Identification of a Ca 2+ -Binding Domain in the Rubella Virus Nonstructural Protease

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Abstract
The rubella virus (RUB) nonstructural protein (NS) open reading frame (ORF) encodes a polypeptide precursor that is proteolytically self cleaved into two replicase components involved in viral RNA replication. A putative EF-hand Ca2+-binding motif that was conserved across different genotypes of RUB was predicted within the nonstructural protease that cleaves the precursor by using bioinformatics tools. To probe the metal-binding properties of this motif, we used an established grafting approach and engineered the 12-residue Ca2+-coordinating loop into a non-Ca2+-binding scaffold protein, CD2. The grafted EF-loop bound to Ca2+ and its trivalent analogs Tb3+ and La3+ with Kds of 214, 47, and 14 μM, respectively. Mutations (D1210A and D1217A) of two of the potential Ca2+-coordinating ligands in the EF-loop led to the elimination of Tb3+ binding. Inductive coupled plasma mass spectrometry was used to confirm the presence of Ca2+ ([Ca2+]/[protein] = 0.7 ± 0.2) in an NS protease minimal metal-binding domain, RUBCa, that spans the EF-hand motif. Conformational studies on RUBCa revealed that Ca2+ binding induced local conformational changes and increased thermal stability (ΔTm = 4.1°C). The infectivity of an RUB infectious cDNA clone containing the mutations D1210A/D1217A was decreased by ∼20-fold in comparison to the wild-type (wt) clone, and these mutations rapidly reverted to the wt sequence. The NS protease containing these mutations was less efficient at precursor cleavage than the wt NS protease at 35°C, and the mutant NS protease was temperature sensitive at 39°C, confirming that the Ca2+-binding loop played a structural role in the NS protease and was specifically required for optimal stability under physiological conditions.