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

Biochemistry
Nicholas J SchnickerMishtu Dey

Abstract

Enormous amounts of the organic osmolyte dimethylsulfoniopropionate (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 clade 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 β-helical motif utilizes various divalent metal ions 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 initiat...Continue Reading

References

Nov 1, 2001·Journal of the American Chemical Society·E Skrzypczak-JankunM O Funk
Dec 12, 2001·Trends in Biochemical Sciences·J M DunwellP W Goodenough
Nov 7, 1996·Chemical Reviews·William N. Lipscomb, Norbert Sträter
Dec 20, 2002·Nature·Robert M MorrisStephen J Giovannoni
Mar 26, 2003·Proceedings of the National Academy of Sciences of the United States of America·Mario A PennellaDavid P Giedroc
Nov 25, 2003·Nature Structural Biology·Helen BermanHaruki Nakamura
Dec 31, 2003·Phytochemistry·Jim M DunwellSawsan Khuri
Nov 24, 2004·Inorganic Chemistry·Yuichi ShimazakiOsamu Yamauchi
Nov 10, 2005·Biochimica Et Biophysica Acta·Etana PadanTerry A Krulwich
Jul 11, 2008·Journal of Inorganic Biochemistry·Heping ZhengWladek Minor
Sep 5, 2008·The ISME Journal·Sarah M SowellStephen J Giovanonni
Aug 1, 2007·Journal of Applied Crystallography·Airlie J McCoyRandy J Read
Aug 29, 2009·Chemical Reviews·Yanjie Li, Deborah B Zamble
Dec 2, 2009·Journal of the American Chemical Society·Harini KaluarachchiDeborah B Zamble
Jan 9, 2010·Acta Crystallographica. Section D, Biological Crystallography·Vincent B ChenDavid C Richardson
Feb 4, 2010·Acta Crystallographica. Section D, Biological Crystallography·Wolfgang Kabsch
Sep 8, 2010·Dalton Transactions : an International Journal of Inorganic Chemistry·Himanshu AroraFabrice Thomas
Jan 1, 2009·Annual Review of Marine Science·Julia M Vraspir, Alison Butler
Jun 21, 2011·Journal of the American Chemical Society·Danny YunCatherine L Drennan
Sep 3, 2011·Frontiers in Microbiology·Chris R ReischWilliam B Whitman
Sep 29, 2011·Genome Research·Allison K HansenNancy A Moran
Oct 12, 2011·Nature Reviews. Microbiology·Andrew R J CursonAndrew W B Johnston
Mar 15, 2012·Dalton Transactions : an International Journal of Inorganic Chemistry·Colin D DouglasDeborah B Zamble
Mar 31, 2012·Annual Review of Marine Science·Mary Ann MoranWilliam B Whitman
Apr 17, 2012·Acta Crystallographica. Section D, Biological Crystallography·Pavel V AfoninePaul D Adams
Jun 26, 2013·Acta Crystallographica. Section D, Biological Crystallography·Philip R Evans, Garib N Murshudov
Sep 17, 2013·Archives of Biochemistry and Biophysics·Jodi L BoerRobert P Hausinger
Sep 17, 2013·ELife·Andrew MorinPiotr Sliz
Jan 8, 2014·Proceedings of the National Academy of Sciences of the United States of America·Chun-Yang LiYu-Zhong Zhang
Apr 25, 2014·Proceedings of the National Academy of Sciences of the United States of America·Uria AlcolombriDan S Tawfik
Aug 8, 2014·Dalton Transactions : an International Journal of Inorganic Chemistry·Roland SchnitterBerthold Kersting
Jan 3, 2015·Organic & Biomolecular Chemistry·Jeroen S DickschatChristian A Citron
Jan 6, 2016·Applied and Environmental Microbiology·Shane L HogleKatherine A Barbeau
Feb 7, 2016·Current Opinion in Chemical Biology·Andrew Wb JohnstonJonathan D Todd

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Citations

Jun 25, 2019·Science China. Life Sciences·Xiao-Hua ZhangJonathan D Todd
Jan 16, 2019·Nature Communications·Zhijuan HuIkuro Abe
Nov 7, 2017·Journal of Molecular Biology·Chun-Yang LiYu-Zhong Zhang
Aug 14, 2020·Chembiochem : a European Journal of Chemical Biology·Xiaojing AnJiangyun Wang

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