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J. Biol. Chem., Vol. 282, Issue 37, 27115-27125, September 14, 2007

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Phylogenetic Diversity and the Structural Basis of Substrate Specificity in the /-Barrel Fold Basic Amino Acid Decarboxylases^*

Jeongmi Lee, Anthony J. Michael, Dariusz Martynowski^¶, Elizabeth J. Goldsmith^¶, and Margaret A. Phillips¹

From the Departments of Pharmacology and ^¶Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9041 and the Institute of Food Research, Norwich Research Park, Colney, Norwich NR4 7UA, United Kingdom

The /-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 3₁₀-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 2.15Å, respectively. The overall structure is similar to eukaryotic ODC; however, reorientation of the 3₁₀-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.

Received for publication, May 16, 2007 , and in revised form, June 29, 2007.

The atomic coordinates and structure factors (code 2PLJ and 2PLK) have been deposited in the Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers University, New Brunswick, NJ (http://www.rcsb.org/).

^* This work was supported by National Institutes of Health Grant R01 AI34432 (to M. A. P.), Welch Foundation Grants I-1257 (to M. A. P.) and I-1128 (to E. J. G.), and a grant from the Department of Trade and Industry, UK/United States Collaborative Initiative in Bioscience (to A. J. M.). The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

The on-line version of this article (available at http://www.jbc.org) contains supplemental Table I and Fig. 1.

¹ To whom correspondence should be addressed. Tel.: 214-645-6164; Fax: 214-645-6166; E-mail: margaret.phillips{at}UTSouthwestern.edu.

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