Structure determination of histidine decarboxylase from Lactobacillus 30a at 3.0 Å resolution

Abstract

The crystal structure of histidine decarboxylase from Lactobacillus 30a has been determined by X-ray diffraction methods to a resolution of 3.0 Å. This protein is a pyruvoyl-dependent enzyme that is formed by an unusual self-activation process. The structure was determined from an electron density map calculated using multiple isomorphous replacement phases from two heavy-atom derivatives and included contributions from anomalous scattering measurements. The final mean figure of merit was 0.79, based on 28,805 independent reflections. The molecule has an ( αβ) 6 subunit composition and crystallizes in the space group I4 122 with a = b = 221.7 A ̊ and c = 107.1 A ̊ . There is one ( αβ) 3 half molecule per asymmetric unit. The ( αβ) 6 particle is dumbbell-shaped, with each ( αβ) 3 unit being approximately spherical, with a diameter of about 65 Å. There is a large central cavity approximately 30 Å deep around the molecular 3-fold axis of the ( αβ) 3 unit. The 3-fold related active site pockets are located around the bottom of this cavity and are separated from each other by a distance of approximately 23 Å. The inner portion of each (αβ) unit, which lies near the interface between the two ( αβ) 3 particles, consists mainly of random coil with several small helical and sheet regions. The outer region of each (αβ) unit has an unusual structure consisting of two overlapping, predominantly antiparallel β-pleated sheets, lined on each side by an α-helix. The walls of the central cavity are formed by the 3-fold repeat of two strands from this β-sandwich structure and one of the helices.