Site 2 of the Yersinia pestis substrate-binding protein YfeA is a dynamic surface metal-binding site

Christopher D. Radka, Stephen G. Aller

Research output: Contribution to journalArticlepeer-review

3 Scopus citations


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.

Original languageEnglish
Pages (from-to)286-293
Number of pages8
JournalActa Crystallographica Section F:Structural Biology Communications
StatePublished - Sep 1 2021

Bibliographical note

Publisher Copyright:
© 2021.


  • Crystallography
  • Inter-protein metal coordination
  • Manganese
  • Plague
  • Substrate-binding proteins
  • Transition-metal homeostasis
  • Yersinia pestis
  • YfeA site 2
  • Zinc

ASJC Scopus subject areas

  • Biophysics
  • Structural Biology
  • Biochemistry
  • Genetics
  • Condensed Matter Physics


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