2PLK

Crystal structure of lysine/ornithine decarboxylase complexed with cadaverine from Vibrio vulnificus

Summary for 2PLK

• Entry DOI: 10.2210/pdb2plk/pdb
• Related: 2PLJ
• Descriptor: lysine/ornithine decarboxylase, (4-{(E)-[(5-AMINOPENTYL)IMINO]METHYL}-5-HYDROXY-6-METHYLPYRIDIN-3-YL)METHYL DIHYDROGEN PHOSPHATE (3 entities in total)
• Functional Keywords: type iv decarboxylase, beta/alpha barrel, beta barrel, lyase
• Biological source: Vibrio vulnificus
• Total number of polymer chains: 2
• Total formula weight: 92500.71

Authors

Lee, J.,Goldsmith, E.J.,Phillips, M.A. (deposition date: 2007-04-19, release date: 2007-07-10, Last modification date: 2023-08-30)

Primary citation

Lee, J.,Michael, A.J.,Martynowski, D.,Goldsmith, E.J.,Phillips, M.A.
Phylogenetic diversity and the structural basis of substrate specificity in the beta/alpha-barrel fold basic amino acid decarboxylases.
J.Biol.Chem., 282:27115-27125, 2007

PubMed 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.

PubMed: 17626020
DOI: 10.1074/jbc.M704066200

Experimental method

X-RAY DIFFRACTION (2.14 Å)