Structure of SurE protein from Aquifex aeolicus VF5 at 1.5 A resolution

Abstract

SurE is a stationary-phase survival protein found in bacteria, eukaryotes and archaea that exhibits a divalent-metal-ion-dependent phosphatase activity and acts as a nucleotidase and polyphosphate phosphohydrolase. The structure of the SurE protein from the hyperthermophile Aquifex aeolicus has been solved at 1.5 A resolution using molecular replacement with one dimer in the asymmetric unit and refined to an R factor of 15.6%. The crystal packing reveals that two dimers assemble to form a tetramer, although gel-filtration chromatography showed the presence of only a dimer in solution. The phosphatase active-site pocket was occupied by sulfate ions from the crystallization medium.

Figure 1

Crystals of A. aeolicus VF5 SurE.

Figure 2

(a) Two orthogonal orientations of the AaSurE subunit showing the secondary structure and overall fold. The core globular domain consists of nine β-strands (yellow) and six helices (red cylinders), with helix α7 linking the C-terminal β-hairpin to the main body of the molecule. The dimer interface is located on the subunit edge where the β-­hairpin (strands β9 and β10) and helix α8 project away from the main body of the molecule. (b) The AaSurE dimer (right) as found in the asymmetric unit, indicating the secondary-structure elements involved in forming salt bridges and/or hydrogen bonds between the two subunits A (red) and B (green). The domain-swapped α8 helices are well ordered. The quality of the electron-density map (left) is shown for A α8 at the 1σ contour level. The overall fold of AaSurE compared with the SurE dimers from other organisms give root-mean-square deviations for C^α atoms of 2.9 Å (PDB code 1j9j, the molecular-replacement search model) and 2.6 Å for 1ilv (both from Thermotoga maritima), 2.1 Å for 1l5x from P. aerophilum and 6.7 Å for 2e6e from Thermus thermophilus. This figure was drawn using Coot (Emsley & Cowtan, 2004 ▶) and PyMOL (DeLano, 2008 ▶).

Figure 3

(a) A tetramer of AaSurE, generated by applying symmetry operations to the dimer, is shown in two orthogonal views. The main contacts forming the tetramer interfaces occur between the β-hairpin strands of adjacent A (red) subunits and adjacent B (green) subunits. The metal-binding site that gives the enzyme its phosphatase activity is shown for each subunit, with a water molecule or Na ion (magenta sphere) occupying the position usually taken by a divalent metal ion and with a sulfate ion (red and yellow spheres) filling the active-site pocket. (b) Close-up of the active site of subunit A (red sticks) compared with the equivalent sites in SurE from Thermotoga maritima with Mg²⁺ (PDB entry 1j9j, green) or water (1ilv, magenta) at the metal-binding site, from Thermus thermophilus with water and a sulfate ion in the active site (2e69, cyan) or an empty active site (2e6e, yellow) and from P. aerophilum (1l5x, blue) with water at the active site. The numbering of the active-site ligands follows the sequence of AaSurE.