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Volume 170, Issue 2

Structure and ligand binding in the putative anti-microbial peptide transporter protein, YejA Open Access

Abstract

YejABEF is an ATP-binding cassette transporter that is implicated in the sensitivity of to anti-microbial peptides, the best-characterized example being microcin C, a peptide-nucleotide antibiotic that targets aspartyl-tRNA synthetase. Here the structure of the extracellular solute binding protein, YejA, has been determined, revealing an oligopeptide-binding protein fold enclosing a ligand-binding pocket larger than those of other peptide-binding proteins of known structure. Prominent electron density in this cavity defines an undecapeptide sequence LGEPRYAFNFN, an observation that is confirmed by mass spectrometry. In the structure, the peptide interactions with the protein are mediated by main chain hydrogen bonds with the exception of Arg5 whose guanidinium side chain makes a set of defining polar interactions with four YejA residues. More detailed characterization of purified recombinant YejA, by a combination of ESI and MALDI-mass spectrometry as well as thermal shift assays, reveals a set of YejA complexes containing overlapping peptides 10–19 residues in length. All contain the sequence LGEPRYAFN. Curiously, these peptides correspond to residues 8–26 of the mature YejA protein, which belong to a unique N-terminal extension that distinguishes YejA from other cluster C oligopeptide binding proteins of known structure. This 35-residue extension is well-ordered and packs across the surface of the protein. The undecapeptide ligand occupies only a fraction of the enclosed pocket volume suggesting the possibility that much larger peptides or peptide conjugates could be accommodated, though thermal shift assays of YejA binding to antimicrobial peptides and peptides unrelated to LGEPRYAFNFN have not provided evidence of binding. While the physiological significance of this ‘auto-binding’ is not clear, the experimental data suggest that it is not an artefact of the crystallization process and that it may have a function in the sensing of periplasmic or membrane stress.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): ABC transporter , anti-microbial peptide , crystal structure , mass spectrometry and YejA
Funding
This study was supported by the:
  • Wellcome Trust (Award 105501/Z/14/Z)
    • Principle Award Recipient: BryonyK Ackroyd
© 2024 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2024-02-09
2024-04-27
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Structure and ligand binding in the putative anti-microbial peptide transporter protein, YejA
Microbiology 170, 001430 (2024); https://doi.org/10.1099/mic.0.001430
/content/journal/micro/10.1099/mic.0.001430
/content/journal/micro/10.1099/mic.0.001430
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