The C-terminal cytoplasmic tail of polycystin-2 (PC2/TRPP2), a Ca
2+
-permeable channel, is frequently mutated or truncated in autosomal dominant polycystic kidney disease. We have previously shown that this tail consists of three functional regions: an EF-hand domain (PC2-EF, 720–797), a flexible linker (798–827), and an oligomeric coiled coil domain (828–895). We found that PC2-EF binds Ca
2+
at a single site and undergoes Ca
2+
-dependent conformational changes, suggesting it is an essential element of Ca
2+
-sensitive regulation of PC2 activity. Here we describe the NMR structure and dynamics of Ca
2+
-bound PC2-EF. Human PC2-EF contains a divergent non-Ca
2+
-binding helix-loop-helix (HLH) motif packed against a canonical Ca
2+
-binding EF-hand motif. This HLH motif may have evolved from a canonical EF-hand found in invertebrate PC2 homologs. Temperature-dependent steady-state NOE experiments and NMR
R
1
and
R
2
relaxation rates correlate with increased molecular motion in the EF-hand, possibly due to exchange between apo and Ca
2+
-bound states, consistent with a role for PC2-EF as a Ca
2+
-sensitive regulator. Structure-based sequence conservation analysis reveals a conserved hydrophobic surface in the same region, which may mediate Ca
2+
-dependent protein interactions. We propose that Ca
2+
-sensing by PC2-EF is responsible for the cooperative nature of PC2 channel activation and inhibition. Based on our results, we present a mechanism of regulation of the Ca
2+
dependence of PC2 channel activity by PC2-EF.