Multistep phosphorelay (MSP) cascades mediate responses to a wide spectrum of stimuli, including plant hormonal signaling, but several aspects of MSP await elucidation. Here, we provide first insight into the key step of MSP- mediated phosphotransfer in a eukaryotic system, the phosphorylation of the receiver domain of the histidine kinase CYTOKININ-INDEPENDENT 1 (CKI1(RD)) from Arabidopsis thaliana. We observed that the crystal structures of free, Mg2+-bound, and beryllofluoridated CKI1(RD) (a stable analogue of the labile phosphorylated form) were identical and similar to the active state of receiver domains of bacterial response regulators. However, the three CKI1(RD) variants exhibited different conformational dynamics in solution. NMR studies revealed that Mg2+ binding and beryllofluoridation alter the conformational equilibrium of the beta 3-beta 3 loop close to the phosphorylation site. Mutations that perturbed the conformational behavior of the beta 3-beta 3 loop while keeping the active- site aspartate intact resulted in suppression of CKI1 function. Mechanistically, homology modeling indicated that the beta 3 beta 3 loop directly interacts with the ATP- binding site of the CKI1 histidine kinase domain. The functional relevance of the conformational dynamics observed in the beta 3-beta 3 loop of CKI1(RD) was supported by a comparison with another A. thaliana histidine kinase, ETR1. In contrast to the highly dynamic beta 3- beta 3 loop of CKI1(RD), the corresponding loop of the ETR1 receiver domain (ETR1(RD)) exhibited little conformational exchange and adopted a different orientation in crystals. Biochem-ical data indicated that ETR1(RD) is involved in phosphorylation-independent signaling, implying a direct link between conformational behavior and the ability of eukaryotic receiver domains to participate in MSP.