Nuclear magnetic resonance structure of calcium‐binding protein 1 in a Ca²⁺‐bound closed state: Implications for target recognition

Abstract

Calcium-binding protein 1 (CaBP1), a neuron-specific member of the calmodulin (CaM) superfamily, regulates the Ca 21 -dependent activity of inositol 1,4,5-triphosphate receptors (InsP3Rs) and various voltage-gated Ca 21 channels. Here, we present the NMR structure of fulllength CaBP1 with Ca 21 bound at the first, third, and fourth EF-hands. A total of 1250 nuclear Overhauser effect distance measurements and 70 residual dipolar coupling restraints define the overall main chain structure with a root-mean-squared deviation of 0.54 Å (N-domain) and 0.48 Å (C-domain). The first 18 residues from the N-terminus in CaBP1 (located upstream of the first EFhand) are structurally disordered and solvent exposed. The Ca 21 -saturated CaBP1 structure contains two independent domains separated by a flexible central linker similar to that in calmodulin and troponin C. The N-domain structure of CaBP1 contains two EF-hands (EF1 and EF2), both in a closed conformation [interhelical angles 5 129°(EF1) and 142°(EF2)]. The C-domain contains EF3 and EF4 in the familiar Ca 21 -bound open conformation [interhelical angles 5 105°( EF3) and 91°(EF4)]. Surprisingly, the N-domain adopts the same closed conformation in the presence or absence of Ca 21 bound at EF1. The Ca 21 -bound closed conformation of EF1 is reminiscent of Ca 21 -bound EF-hands in a closed conformation found in cardiac troponin C and calpain. We propose that the Ca 21 -bound closed conformation of EF1 in CaBP1 might undergo an induced-fit opening only in the presence of a specific target protein, and thus may help explain the highly specialized target binding by CaBP1.

Molecular Dynamics of the Neuronal EF-Hand Ca2+-Sensor Caldendrin

“…Accordingly a close to open conformational change upon Ca 2+ binding was observed in the NMR and crystal structures of the C-terminal EF-hand domain of S-CaBP1 [16]–[18]. To increase the sensitivity of the method we next generated mutant Caldendrin proteins having single Trp reporter groups in EF-hand 1 (F162W) and 3 (F239W).…”

Calcium triggers reversal of calmodulin on nested anti-parallel sites in the IQ motif of the neuronal voltage-dependent sodium channel Na V 1.2

“…CaBP1 (Calcium Binding Protein 1) binds only 3 Ca 2+ , suggesting that there are some neuronal targets that prefer this stoichiometry. [140] Wild-type CaM with 4 functional sites is unlikely to adopt states with only one site filled in a domain because of the high degree of cooperativity between calcium-binding sites in the same domains. However, interactions between binding-site residues in CaM and side chains of residues in a target protein could alter the energetic balance to tip it in favor of an unoccupied site as proposed in the analysis of 4DCK.…”

Calmodulin Lobes Facilitate Dimerization and Activation of Estrogen Receptor-α

“…Structure Calculation-The NMR structure of full-length CaM bound to ER(287-305) was calculated using NMR-derived distance restraints and residual dipolar couplings as described previously (15,(31)(32)(33). The structure of ER(287-305) bound to full-length CaM was verified to form an ␣-helix based on NOE distance restraints (H N -H N connectivity), chemical shift index (34), and circular dichroism analysis as described previously (15).…”