The DxDxDG motif for calcium binding: multiple structural contexts and implications for evolution

J Mol Biol. 2004 Oct 29;343(4):971-84. doi: 10.1016/j.jmb.2004.08.077.

Abstract

Calcium ions regulate many cellular processes and have important structural roles in living organisms. Despite the great variety of calcium-binding proteins (CaBPs), many of them contain the same Ca(2+)-binding helix-loop-helix structure, referred to as the EF-hand. In the canonical EF-hand, the loop contains three calcium-binding aspartic acid residues, which form the DxDxDG sequence motif, and is flanked by two alpha-helices. Recently, other CaBPs containing the same motif, but lacking one or both helices, have been described. Here, structural motif searches were used to analyse the full diversity of structural context in the known set of DxDxDG-containing CaBPs, including those where the structural resemblance of a given DxDxDG motif to that of EF-hands had not been noted. The results obtained indicate that the EF-hand represents but one, among many, structural context for the DxDxDG-like Ca(2+)-binding loops. While the structural similarity of the binuclear calcium-binding sites in anthrax protective antigen and human thrombospondin suggests that they are homologous, evolutionary relationships for mononuclear sites are harder to discern. The possible scenarios for the evolution of DxDxDG motif-containing calcium-binding loops in a variety of non-homologous proteins suggested loop transplant as a mechanism perhaps responsible for much of the diversity in structural contexts of present day DxDxDG-type CaBPs. Additionally, while it can be shown that existence of a DxDxDG sequence is not enough to confer a conformation suitable for calcium binding, local convergent evolution may still have a role. The analysis presented here has consequences for the prediction of calcium binding from sequence alone.

MeSH terms

  • Amino Acid Motifs / genetics
  • Amino Acid Motifs / physiology
  • Amino Acid Sequence
  • Aspartic Acid / metabolism*
  • Bacteria / chemistry
  • Bacteria / genetics
  • Bacteria / metabolism
  • Calcium / metabolism*
  • Calcium-Binding Proteins / chemistry
  • Calcium-Binding Proteins / genetics
  • Calcium-Binding Proteins / metabolism*
  • Crystallography, X-Ray
  • Data Interpretation, Statistical
  • Evolution, Molecular
  • Glycine / metabolism*
  • Humans
  • Molecular Sequence Data
  • Protein Binding
  • Protein Structure, Tertiary

Substances

  • Calcium-Binding Proteins
  • Aspartic Acid
  • Calcium
  • Glycine