Molecular basis of C-S bond cleavage in the glycyl radical enzyme isethionate sulfite-lyase

Christopher D Dawson; Stephania M Irwin; Lindsey R F Backman; Chip Le; Jennifer X Wang; Vyshnavi Vennelakanti; Zhongyue Yang; Heather J Kulik; Catherine L Drennan; Emily P Balskus

doi:10.1016/j.chembiol.2021.03.001

Molecular basis of C-S bond cleavage in the glycyl radical enzyme isethionate sulfite-lyase

Cell Chem Biol. 2021 Sep 16;28(9):1333-1346.e7. doi: 10.1016/j.chembiol.2021.03.001. Epub 2021 Mar 26.

Authors

Affiliations

¹ Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
² Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.
³ Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
⁴ Harvard Center for Mass Spectrometry, Faculty of Arts and Sciences Division of Science, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA.
⁵ Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
⁶ Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
⁷ Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Electronic address: hjkulik@mit.edu.
⁸ Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Electronic address: cdrennan@mit.edu.
⁹ Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA; Broad Institute, Cambridge, MA 02139, USA. Electronic address: balskus@chemistry.harvard.edu.

Abstract

Desulfonation of isethionate by the bacterial glycyl radical enzyme (GRE) isethionate sulfite-lyase (IslA) generates sulfite, a substrate for respiration that in turn produces the disease-associated metabolite hydrogen sulfide. Here, we present a 2.7 Å resolution X-ray structure of wild-type IslA from Bilophila wadsworthia with isethionate bound. In comparison with other GREs, alternate positioning of the active site β strands allows for distinct residue positions to contribute to substrate binding. These structural differences, combined with sequence variations, create a highly tailored active site for the binding of the negatively charged isethionate substrate. Through the kinetic analysis of 14 IslA variants and computational analyses, we probe the mechanism by which radical chemistry is used for C-S bond cleavage. This work further elucidates the structural basis of chemistry within the GRE superfamily and will inform structure-based inhibitor design of IsIA and thus of microbial hydrogen sulfide production.

Keywords: Bilophila wadsworthia; carbon-sulfur bond cleavage; glycyl radical enzyme; human gut microbiome; hydrogen sulfide; isethionate; lyase; structural enzymology; sulfate-reducing bacteria; sulfite.

Publication types

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

MeSH terms

Bilophila / enzymology
Carbon / chemistry
Carbon / metabolism*
Crystallography, X-Ray
Lyases / chemistry
Lyases / metabolism*
Models, Molecular
Sulfur / chemistry
Sulfur / metabolism*

Substances

Sulfur
Carbon
Lyases

Abstract

Publication types

MeSH terms

Substances

Grants and funding