Bioinorganic motifs: towards functional classification of metalloproteins

Abstract

The habitat of bioinorganic motifs (BIMs) is at the interface of biological inorganic chemistry and bioinformatics. BIM is defined as a common structural feature shared by functionally related, but not necessarily homologous, proteins, and consisting of the metal atom(s) and first coordination shell ligands. BIMs appear to be suitable for classification of metal centres at any level, from groups of unrelated proteins with similar function to different functional states of the same protein, and for description of possible evolutionary relationships of metalloproteins. However, they have not attracted wide attention from the bioinformatics community. Although their presence is appreciated, they are difficult to predict—therefore the current ‘high-throughput’ initiatives are likely to miss or ignore them altogether. The protein sequence databases do not distinguish between proteins containing different prosthetic groups (unless they have different sequences) or between apo- and holoprotein. On the other hand, the protein structure databases include data on ‘hetero compounds’ of various origin but these data are often inconsistent. A number of specialized databases dealing with BIMs and attempts to classify them are reviewed. Supplementary information: The additional bibliography and list of Internet resources on bioinorganic chemistry are available at http://www.ebi.ac.uk/~kirill/biometal/