5tfz

Crystal structure of the dimethylsulfoniopropionate (DMSP) lyase DddK complexed with nickel and diacrylate

spinqualitylabelsall models 5tfz, resolution 2.20Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 5tfz is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: 7BC, NI, PEG Related: 5tg0 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed 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 beta-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 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. Structural and Biochemical Insights into Dimethylsulfoniopropionate Cleavage by Cofactor-Bound DddK from the Prolific Marine Bacterium Pelagibacter.,Schnicker NJ, De Silva SM, Todd JD, Dey M Biochemistry. 2017 Jun 13;56(23):2873-2885. doi: 10.1021/acs.biochem.7b00099., Epub 2017 May 30. PMID:28511016 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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