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

Nat Commun. 2016 Aug 31:7:12481. doi: 10.1038/ncomms12481.

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.

Publication types

  • Research Support, N.I.H., Intramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine Triphosphatases / chemistry
  • Adenosine Triphosphatases / metabolism*
  • Amino Acid Motifs / physiology
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / metabolism
  • Biofilms
  • Crystallography, X-Ray
  • Cyclic GMP / analogs & derivatives*
  • Cyclic GMP / chemistry
  • Cyclic GMP / metabolism
  • Mutation
  • Protein Binding / physiology
  • Protein Domains / physiology*
  • Type II Secretion Systems / chemistry
  • Type II Secretion Systems / metabolism
  • Vibrio cholerae / physiology*

Substances

  • Bacterial Proteins
  • Type II Secretion Systems
  • bis(3',5')-cyclic diguanylic acid
  • Adenosine Triphosphatases
  • Cyclic GMP