X-ray structure of Paramecium bursaria chlorella virus arginine decarboxylase:: Insight into the structural basis for substrate specificity

The group IV pyridoxal-5'-phosphate (PLP)-dependent decarboxylases belong to the, beta/alpha barrel structural family, and include enzymes with substrate specificity for a range of basic amino acids. A unique homolog of this family, the Paramecium bursaria Chlorella virus arginine decarboxylase ( cvADC), shares about 40% amino acid sequence identity with the eukaryotic ornithine decarboxylases (ODCs). The X-ray structure of cvADC has been solved to 1.95 and 1.8 angstrom resolution for the free and agmatine (product)-bound enzymes. The global structural differences between cvADC and eukaryotic ODC are minimal (rmsd of 1.2-1.4 angstrom); however, the active site has significant structural rearrangements. The key specificity element, is identified as the 3(10)-helix that contains and positions substrate-binding residues such as E296 cvADC (D332 in T. brucei ODC). In comparison to the ODC structures, the 3(10)-helix in cvADC is shifted over 2 angstrom away from the PLP cofactor, thus accommodating the larger arginine substrate. Within the context of this conserved fold, the protein is designed to be flexible in the positioning and amino acid sequence of the 3(10)-helix, providing a mechanism to evolve different substrate preferences within the family without large structural rearrangements. Also, in the structure, the K148-loop (homologous to the K169-loop of ODC) is observed in a closed, substrate-bound conformation for the first time. Apparently the K148 loop is a mobile loop, analogous to those observed in triose phosphate isomerase and tryptophan synthetase. In conjunction with prior structural studies these data predict that this loop adopts different conformations throughout the catalytic cycle, and that loop movement may be kinetically linked to the rate-limiting step of product release.