title: The structure of RdDddP from Roseobacter denitrificans reveals that DMSP lyases in the DddP-family are metalloenzymes.
abstract: Marine microbes degrade dimethylsulfoniopropionate (DMSP), which is produced in large quantities by marine algae and plants, with DMSP lyases into acrylate and the gas dimethyl sulfide (DMS). Approximately 10% of the DMS vents from the sea into the atmosphere and this emission returns sulfur, which arrives in the sea through rivers and runoff, back to terrestrial systems via clouds and rain. Despite their key role in this sulfur cycle DMSP lyases are poorly understood at the molecular level. Here we report the first X-ray crystal structure of the putative DMSP lyase RdDddP from Roseobacter denitrificans, which belongs to the abundant DddP family. This structure, determined to 2.15 Å resolution, shows that RdDddP is a homodimeric metalloprotein with a binuclear center of two metal ions located 2.7 Å apart in the active site of the enzyme. Consistent with the crystallographic data, inductively coupled plasma mass spectrometry (ICP-MS) and total reflection X-ray fluorescence (TRXF) revealed the bound metal species to be primarily iron. A 3D structure guided analysis of environmental DddP lyase sequences elucidated the critical residues for metal binding are invariant, suggesting all proteins in the DddP family are metalloenzymes.
authors: Department of Biochemistry & Microbiology, University of Victoria, Victoria, British Columbia, Canada.
authors: Jan-Hendrik
authors: JH
authors: Hehemann
authors: Department of Biochemistry & Microbiology, University of Victoria, Victoria, British Columbia, Canada.
authors: Adrienne
authors: A
authors: Law
authors: Joint Laboratory for Structural Biology of Infection and Inflammation of the Universities of Hamburg and Lübeck, c/o DESY, Hamburg, Germany.
authors: Lars
authors: L
authors: Redecke
authors: Department of Biochemistry & Microbiology, University of Victoria, Victoria, British Columbia, Canada.
authors: Alisdair B
authors: AB
authors: Boraston
mesh_terms: D000595:Amino Acid Sequence; D013437:Carbon-Sulfur Lyases / Q000737:chemistry* / Q000378:metabolism; D018360:Crystallography, X-Ray; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D041904:Roseobacter / Q000737:chemistry / Q000201:enzymology* / Q000378:metabolism; D013440:Sulfides / Q000378:metabolism; D013452:Sulfonium Compounds / Q000378:metabolism; D013455:Sulfur / Q000378:metabolism
chemical_list: D013440:Sulfides; D013452:Sulfonium Compounds; D013455:Sulfur; C068078:dimethylpropiothetin; D013437:Carbon-Sulfur Lyases; C400924:dimethylsulfoniopropionate lyase; C004784:dimethyl sulfide