1X7D

Crystal Structure Analysis of Ornithine Cyclodeaminase Complexed with NAD and ornithine to 1.6 Angstroms

Summary for 1X7D

• Entry DOI: 10.2210/pdb1x7d/pdb
• Related: 1U7H
• Descriptor: ornithine cyclodeaminase, SODIUM ION, NICOTINAMIDE-ADENINE-DINUCLEOTIDE, ... (7 entities in total)
• Functional Keywords: deaminase, binds nad+, binds l-ornithine, binds l-proline, 2 helix bundle, beta barrel, rossmann fold, lyase
• Biological source: Pseudomonas putida
• Total number of polymer chains: 2
• Total formula weight: 80237.39

Authors

Alam, S.,Goodman, J.L.,Wang, S.,Ruzicka, F.J.,Frey, P.A.,Wedekind, J.E. (deposition date: 2004-08-13, release date: 2004-11-09, Last modification date: 2023-11-15)

Primary citation

Goodman, J.L.,Wang, S.,Alam, S.,Ruzicka, F.J.,Frey, P.A.,Wedekind, J.E.
Ornithine Cyclodeaminase: Structure, Mechanism of Action, and Implications for the u-Crystallin Family
Biochemistry, 43:13883-13891, 2004

PubMed Abstract: 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.

PubMed: 15518536
DOI: 10.1021/bi048207i

Experimental method

X-RAY DIFFRACTION (1.6 Å)