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

2 Scopus citations

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

Funding

The authors thank Marin Cymborowski, Sarah Grimshaw, Lukasz Jaroszewski, Olga Kiryukhina, Keewhon Kwon, Nathan Mih, Zdzislaw Warwzak, and James Windsor for target selection, cloning, crystallization, and protein purification, as well as for assistance in solving the structures. This project has been funded in whole or in part with Federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contract Nos. HHSN272201200026C and HHSN272201700060C and under Grant No. U01AI124316. M. R. L. was funded by an Undergraduate Research Fellowship from Northwestern University. Undergraduate Research Fellowship from Northwestern University; National Institute of Allergy and Infectious Diseases, National Institutes of Health, Grant/Award Numbers: HHSN272201200026C, HHSN272201700060C, U01AI124316 Funding information

Keywords

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

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

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