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

Protein Sci. 2020 Jul;29(7):1618-1628. doi: 10.1002/pro.3876. Epub 2020 May 8.


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.

Keywords: Escherichia coli; Yersinia pestis; PepB; X-ray crystallography; aminopeptidase; hexamer; metalloprotease.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aminopeptidases / chemistry*
  • Crystallography, X-Ray
  • Escherichia coli / enzymology*
  • Escherichia coli Proteins / chemistry*
  • Manganese / chemistry*
  • Protein Domains
  • Yersinia pestis / enzymology*
  • Zinc / chemistry*


  • Escherichia coli Proteins
  • Manganese
  • Aminopeptidases
  • Zinc