Structural insights into ATP hydrolysis by the MoxR ATPase RavA and the LdcI-RavA cage-like complex

Commun Biol. 2020 Jan 28;3(1):46. doi: 10.1038/s42003-020-0772-0.

Abstract

The hexameric MoxR AAA+ ATPase RavA and the decameric lysine decarboxylase LdcI form a 3.3 MDa cage, proposed to assist assembly of specific respiratory complexes in E. coli. Here, we show that inside the LdcI-RavA cage, RavA hexamers adopt an asymmetric spiral conformation in which the nucleotide-free seam is constrained to two opposite orientations. Cryo-EM reconstructions of free RavA reveal two co-existing structural states: an asymmetric spiral, and a flat C2-symmetric closed ring characterised by two nucleotide-free seams. The closed ring RavA state bears close structural similarity to the pseudo two-fold symmetric crystal structure of the AAA+ unfoldase ClpX, suggesting a common ATPase mechanism. Based on these structures, and in light of the current knowledge regarding AAA+ ATPases, we propose different scenarios for the ATP hydrolysis cycle of free RavA and the LdcI-RavA cage-like complex, and extend the comparison to other AAA+ ATPases of clade 7.

MeSH terms

  • Adenosine Diphosphate / metabolism
  • Adenosine Triphosphatases / chemistry*
  • Adenosine Triphosphatases / metabolism*
  • Adenosine Triphosphate / metabolism*
  • Carboxy-Lyases / chemistry*
  • Carboxy-Lyases / metabolism*
  • Catalytic Domain
  • Cryoelectron Microscopy
  • Crystallization
  • Crystallography, X-Ray
  • Electron Transport Complex I / chemistry*
  • Electron Transport Complex I / metabolism*
  • Escherichia coli / metabolism
  • Escherichia coli Proteins / chemistry*
  • Escherichia coli Proteins / metabolism*
  • Hydrogen-Ion Concentration
  • Hydrolysis
  • Protein Binding
  • Protein Conformation, alpha-Helical

Substances

  • Escherichia coli Proteins
  • Adenosine Diphosphate
  • Adenosine Triphosphate
  • Adenosine Triphosphatases
  • RavA protein, E coli
  • Carboxy-Lyases
  • lysine decarboxylase
  • Electron Transport Complex I