Structural and Biochemical Insights into Dimethylsulfoniopropionate Cleavage by Cofactor-Bound DddK from the Prolific Marine Bacterium Pelagibacter

Nicholas J. Schnicker; Saumya M. De Silva; Jonathan D. Todd; Mishtu Dey

doi:10.1021/acs.biochem.7b00099

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Structural and Biochemical Insights into Dimethylsulfoniopropionate Cleavage by Cofactor-Bound DddK from the Prolific Marine Bacterium Pelagibacter

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Structural and Biochemical Insights into Dimethylsulfoniopropionate Cleavage by Cofactor-Bound DddK from the Prolific Marine Bacterium Pelagibacter

Nicholas J. Schnicker, Saumya M. De Silva, Jonathan D. Todd and Mishtu Dey

Biochemistry (Easton), Vol.56(23), pp.2873-2885

06/13/2017

DOI: 10.1021/acs.biochem.7b00099

PMID: 28511016

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https://ueaeprints.uea.ac.uk/id/eprint/63554/1/Accepted_manuscript.pdfView

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Abstract

Enormous amounts of,the organic osmolyte drmethylsulfoniopro-pionate (DMSP) are produced in marine environments where bacterial DMSP lyases cleave it, yielding acrylate and the climate-active gas dimethyl sulfide (DMS). SAR11 bacteria are the most abundant Glade of heterotrophic bacteria in the oceans and play a key role in DMSP catabolism: An important environmental factor affecting DMS generation via DMSP lyases is the availability of metal ions because they are essential cofactors for many of these enzymes. Here we examine the structure and activity of DddK in the presence of various metal ions. We have established that DddK containing a double-stranded beta-helical, motif utilizes various divalent metal Rills as cofactors for catalytic activity. However, nickel, an abundant metal ion in marine environments, adopts a distorted octahedral coordination,environment and conferred the highest DMSP lyase activity. Crystal structures of cofactor-bound DddK reveal key metal ion binding. and catalytic residues and provide the first rationalization for varying activities with different Metal ions. The structures of DddK along with site-directed mutagenesis and ultraviolet-visible studies are consistent with Tyr 64 acting as a base to initiate the beta-elimination reaction of,DMSP. Our biochemical and structural studies provide a detailed understanding of DMS generation by one of the ocean's most prolific bacteria.

Biochemistry & Molecular Biology

Life Sciences & Biomedicine

Science & Technology

Details

Title: Subtitle: Structural and Biochemical Insights into Dimethylsulfoniopropionate Cleavage by Cofactor-Bound DddK from the Prolific Marine Bacterium Pelagibacter
Creators: Nicholas J. Schnicker - University of Iowa
Saumya M. De Silva - University of Iowa
Jonathan D. Todd - University of East Anglia
Mishtu Dey - University of Iowa
Resource Type: Journal article
Publication Details: Biochemistry (Easton), Vol.56(23), pp.2873-2885
DOI: 10.1021/acs.biochem.7b00099
PMID: 28511016
NLM abbreviation: Biochemistry
ISSN: 0006-2960
eISSN: 1520-4995
Publisher: Amer Chemical Soc
Number of pages: 13
Grant note: NE/P012671/1 / Natural Environment Research Council; UK Research & Innovation (UKRI); Natural Environment Research Council (NERC) NE/J01138X; NE/M004449; NE/N002385 / Natural Environmental Research Council; UK Research & Innovation (UKRI); Natural Environment Research Council (NERC) CLP 1506181 / National Science Foundation; National Science Foundation (NSF) University of Iowa College of Liberal Arts and Sciences NE/N002385/1 / NERC; UK Research & Innovation (UKRI); Natural Environment Research Council (NERC)
Language: English
Date published: 06/13/2017
Academic Unit: Molecular Physiology and Biophysics; Chemistry; Medicine Administration
Record Identifier: 9984622051902771

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