7ME1

YfeA oligomer crystal 1, form 1

Summary for 7ME1

• Entry DOI: 10.2210/pdb7me1/pdb
• Descriptor: Periplasmic chelated iron-binding protein YfeA, FE (III) ION, ZINC ION, ... (5 entities in total)
• Functional Keywords: metal coordination, metal transport
• Biological source: Yersinia pestis
• Total number of polymer chains: 2
• Total formula weight: 72460.47

Authors

Radka, C.D.,Aller, S.G. (deposition date: 2021-04-06, release date: 2021-08-25, Last modification date: 2023-10-18)

Primary citation

Radka, C.D.,Aller, S.G.
Site 2 of the Yersinia pestis substrate-binding protein YfeA is a dynamic surface metal-binding site.
Acta Crystallogr.,Sect.F, 77:286-293, 2021

PubMed Abstract: The substrate-binding protein YfeA (also known as YPO2439 or y1897) is a polyspecific metal-binding protein that is crucial for nutrient acquisition and virulence in Yersinia pestis, the causative microbe of plague. YfeA folds into a monomeric c-clamp like other substrate-binding proteins and has two metal-binding sites (sites 1 and 2). Site 2 is a bidentate surface site capable of binding Zn and Mn atoms and is a unique feature of YfeA. Occasionally, the site 2 residues of two YfeA molecules will cooperate with the histidine tag of a third YfeA molecule in coordinating the same metal and lead to metal-dependent crystallographic packing. Here, three crystal structures of YfeA are presented at 1.85, 2.05 and 2.25 Å resolution. A comparison of the structures reveals that the metal can be displaced at five different locations ranging from ∼4 to ∼16 Å away from the canonical site 2. These observations reveal different configurations of site 2 that enable cooperative metal binding and demonstrate how site 2 is dynamic and freely available for inter-protein metal coordination.

PubMed: 34473105
DOI: 10.1107/S2053230X21008086

Experimental method

X-RAY DIFFRACTION (2.05 Å)