity binding between unphosphorylated AdeR and DNA with a dissociation constant of 20 nM. In addition, we provide a 2.75 Å crystal structure of AdeR DNA-binding-domain complexed with the intercistronic DNA. This structure shows that the α3 and β hairpin formed by β5-β6 interacts with the major and minor groove of the DNA, which in turn leads to the introduction of a bend. The AdeR receiver domain structure revealed a dimerization motif mediated by a gearwheel-like structure involving the D108F109-R122 motif through cation π stack interaction. The structure of AdeR receiver domain bound with magnesium indicated a conserved Glu19Asp20-Asp63 magnesium-binding motif, and revealed that the potential phosphorylation site Asp63OD1 forms a hydrogen bond with Lys112. We thus dissected the mechanism of how AdeR recognizes the intercistronic DNA, which leads to a diverse mode of response regulation. Unlocking the AdeRS mechanism provides ways to circumvent A. baumannii antibiotic resistance.