STRUCTURE OF THE ESCHERICHIA-COLI RESPONSE REGULATOR NARL

The crystal structure analysis of the NarL protein provides a first lo ok at interactions between receiver and effector domains of a full-len gth bacterial response regulator. The N-terminal receiver domain, with 131 amino acids, is folded into a 5-strand beta sheet flanked by 5 al pha helices, as seen in CheY and in the N-terminal domain of NTRC. The C-terminal DNA-binding domain, with 62 amino acids, is a compact bund le of 4 alpha helices, of which the middle 2 form a helix-turn-helix m otif closely related to that of Drosophila paired protein and other H- T-H DNA-binding proteins. The 2 domains are connected by an alpha heli x of 10 amino acids and a 13-residue flexible tether that is not visib le and presumably disordered in the X-ray structure. In this unphospho rylated form of NarL, the C-terminal domain is turned against the rece iver domain in a manner that would preclude DNA binding. Activation of NarL via phosphorylation of Asp59 must involve transfer of informatio n to the interdomain interface and either rotation or displacement of the DNA-binding C-terminal domain. Docking of a B-DNA duplex against t he isolated C-terminal domain in the manner observed in paired protein and other H-T-H proteins suggests a stereochemical basis for DNA sequ ence preference: T-R-C-C-Y (high affinity) or T-R-C-T-N (low affinity) , which is close to the experimentally observed consensus sequence: T- A-C-Y-N. The NarL structure is a model for other members of the FixJ o r LuxR family of bacterial transcriptional activators, and possibly to the more distant OmpR and NtrC families as well.