Research Article: Crystal structure of Yersinia pestis virulence factor YfeA reveals two polyspecific metal-binding sites

Date Published: July 01, 2017

Publisher: International Union of Crystallography

Author(s): Christopher D. Radka, Lawrence J. DeLucas, Landon S. Wilson, Matthew B. Lawrenz, Robert D. Perry, Stephen G. Aller.


YfeA, a substrate-binding protein that is important for the virulence of Yersinia pestis, has two polyspecific metal-binding sites that may play different roles during infection. A flexible lobe at the carboxy-terminus suggests that structural rearrangement is required for metal transfer to binding partners.

Partial Text

In Gram-negative bacteria, the periplasm plays a crucial role in the homeostasis of essential transition metals by serving as a nutrient bank to supply or deplete the cytoplasm (Andrews et al., 2003 ▸). When resources are limited, extracellular metal ions are sequestered and returned to the cell by high-affinity metal-chelating siderophores and cognate receptors (Andrews et al., 2003 ▸). Trafficking of transition-metal ions through the periplasm is mitigated by siderophores and substrate-binding proteins (SBPs; Couñago et al., 2012 ▸). SBPs similarly chelate and deliver metal ions to inner membrane transporters for passage into the cytoplasm (Argüello et al., 2011 ▸). For pathogenic bacteria, infection presents significant challenges in acquiring nutrients, as metals are in variable abundance according to the site of infection and pathogens must compete with the host for essential metals (Ma et al., 2009 ▸).

YfeA is a polyspecific cluster A-1 SBP that is important for Y. pestis infection and transition-metal homeostasis (Bearden & Perry, 1999 ▸; Desrosiers et al., 2010 ▸; Fetherston et al., 2012 ▸; Perry et al., 2012 ▸). YfeA contains a canonical metal-binding site that we refer to as site 1, with ligands that are evolutionarily conserved across SBPs from Gram-positive and Gram-negative genera (Fig. 5 ▸). EDS and anomalous X-ray scattering data confirm that site 1 binds zinc, iron and manganese in a manner that appears to be irreversible in the absence of physiological downstream binding partners for metal exchange. Site 1 appears to show a preference for zinc across all growth-condition experiments, including conditions where YfeA is produced in the context of its cognate transporter. It may be possible to achieve higher occupancies of manganese or iron by either adding more metal at the time of induction and harvesting cells sooner, or continuously supplementing with metal over the course of overexpression. However, such experiments would deviate from the physiological setting considerably given that the host and pathogen compete for limited metal nutrients.




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