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Title: Structures of the peptide-modifying radical SAM enzyme SuiB elucidate the basis of substrate recognition

Abstract

Posttranslational modification of ribosomally synthesized peptides provides an elegant means for the production of biologically active molecules known as RiPPs (ribosomally synthesized and posttranslationally modified peptides). Although the leader sequence of the precursor peptide is often required for turnover, the exact mode of recognition by the modifying enzymes remains unclear for many members of this class of natural products. In this report, we have used X-ray crystallography and computational modeling to examine the role of the leader peptide in the biosynthesis of a homolog of streptide, a recently identified peptide natural product with an intramolecular lysine–tryptophan cross-link, which is installed by the radicalS-adenosylmethionine (SAM) enzyme, StrB. We present crystal structures of SuiB, a close ortholog of StrB, in various forms, including apo SuiB, SAM-bound SuiB, and a complex of SuiB with SAM and its peptide substrate, SuiA. Although the N-terminal domain of SuiB adopts a typical RRE (RiPP recognition element) motif, which has been implicated in precursor peptide recognition, we observe binding of the leader peptide in the catalytic barrel rather than the N-terminal domain. Computational simulations support a mechanism in which the leader peptide guides posttranslational modification by positioning the cross-linking residues of the precursor peptide within the activemore » site. Together the results shed light onto binding of the precursor peptide and the associated conformational changes needed for the formation of the unique carbon–carbon cross-link in the streptide family of natural products.« less

Authors:
 [1];  [1];  [2];  [1]; ORCiD logo [2];  [1];  [1]
  1. Princeton Univ., NJ (United States)
  2. Rutgers Univ., New Brunswick, NJ (United States)
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
National Institutes of Health (NIH)
OSTI Identifier:
1436804
Grant/Contract Number:  
AC02- 06CH11357
Resource Type:
Accepted Manuscript
Journal Name:
Proceedings of the National Academy of Sciences of the United States of America
Additional Journal Information:
Journal Volume: 114; Journal Issue: 39; Journal ID: ISSN 0027-8424
Publisher:
National Academy of Sciences
Country of Publication:
United States
Language:
ENGLISH
Subject:
59 BASIC BIOLOGICAL SCIENCES; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; radical SAM enzyme; SPASM domain; RRE domain; RiPP; streptide

Citation Formats

Davis, Katherine M., Schramma, Kelsey R., Hansen, William A., Bacik, John P., Khare, Sagar D., Seyedsayamdost, Mohammad R., and Ando, Nozomi. Structures of the peptide-modifying radical SAM enzyme SuiB elucidate the basis of substrate recognition. United States: N. p., 2017. Web. doi:10.1073/pnas.1703663114.
Davis, Katherine M., Schramma, Kelsey R., Hansen, William A., Bacik, John P., Khare, Sagar D., Seyedsayamdost, Mohammad R., & Ando, Nozomi. Structures of the peptide-modifying radical SAM enzyme SuiB elucidate the basis of substrate recognition. United States. doi:10.1073/pnas.1703663114.
Davis, Katherine M., Schramma, Kelsey R., Hansen, William A., Bacik, John P., Khare, Sagar D., Seyedsayamdost, Mohammad R., and Ando, Nozomi. Mon . "Structures of the peptide-modifying radical SAM enzyme SuiB elucidate the basis of substrate recognition". United States. doi:10.1073/pnas.1703663114. https://www.osti.gov/servlets/purl/1436804.
@article{osti_1436804,
title = {Structures of the peptide-modifying radical SAM enzyme SuiB elucidate the basis of substrate recognition},
author = {Davis, Katherine M. and Schramma, Kelsey R. and Hansen, William A. and Bacik, John P. and Khare, Sagar D. and Seyedsayamdost, Mohammad R. and Ando, Nozomi},
abstractNote = {Posttranslational modification of ribosomally synthesized peptides provides an elegant means for the production of biologically active molecules known as RiPPs (ribosomally synthesized and posttranslationally modified peptides). Although the leader sequence of the precursor peptide is often required for turnover, the exact mode of recognition by the modifying enzymes remains unclear for many members of this class of natural products. In this report, we have used X-ray crystallography and computational modeling to examine the role of the leader peptide in the biosynthesis of a homolog of streptide, a recently identified peptide natural product with an intramolecular lysine–tryptophan cross-link, which is installed by the radicalS-adenosylmethionine (SAM) enzyme, StrB. We present crystal structures of SuiB, a close ortholog of StrB, in various forms, including apo SuiB, SAM-bound SuiB, and a complex of SuiB with SAM and its peptide substrate, SuiA. Although the N-terminal domain of SuiB adopts a typical RRE (RiPP recognition element) motif, which has been implicated in precursor peptide recognition, we observe binding of the leader peptide in the catalytic barrel rather than the N-terminal domain. Computational simulations support a mechanism in which the leader peptide guides posttranslational modification by positioning the cross-linking residues of the precursor peptide within the active site. Together the results shed light onto binding of the precursor peptide and the associated conformational changes needed for the formation of the unique carbon–carbon cross-link in the streptide family of natural products.},
doi = {10.1073/pnas.1703663114},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = 39,
volume = 114,
place = {United States},
year = {2017},
month = {9}
}

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    The hidden enzymology of bacterial natural product biosynthesis
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