HutP regulates the expression of the hut structural genes of Bacillus subtilis by an anti-termination mechanism. A study of the crystal structure of HutP protein bound to a conserved sequence of the terminator of the hut mRNA show how HutP specifically recognizes the RNA and reveals the unexpected direct role of the Mg²⁺ ion for mediating the L-histidine-dependent structural rearrangement in the protein. Additional structural analyses revealed intermediate structures and allowed us to conclude that the Mg²⁺ ion together with L-histidine plays a major role to activate the HutP protein for binding to its cognate RNA.