The intricacies of the calcium ion-binding motif in the βγ-crystallin domain

What do a bacterial spore coat and a human eye lens have in common? For one, the presence of βγ-crystallins. The βγ-crystallins are a superfamily of Ca2+-binding proteins, grouped on the basis of their characteristic Greek key topology, that share a calcium-binding motif. Because the Ca2+-binding motif is evolutionarily conserved, learning more about it in bacteria could improve our understanding of it in other domains of life.
In the Journal of Biological Chemistry, biophysicist Yogendra Sharma and his group at the Centre for Cellular and Molecular Biology in India review the intricacies of the Ca2+-binding motif in the βγ-crystallin domain. The authors cover the architecture of the Ca2+-binding motif and Ca2+ coordination, paying special attention to Ca2+ coordination by the signature sequence residues of the Ca2+-binding site.
In the crystal structure of a typical βγ-crystallin, such as Clostrillin from the bacterium Clostridium beijerinckii, two Greek key motifs together form the Ca2+-binding sites. The partner Greek key motifs share one β-strand (out of four). On top of the domain lie two (N/D)-(N/D)-(X)-(X)-(T/S)-(S) sequence stretches that connect the third and fourth strands from their respective Greek key motifs. Each calcium ion is coordinated by residues from both sequence stretches and the β-hairpin loop between the first and second β-strand.

Figure 2
a) formation of a double clamp using two (N/D)(N/D)XX(T/S)S motifs.
b) Ca2-binding sites of Clostrillin (PDB ID: 3I9H) showing the Ca2 coordination sphere.

In a βγ-crystallin domain, the Ca2+-binding site generally has a coordination number of seven, including four protein ligands and three water molecules, and forms a pentagonal bipyramidal geometry. Ca2+-coordination is mediated via second, third and fifth residues of the (N/D)-(N/D)-(X)-(X)-(T/S)-(S) stretch, along with one residue of the β-hairpin, while the first residue of the (N/D)-(N/D)-(X)-(X)-(T/S)-(S) stretch may play a role in stabilizing the pocket through hydrogen bonding. Meanwhile, the fourth residue of the stretch is involved in forming a hydrophobic core. Ca2+ binding is important for stabilizing the βγ-crystallin domain, and the extent of gain in stability varies from domain to domain.
“The Ca2+-binding motif of βγ-crystallins is spectacular not only in its composition of a nonlinear sequence of amino acids but also in that it acts as a thread to connect an extensively diverse and chronologically vast array of proteins,” says Sharma. “Evolution of this motif displays the footprint of adaptations that the βγ-crystallin superfamily has undergone.”
While the Ca2+ coordination pattern has been well studied, very little is known regarding the functions of many βγ-crystallins. Current data suggest that many of these Ca2+-binding βγ-crystallins are relevant with stress, virulency or adhesion. As more members of this group are being identified, further research is needed to explore the Ca2+-dependent functions of βγ-crystallins.

Emily TsaiEmily Tsai ( recently completed postdoctoral research studies at the Johns Hopkins University School of Medicine department of radiation oncology and molecular radiation sciences.