Publications

• Ornithine cyclodeaminase: structure, mechanism of action, and implications for the mu-crystallin family.

  Goodman J.L., Wang S., Alam S., Ruzicka F.J., Frey P.A., Wedekind J.E.

  Ornithine cyclodeaminase catalyzes the conversion of L-ornithine to L-proline by an NAD(+)-dependent hydride transfer reaction that culminates in ammonia elimination. Phylogenetic comparisons of amino acid sequences revealed that the enzyme belongs to the mu-crystallin protein family whose three-d ... >> More

  Ornithine cyclodeaminase catalyzes the conversion of L-ornithine to L-proline by an NAD(+)-dependent hydride transfer reaction that culminates in ammonia elimination. Phylogenetic comparisons of amino acid sequences revealed that the enzyme belongs to the mu-crystallin protein family whose three-dimensional fold has not been reported. Here we describe the crystal structure of ornithine cyclodeaminase in complex with NADH, refined to 1.80 A resolution. The enzyme consists of a homodimeric fold whose subunits comprise two functional regions: (i) a novel substrate-binding domain whose antiparallel beta-strands form a 14-stranded barrel at the oligomeric interface and (ii) a canonical Rossmann fold that interacts with a single dinucleotide positioned for re hydride transfer. The adenosyl moiety of the cofactor resides in a solvent-exposed crevice on the protein surface and makes contact with a "domain-swapped"-like coil-helix module originating from the dyad-related molecule. Diffraction data were also collected to 1.60 A resolution on crystals grown in the presence of l-ornithine. The structure revealed that the substrate carboxyl group interacts with the side chains of Arg45, Lys69, and Arg112. In addition, the ammonia leaving group hydrogen bonds to the side chain of Asp228 and the site of hydride transfer is 3.8 A from C4 of the nicotinamide. The absence of an appropriately positioned water suggested that a previously proposed mechanism that calls for hydrolytic elimination of the imino intermediate must be reconsidered. A more parsimonious description of the chemical mechanism is proposed and discussed in relation to the structure and function of mu-crystallins. << Less

  Biochemistry 43:13883-13891(2004) [PubMed] [EuropePMC]

• Ornithine cyclase (deaminating). Purification of a protein that converts ornithine to proline and definition of the optimal assay conditions.

  Costilow R.N., Laycock L.

  J Biol Chem 246:6655-6660(1971) [PubMed] [EuropePMC]

• Crystallization and X-ray diffraction analysis of ornithine cyclodeaminase from Pseudomonas putida.

  Alam S., Wang S.C., Ruzicka F.J., Frey P.A., Wedekind J.E.

  Ornithine cyclodeaminase (OCD) is a member of the micro-crystallin protein family, the biological activity of which is the conversion of L-ornithine to L-proline and ammonia. In order to elucidate the functional groups of this enzyme that are involved in catalysis, the crystallization of OCD from ... >> More

  Ornithine cyclodeaminase (OCD) is a member of the micro-crystallin protein family, the biological activity of which is the conversion of L-ornithine to L-proline and ammonia. In order to elucidate the functional groups of this enzyme that are involved in catalysis, the crystallization of OCD from Pseudomonas putida was undertaken. Using microbatch-under-oil screening at the high-throughput crystallization laboratory (HTC) at the Hauptman-Woodward Medical Research Institute Inc. (HWI Buffalo, NY, USA), numerous crystallization conditions were rapidly identified. Several conditions could be reproduced on a larger scale as vapor-diffusion experiments in-house. The best diffraction-quality crystals were obtained from solutions of 40%(v/v) 2-methyl-2,4-pentanediol buffered at pH 6.0 with 0.1 M MES and diffracted X-rays to 1.68 A resolution. Crystals belonged to space group P2(1)2(1)2(1), with unit-cell parameters a = 70.0, b = 78.3, c = 119.4 A. The V(M) was 2.1 A(3) Da(-1), corresponding to 42% solvent, which is consistent with two 38.5 kDa molecules per asymmetric unit. The structure determination is under way using experimental phasing methods. << Less

  Acta Crystallogr. D 60:941-944(2004) [PubMed] [EuropePMC]

• Ornithine cyclase (deaminating). III. Mechanism of the conversion of ornithine to proline.

  Muth W.L., Costilow R.N.

  J Biol Chem 249:7463-7467(1974) [PubMed] [EuropePMC]