Abstract
Virulence-associated proteins (Vaps) contribute to the virulence of the pathogen Rhodococcus equi, but their mode of action has remained elusive. All Vaps share a conserved core of about 105 amino acids that folds into a compact eight-stranded antiparallel β-barrel with a unique topology. At the top of the barrel, four loops connect the eight β-strands. Previous Vap structures did not show concave surfaces that might serve as a ligand-binding site. Here, the structure of VapB in a new crystal form was determined at 1.71 Å resolution. The asymmetric unit contains two molecules. In one of them, the loop regions at the top of the barrel adopt a different conformation from other Vap structures. An outward movement of the loops results in the formation of a hydrophobic cavity that might act as a ligand-binding site. This lends further support to the hypothesis that the structural similarity between Vaps and avidins suggests a potential binding function for Vaps.
Highlights
Rhodococcus equi is a Gram-positive environmental soil bacterium that can cause severe bronchopneumonia in young foals (Vazquez-Boland & Meijer, 2019)
A virulence-associated plasmid of some 85 kbp is absolutely required for infection of foals (Takai et al, 1991; Tkachuk-Saad & Prescott, 1991) and encodes a key factor for infection and intracellular multiplication: virulenceassociated protein A (VapA; Jain et al, 2003)
The critical activity of VapA is the collapse of the pH gradient across the phagosome membrane, as chemical pH neutralization of the endocytic and phagocytic continuum using any of several pH-neutralizing drugs enables virulence-plasmid-deficient R. equi to multiply in macrophages
Summary
Rhodococcus equi is a Gram-positive environmental soil bacterium that can cause severe bronchopneumonia in young foals (Vazquez-Boland & Meijer, 2019). R. equi infects lung alveolar macrophages, where it multiplies in a remodelled compartment, the Rhodococcus-containing vacuole (Zink et al, 1987; Fernandez-Mora et al, 2005) This is an unusual phagolysosome that maintains a near-neutral pH (von Bargen et al, 2019). Whittingham and coworkers noted the structural similarity between VapD and bradavidin 2, an avidin-like protein from Bradyrhizobium japonicum (Leppiniemi et al, 2013), but suggested that VapD is not involved in small-molecule binding due to the absence of a cavity (Whittingham et al, 2014). Vap proteins have less potential for a binding site due to the crossover connections linking strands 3 to 4 and 7 to 8 at the top and the -helix that seals the bottom (Okoko et al, 2015). We present a new structure of VapB that highlights a potential binding site for a putative host cell-derived ligand
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