PMID:8780507

Citation	Baikalov, I, Schröder, I, Kaczor-Grzeskowiak, M, Grzeskowiak, K, Gunsalus, RP and Dickerson, RE (1996) Structure of the Escherichia coli response regulator NarL. Biochemistry 35:11053-61
Abstract	The crystal structure analysis of the NarL protein provides a first look at interactions between receiver and effector domains of a full-length bacterial response regulator. The N-terminal receiver domain, with 131 amino acids, is folded into a 5-strand beta sheet flanked by 5 alpha 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 bundle of 4 alpha helices, of which the middle 2 form a helix-turn-helix motif closely related to that of Drosophila paired protein and other H-T-H DNA-binding proteins. The 2 domains are connected by an alpha helix of 10 amino acids and a 13-residue flexible tether that is not visible and presumably disordered in the X-ray structure. In this unphosphorylated form of NarL, the C-terminal domain is turned against the receiver domain in a manner that would preclude DNA binding. Activation of NarL via phosphorylation of Asp59 must involve transfer of information to the interdomain interface and either rotation or displacement of the DNA-binding C-terminal domain. Docking of a B-DNA duplex against the isolated C-terminal domain in the manner observed in paired protein and other H-T-H proteins suggests a stereochemical basis for DNA sequence 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 or LuxR family of bacterial transcriptional activators, and possibly to the more distant OmpR and NtrC families as well.
Links	PubMed Online version:10.1021/bi960919o
Keywords	Amino Acid Sequence; Bacterial Proteins/chemistry; Bacterial Proteins/metabolism; Binding Sites; Crystallography, X-Ray; DNA-Binding Proteins/chemistry; DNA-Binding Proteins/metabolism; Escherichia coli/chemistry; Escherichia coli Proteins; Models, Molecular; Molecular Sequence Data; Phosphorylation; Protein Conformation; Protein Structure, Secondary; Recombinant Proteins/chemistry; Repressor Proteins; Sequence Alignment; Trans-Activators
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