Crystallographic study of tyrosine phenol-lyase from Erwinia herbicola

Crystal structures of the apo and hole forms of homotetrameric tyrosine phenol-lyase (TPL) from Erwinia herbicola and its complex with a quasisubstrate, N-(5'-phosphopyridoxyl)-L-tyrosine, were studied by the molecular replacement method. The refinement at 2.4, 2.7, and 2.0 Angstrom converged to the R factors of 20.2, 17.0, and 20.6%, respectively. The coordinate errors were 0.24, 0.35, and 0.13 Angstrom, respectively, Crystals of the apo and hole forms of TPL belong to sp, gr. P6(2)22 and contain one subunit per asymmetric unit, There are two molecules per asymmetric unit in the crystal structure of the complex (sp, gr. P2(1)2(1)2(1)). The TPL molecule consists of two catalytic dimers. The side chains of Lys257, Asn98, Arg 100, Asp214, and Arg217 and the nitrogen atom of the main chain of Gly99 are involved in the binding of the cofactor. Binding of the cofactor molecule is accompanied by the displacement of the small domain toward the large one (on the average, by 1,5 Angstrom). In the structure of the complex, one subunit of each crystallographically independent molecule differs from the remaining three subunits both in the conformation of the quasi-substrate molecule (with the perpendicular mutual arrangement of the phenyl and pyridine rings) and in the mutual arrangement of the small and large domains. In this subunit, the small domain is located even closer to the large one (on the average, by 3.0 Angstrom compared to this distance in the structure of the holoenzyme). In three other subunits, the mutual arrangement of the domains is identical to the arrangement in the holoenzyme. In these subunits, the quasi-substrate molecule adopts a conformation such that the angle formed by the phenyl and pyridine rings is similar to 23 degrees.