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

Matthew Jessop,Angélique Fraudeau,Karine Huard,Jan Felix,Patrice Catty,Irina Gutsche,Benoit Arragain,Maria Bacia-Verloop,Roger Miras,Hélène Malet

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.

Highlights

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
AAA+ ATPases of the MoxR family have been suggested to play a role as chaperones in the assembly of multi-protein complexes, but in general the functions of MoxR family members are not well characterised and their structures are scarce[2]
RavA has been implicated in the assembly of E. coli respiratory Complex I and modulation of the activity of fumarate reductase[6,7]

Summary

Introduction

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. AAA+ ATPases of the MoxR family are ubiquitous and found in all major phyla of bacteria and archaea They are proposed to fulfil chaperone-like functions assisting the maturation or assembly of metabolic protein complexes[1,2], and are often found in an operon upstream of a gene encoding a von Willebrand factor A (VWA) domain-containing protein. The most well-characterised representative of the MoxR family is the E. coli ATPase RavA, encoded by the ravAviaA operon, together with the VWA domain-containing protein ViaA These two proteins were proposed to play a role in the maturation of both respiratory Complex I and fumarate reductase[6,7]. Combined with crystal structures of the LdcI decamer (PDB ID: 3N75) and the RavA monomer (PDB ID: 3NBX), our first low resolution cryo-electron microscopy (cryo-EM) map of the LdcI–RavA cage, performed imposing the D5 symmetry of the

Methods

Results

Conclusion