Structure of a Nudix protein fromPyrobaculum aerophilumreveals a dimer with two intersubunit β-sheets

Abstract

Nudix proteins, formerly called MutT homolog proteins, are a large family of proteins that play an important role in reducing the accumulation of potentially toxic compounds inside the cell. They hydrolyze a wide variety of substrates that are mainly composed of a nucleoside diphosphate linked to some other moiety X and thus are called Nudix hydrolases. Here, the crystal structure of a Nudix hydrolase from the hyperthermophilic archaeon Pyrobaculum aerophilum is reported. The structure was determined by the single-wavelength anomalous scattering method with data collected at the peak anomalous wavelength of an iridium-derivatized crystal. It reveals an extensive dimer interface, with each subunit contributing two strands to the beta-sheet of the other subunit. Individual subunits consist of a mixed highly twisted and curved beta-sheet of 11 beta-strands and two alpha-helices, forming an alpha-beta-alpha sandwich. The conserved Nudix box signature motif, which contains the essential catalytic residues, is located at the first alpha-helix and the beta-strand and loop preceding it. The unusually short connections between secondary-structural elements, together with the dimer form of the structure, are likely to contribute to the thermostability of the P. aerophilum Nudix protein.

Structure of a Nudix hydrolase (MutT) in the Mg2+-bound state fromBartonella henselae, the bacterium responsible for cat scratch fever

“…A small hydrophobic pocket formed by the side chains of Leu58 and Val64 is likely to play a conserved role in stabilizing the loop-helix-loop Nudix motif. The similar three-dimensional orientations of the conserved residues in the Nudix box of all known Nudix protein structures suggest that these residues play similar roles in all Nudix hydrolases, binding one or more divalent cations (Wang, Mura et al, 2002). This is true for Bh-MutT, as shown in the electrondensity map in Fig.…”

“…Furthermore, the 1 H-15 N HSQC spectrum of uncleaved 15 N-labeled Bh-MutT featured broad cross-peaks characteristic of a protein much larger than 18 kDa (data not shown). Dimeric Nudix hydrolases have previously been observed both in solution and in the crystalline state and are sometimes required for the Nudix hydrolase to function optimally (Wang, Mura et al, 2002). Fig.…”

The Structure of Irisin Reveals a Novel Intersubunit β-Sheet Fibronectin Type III (FNIII) Dimer

“…This type of intersubunit H-bonding between backbone atoms of separate subunits has been implicated previously in the protein stability for other protein oligomers. An example is the thermostability imparted by two intersubunit ␤-sheets in the Pyrobaculum aerophilum Nudix hydrolase dimer (31).…”

Structure of a Coenzyme A Pyrophosphatase from Deinococcus radiodurans : a Member of the Nudix Family

“…Their preferred substrates are the following: CoA, ADP-ribose (ADPR) (15), nucleoside triphosphates (3), and Ap 4 A. (31) (A fifth structure has been determined [36], but the specificity of this enzyme remains unknown.) Alignment of the three-dimensional structures of these enzymes reveals both common and distinctive features (Fig.…”