title: Phylogenetic diversity and the structural basis of substrate specificity in the beta/alpha-barrel fold basic amino acid decarboxylases.
abstract: The beta/alpha-barrel fold type basic amino acid decarboxylases include eukaryotic ornithine decarboxylases (ODC) and bacterial and plant enzymes with activity on L-arginine and meso-diaminopimelate. These enzymes catalyze essential steps in polyamine and lysine biosynthesis. Phylogenetic analysis suggests that diverse bacterial species also contain ODC-like enzymes from this fold type. However, in comparison with the eukaryotic ODCs, amino acid differences were identified in the sequence of the 3(10)-helix that forms a key specificity element in the active site, suggesting they might function on novel substrates. Putative decarboxylases from a phylogenetically diverse range of bacteria were characterized to determine their substrate preference. Enzymes from species within Methanosarcina, Pseudomonas, Bartonella, Nitrosomonas, Thermotoga, and Aquifex showed a strong preference for L-ornithine, whereas the enzyme from Vibrio vulnificus (VvL/ODC) had dual specificity functioning well on both L-ornithine and L-lysine. The x-ray structure of VvL/ODC was solved in the presence of the reaction products putrescine and cadaverine to 1.7 and 2.15A, respectively. The overall structure is similar to eukaryotic ODC; however, reorientation of the 3(10)-helix enlarging the substrate binding pocket allows L-lysine to be accommodated. The structure of the putrescine-bound enzyme suggests that a bridging water molecule between the shorter L-ornithine and key active site residues provides the structural basis for VvL/ODC to also function on this substrate. Our data demonstrate that there is greater structural and functional diversity in bacterial polyamine biosynthetic decarboxylases than previously suspected.
authors.affiliation: Departments of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9041.
authors.forename: Jeongmi
authors.initials: J
authors.lastname: Lee
authors.affiliation: Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, United Kingdom.
authors.forename: Anthony J
authors.initials: AJ
authors.lastname: Michael
authors.affiliation: Departments of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9041 and the.
authors.forename: Dariusz
authors.initials: D
authors.lastname: Martynowski
authors.affiliation: Departments of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9041 and the.
authors.forename: Elizabeth J
authors.initials: EJ
authors.lastname: Goldsmith
authors.affiliation: Departments of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9041. Electronic address: margaret.phillips@UTSouthwestern.edu.
authors.forename: Margaret A
authors.initials: MA
authors.lastname: Phillips
mesh_terms: D000595:Amino Acid Sequence; D001419:Bacteria / Q000145:classification / Q000201:enzymology*; D000518:Eflornithine / Q000494:pharmacology; D008969:Molecular Sequence Data; D009955:Ornithine Decarboxylase / Q000737:chemistry* / Q000378:metabolism; D065108:Ornithine Decarboxylase Inhibitors; D010802:Phylogeny; D017510:Protein Folding; D013379:Substrate Specificity
chemical_list: D065108:Ornithine Decarboxylase Inhibitors; D009955:Ornithine Decarboxylase; D000518:Eflornithine