Crystal structure of DFA0005 complexed with α-ketoglutarate: A novel member of the ICL/PEPM superfamily from alkali-tolerant Deinococcus ficus

The crystal structure of the DFA0005 protein complexed with α-ketoglutarate (AKG) from an alkali-tolerant bacterium Deinococcus ficus has been determined to a resolution of 1.62 Å. The monomer forms an incomplete α7/β8 barrel with a protruding α8 helix that interacts extensively with another subunit to form a stable dimer of two complete α8/β8 barrels. The aimer is further stabilized by four glycerol molecules situated at the interface. One unique AKG ligand binding pocket per subunit is detected. Fold match using the DALI and SSE servers identifies DFA0005 as belonging to the isocitrate lyase/phosphoenolpyruvate mutase (ICL/PEPM) superfamily. However, further detailed structural and sequence comparison with other members in this superfamily and with other families containing AKG ligand indicate that DFA0005 protein exhibits considerable distinguishing features of its own and can be considered a novel member in this ICL/PEPM superfamily.