Structure of a cupin protein Plu4264 from Photorhabdus luminescens subsp. laumondii TTO1 at 1.35 Å resolution

Abstract

Proteins belonging to the cupin superfamily have a wide range of catalytic and noncatalytic functions. Cupin proteins commonly have the capacity to bind a metal ion with the metal frequently determining the function of the protein. We have been investigating the function of homologous cupin proteins that are conserved in more than 40 species of bacteria. To gain insights into the potential function of these proteins we have solved the structure of Plu4264 from Photorhabdus luminescens TTO1 at a resolution of 1.35 Å and identified manganese as the likely natural metal ligand of the protein.

Keywords: X-ray; cupin; manganese-bound; natural product; structural genomics.

Figure 1. Crystal structure of Plu4264

(A) Cartoon representation of Plu4264, with Ni²⁺ ions represented as green spheres. Chain A is colored in red and chain B is colored blue. The β-strand from chain B (Bβ1) that crosses over to complex with Aβ9 of chain A to form part of the β-sheet for chain A is noted. A similar crossover is observed in chain B. (B) Cartoon representation of chain A Ni²⁺ coordination site with the responsible residues labeled and represented as sticks (carbon atoms are yellow, nitrogen atoms are blue and oxygen atoms are red, hydrogen atoms are not shown). Chain A is rotated approximately 180° relative to the orientation in Fig. 1A. (C) Loop flexibility of Plu4264. All conformations of the loops are represented as separate lines. The dimer is rotated approximately 90° north relative to the orientation in Fig. 1A.

Figure 2. Structural alignment of Tm1287 with Plu4264

(A) Alignment of chain-A β-barrels of Plu4264 and Tm1287, shown as cartoon. Tm1287 is represented in pink along with the magnesium ion represented as a sphere in its binding pocket. Plu4264 is shown in blue, with the nickel ion represented as a green sphere. (B) Plu4264 and Tm1287 binding pockets are shown as surface representation. Panels Bi and Bii show a slice across the binding pocket of Plu4264 and Tm1287, respectively, with the grey area represents the protein interior. Panels Biii and Biv show the cavity entry sites of Plu4264 and Tm1287, respectively. Carbon atoms are colored white, oxygen atoms are colored red, nitrogen atoms are colored blue and sulfur atoms are colored yellow. The metal ions are represented as spheres in their respective binding pockets, where the nickel is colored green and the manganese is colored pink. The oxalate from the Tm1287 structure, represented as sticks, was shown in both binding pockets for size comparison.