Structural insight of a concentration-dependent mechanism by which YdiV inhibits Escherichia coli flagellum biogenesis and motility

Nucleic Acids Res. 2012 Nov;40(21):11073-85. doi: 10.1093/nar/gks869. Epub 2012 Sep 21.


YdiV is a negative regulator of cell motility. It interacts with FlhD(4)C(2) complex, a product of flagellar master operon, which works as the transcription activator of all other flagellar operons. Here, we report the crystal structures of YdiV and YdiV(2)-FlhD(2) complex at 1.9 Å and 2.9 Å resolutions, respectively. Interestingly, YdiV formed multiple types of complexes with FlhD(4)C(2). YdiV(1)-FlhD(4)C(2) and YdiV(2)-FlhD(4)C(2) still bound to DNA, while YdiV(3)-FlhD(4)C(2) and YdiV(4)-FlhD(4)C(2) did not. DNA bound FlhD(4)C(2) through wrapping around the FlhC subunit rather than the FlhD subunit. Structural analysis showed that only two peripheral FlhD subunits were accessible for YdiV binding, forming the YdiV(2)-FlhD(4)C(2) complex without affecting the integrity of ring-like structure. YdiV(2)-FlhD(2) structure and the negative staining electron microscopy reconstruction of YdiV(4)-FlhD(4)C(2) suggested that the third and fourth YdiV molecule bound to the FlhD(4)C(2) complex through squeezing into the ring-like structure of FlhD(4)C(2) between the two internal D subunits. Consequently, the ring-like structure opened up, and the complex lost DNA-binding ability. Thus, YdiV inhibits FlhD(4)C(2) only at relatively high concentrations.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Carrier Proteins / chemistry*
  • Carrier Proteins / genetics
  • Carrier Proteins / metabolism
  • DNA, Bacterial / metabolism
  • Escherichia coli / genetics
  • Escherichia coli / metabolism
  • Escherichia coli Proteins / chemistry*
  • Escherichia coli Proteins / genetics
  • Escherichia coli Proteins / metabolism
  • Flagella / metabolism
  • Models, Molecular
  • Movement
  • Mutation
  • Protein Binding
  • Protein Subunits / chemistry
  • Protein Subunits / metabolism
  • Trans-Activators / chemistry*
  • Trans-Activators / metabolism


  • Carrier Proteins
  • DNA, Bacterial
  • Escherichia coli Proteins
  • Protein Subunits
  • Trans-Activators
  • YdiV protein, E coli
  • flhC protein, E coli
  • flhD protein, E coli

Associated data

  • PDB/3TLQ
  • PDB/4ES4