Comparison of metal-bound and unbound structures of aminopeptidase B proteins from Escherichia coli and Yersinia pestis

George Minasov, Matthew R. Lam, Monica Rosas-Lemus, Joanna Sławek, Magdalena Woinska, Ivan G. Shabalin, Ludmilla Shuvalova, Bernhard Palsson, Adam Godzik, Wladek Minor, Karla J.F. Satchell*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

Protein degradation by aminopeptidases is involved in bacterial responses to stress. Escherichia coli produces two metal-dependent M17 family leucine aminopeptidases (LAPs), aminopeptidase A (PepA) and aminopeptidase B (PepB). Several structures have been solved for PepA as well as other bacterial M17 peptidases. Herein, we report the first structures of a PepB M17 peptidase. The E. coli PepB protein structure was determined at a resolution of 2.05 and 2.6 Å. One structure has both Zn2+ and Mn2+, while the second structure has two Zn2+ ions bound to the active site. A 2.75 Å apo structure is also reported for PepB from Yersinia pestis. Both proteins form homohexamers, similar to the overall arrangement of PepA and other M17 peptidases. However, the divergent N-terminal domain in PepB is much larger resulting in a tertiary structure that is more expanded. Modeling of a dipeptide substrate into the C-terminal LAP domain reveals contacts that account for PepB to uniquely cleave after aspartate.

Original languageEnglish (US)
Pages (from-to)1618-1628
Number of pages11
JournalProtein Science
Volume29
Issue number7
DOIs
StatePublished - Jul 1 2020

Keywords

  • Escherichia coli
  • PepB
  • X-ray crystallography
  • Yersinia pestis
  • aminopeptidase
  • hexamer
  • metalloprotease

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

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