Gram-negative bacteria use siderophores, outer membrane receptors, inner membrane transporters and substrate-binding proteins (SBPs) to transport transition metals through the periplasm. The SBPs share a similar protein fold that has undergone significant structural evolution to communicate with a variety of differentially regulated transporters in the cell. In Yersinia pestis, the causative agent of plague, YfeA (YPO2439, y1897), an SBP, is important for full virulence during mammalian infection. To better understand the role of YfeA in infection, crystal structures were determined under several environmental conditions with respect to transition-metal levels. Energy-dispersive X-ray spectroscopy and anomalous X-ray scattering data show that YfeA is polyspecific and can alter its substrate specificity. In minimal-media experiments, YfeA crystals grown after iron supplementation showed a threefold increase in iron fluorescence emission over the iron fluorescence emission from YfeA crystals grown from nutrient-rich conditions, and YfeA crystals grown after manganese supplementation during overexpression showed a fivefold increase in manganese fluorescence emission over the manganese fluorescence emission from YfeA crystals grown from nutrient-rich conditions. In all experiments, the YfeA crystals produced the strongest fluorescence emission from zinc and could not be manipulated otherwise. Additionally, this report documents the discovery of a novel surface metal-binding site that prefers to chelate zinc but can also bind manganese. Flexibility across YfeA crystal forms in three loops and a helix near the buried metal-binding site suggest that a structural rearrangement is required for metal loading and unloading.
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The research described in this paper was performed using beamline 08ID-1 at the Canadian Light Source, which is supported by the Canada Foundation for Innovation, Natural Sciences and Engineering Research Council of Canada, the University of Saskatchewan, the Government of Saskatchewan, Western Economic Diversification Canada, the National Research Council Canada and the Canadian Institutes of Health Research. Data were also collected at GM/CA@APS, which has been funded in whole or in part with Federal funds from the National Cancer Institute (ACB-12002) and the National Institute of General Medical Sciences (AGM-12006). This research used resources of the Advanced Photon Source (APS), a US Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Argonne National Laboratory under Contract No. DE-AC02-06CH11357. Use of the Advanced Photon Source was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences under Contract No. W-31-109-Eng-38. Purchase of the mass spectrometers in the Targeted Metabolomics and Proteomics Laboratory came from funds provided by the following NCRR grants: AB Sciex 5600 TripleTOF S10, RR027822-01. Funds for the operation of the Targeted Metabolomics and Proteomics Laboratory come in part from the UAB O'Brien Acute Kidney Injury Center (P30 DK079337), the UAB Lung Health Center and the UAB Center for Free Radical Biology. CDR was supported by a grant from the University of Alabama at Birmingham Office of Diversity, Equity and Inclusion.
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PDB references: YfeA, 5uxs; YfeA + EDTA, 5uxu; YfeA, site 2 (λZn), 5uyg; YfeA, site 2 (λMn), 5uyh; YfeA, apo site 2, ancillary sites, 5uyv; YfeA, bound site 2, ancillary sites, 5uyw; YfeA, M9–Fe (λZn), 5uy0; YfeA, M9–Fe (λFe), 5uy4; YfeA, M9–Fe (λMn), 5uy5; YfeA, M9–Mn (λZn), 5uya; YfeA, M9–Mn (λFe), 5uyb; YfeA, M9–Mn (λMn), 5uyc; YfeA, M9–Zn (λZn), 5uyd; YfeA, M9–Zn (λFe), 5uye; YfeA, M9–Zn (λMn), 5uyf
Radka, Christopher D.; DeLucas, Lawrence J.; Wilson, Landon S.; Lawrenz, Matthew B.; Perry, Robert D.; and Aller, Stephen G., "Crystal Structure of Yersinia pestis Virulence Factor YfeA Reveals Two Polyspecific Metal-Binding Sites" (2017). Microbiology, Immunology, and Molecular Genetics Faculty Publications. 98.