Solution structure of hypothetical nudix hydrolase DR0079 from extremely radiation-resistant Deinococcus radiodurans bacterium

Using nuclear magnetic resonance (NMR) based methods, including residual dipolar coupling restraints, we have determined the solution structure of the hypothetical Deinococcus radiodurans Nudix protein DR0079 (171 residues, MW = 19.3 kDa). The protein contains eight β-strands and three α-helices organized into three subdomains: an N-terminal β-sheet (1–34), a central Nudix core (35–140), and a C-terminal helix-turn-helix (141–171). The Nudix core and the C-terminal helix-turn-helix form the fundamental fold common to the Nudix family, a large mixed β-sheet sandwiched between α-helices. The residues that compose the signature Nudix sequence, GX₅EX₇REUXEEXGU (where U = I, L, or V and X = any amino acid), are contained in a turn-helix-turn motif on the face of the mixed β-sheet. Chemical shift mapping experiments suggest that DR0079 binds Mg²⁺. Experiments designed to determine the biological function of the protein indicate that it is not a type I isopentenyl-diphosphate δ-isomerase and that it does not bind α,β-methyleneadenosine 5′-triphosphate (AMPCPP) or guanosine 5′-[β,γ-imido]triphosphate (GMPPNP). In this article, the structure of DR0079 is compared to other known Nudix protein structures, a potential substrate-binding surface is proposed, and its possible biological function is discussed. Proteins 2004;55:000–000. © 2004 Wiley-Liss, Inc.