His-to-Asp phosphorelay mechanisms are evolutionary-conserved powerful biological tactics for intracellular signal transduction. Such a phosphorelay is generally made up of “sensor histidine kinase”, “response regulator” and “histidine-containing transmitter”. In higher plant, Arabidopsis thaliana, the same mechanism is involved in propagation of environmental stimuli. Recent studies have revealed that this higher plant has, at least, 20 members of the family of response regulators that can be classified into two distinct subtypes (type-A and type-B) [1]. Type-B regulators have a common motif (B-motif) consisting of ca 60–70 amino acids in their C-terminal extensions after the receiver domain. The B-motif shows a weak, limited similarity in primary sequence to Myb-related domains found in various transcription factors, but its precise function has not been yet identified. Here we present the three-dimensional solution structure of B-motif determined by NMR spectroscopy. Comparison of the structure with other proteins which have known biological functions suggests that B-motif functions by binding to a DNA target. We have experimentally confirmed our structure-based hypothesis, and have identified a target DNA sequence. In addition, we have identified DNA-binding sites of B-motif by analyzing NMR chemical shift changes upon complex formation with the target DNA.