Nucleotide binding by the widespread high-affinity cyclic di-GMP receptor MshEN domain

Yu-Chuan Wang, Ko-Hsin Chin, Zhi-Le Tu, Jin He, Christopher J. Jones, David Zamorano Sanchez, Fitnat H. Yildiz, Michael Y. Galperin and Shan-Ho Chou ()
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Yu-Chuan Wang: Institute of Biochemistry, National Chung Hsing University
Ko-Hsin Chin: Agricultural Biotechnology Center, National Chung Hsing University
Zhi-Le Tu: Institute of Biochemistry, National Chung Hsing University
Jin He: State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University
Christopher J. Jones: University of California, Santa Cruz
David Zamorano Sanchez: University of California, Santa Cruz
Fitnat H. Yildiz: University of California, Santa Cruz
Michael Y. Galperin: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health
Shan-Ho Chou: Institute of Biochemistry, National Chung Hsing University

Nature Communications, 2016, vol. 7, issue 1, 1-12

Abstract: Abstract C-di-GMP is a bacterial second messenger regulating various cellular functions. Many bacteria contain c-di-GMP-metabolizing enzymes but lack known c-di-GMP receptors. Recently, two MshE-type ATPases associated with bacterial type II secretion system and type IV pilus formation were shown to specifically bind c-di-GMP. Here we report crystal structure of the MshE N-terminal domain (MshEN1-145) from Vibrio cholerae in complex with c-di-GMP at a 1.37 Å resolution. This structure reveals a unique c-di-GMP-binding mode, featuring a tandem array of two highly conserved binding motifs, each comprising a 24-residue sequence RLGxx(L/V/I)(L/V/I)xxG(L/V/I)(L/V/I)xxxxLxxxLxxQ that binds half of the c-di-GMP molecule, primarily through hydrophobic interactions. Mutating these highly conserved residues markedly reduces c-di-GMP binding and biofilm formation by V. cholerae. This c-di-GMP-binding motif is present in diverse bacterial proteins exhibiting binding affinities ranging from 0.5 μM to as low as 14 nM. The MshEN domain contains the longest nucleotide-binding motif reported to date.

Date: 2016
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DOI: 10.1038/ncomms12481

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