New Structural and Functional Contexts of the Dx[DN]xDG Linear Motif: Insights into Evolution of Calcium-Binding Proteins

Abstract

Binding of calcium ions (Ca2+) to proteins can have profound effects on their structure and function. Common roles of calcium binding include structure stabilization and regulation of activity. It is known that diverse families – EF-hands being one of at least twelve – use a Dx[DN]xDG linear motif to bind calcium in near-identical fashion. Here, four novel structural contexts for the motif are described. Existing experimental data for one of them, a thermophilic archaeal subtilisin, demonstrate for the first time a role for Dx[DN]xDG-bound calcium in protein folding. An integrin-like embedding of the motif in the blade of a β-propeller fold – here named the calcium blade – is discovered in structures of bacterial and fungal proteins. Furthermore, sensitive database searches suggest a common origin for the calcium blade in β-propeller structures of different sizes and a pan-kingdom distribution of these proteins. Factors favouring the multiple convergent evolution of the motif appear to include its general Asp-richness, the regular spacing of the Asp residues and the fact that change of Asp into Gly and vice versa can occur though a single nucleotide change. Among the known structural contexts for the Dx[DN]xDG motif, only the calcium blade and the EF-hand are currently found intracellularly in large numbers, perhaps because the higher extracellular concentration of Ca2+ allows for easier fixing of newly evolved motifs that have acquired useful functions. The analysis presented here will inform ongoing efforts toward prediction of similar calcium-binding motifs from sequence information alone.

A Rice Ca2+ Binding Protein Is Required for Tapetum Function and Pollen Formation

“…EF-hand usually form a helix-loop-helix structure (Day et al, 2002;Derbyshire et al, 2007;Rigden et al, 2011). However, there are some b-propeller structure proteins shown to possess Ca 2+ binding activity (Cioci et al, 2006).…”

“…Many Ca 2+ sensors contain domain E and F (EF)-hand domains for Ca 2+ binding (Snedden and Fromm, 1998). The typical EF-hand is a helix-loop-helix structure, in which the residues with +X*+Y*+Z*-Y*-X**-Z are associated with Ca 2+ binding (Day et al, 2002;Derbyshire et al, 2007;Rigden et al, 2011). In addition, other motifs such as helix-loopstrand, helix-loop-turn, strand-loop-helix, strand-loopstrand, and several structural contexts without regular secondary structure elements either before or after the DxDxDG-containing loop can provide affinity for binding Ca 2+ (Rigden and Galperin, 2004).…”

Integrin-α FG-GAP Repeat-Containing Protein 2 Is Critical for Normal B Cell Differentiation and Controls Disease Development in a Lupus Model

“…These domains are usually expressed in multiple repeats in a-integrin proteins, assembled into a b-propeller structure (4). It has been suggested that most FG-GAP domains contain calcium-binding propeller blades that regulate the folding, activation status, and heterodimerization of integrins, and presumably affect ligand binding (47)(48)(49). Indeed, the second FG-GAP domain of Iftg2 contains the sequence Dx[DN]xDG (aa 134-139), which is the consensus sequence of such calcium blades (48).…”

“…It has been suggested that most FG-GAP domains contain calcium-binding propeller blades that regulate the folding, activation status, and heterodimerization of integrins, and presumably affect ligand binding (47)(48)(49). Indeed, the second FG-GAP domain of Iftg2 contains the sequence Dx[DN]xDG (aa 134-139), which is the consensus sequence of such calcium blades (48). However, our data showed that Itfg2 is an intracellular protein; therefore, it cannot be directly involved in extracellular ligand binding like the majority of cellsurface a-integrin molecules.…”

“…However, our data showed that Itfg2 is an intracellular protein; therefore, it cannot be directly involved in extracellular ligand binding like the majority of cellsurface a-integrin molecules. Only two other intracellular proteins have been identified to date that contain FG-GAP domains with the calcium blade sequence, kaptin, and the BBS2 protein (48). Interestingly, both proteins are involved in processes that regulate dynamic change in cell shape and locomotion, and require actin rearrangements and polymerization.…”