Domain atrophy creates rare cases of functional partial protein domains.
BACKGROUND
Protein domains display a range of structural diversity, with numerous additions and deletions of secondary structural elements between related domains. We have observed a small number of cases of surprising large-scale deletions of core elements of structural domains. We propose a new concept called domain atrophy, where protein domains lose a significant number of core structural elements.


RESULTS
Here, we implement a new pipeline to systematically identify new cases of domain atrophy across all known protein sequences. The output of this pipeline was carefully checked by hand, which filtered out partial domain instances that were unlikely to represent true domain atrophy due to misannotations or un-annotated sequence fragments. We identify 75 cases of domain atrophy, of which eight cases are found in a three-dimensional protein structure and 67 cases have been inferred based on mapping to a known homologous structure. Domains with structural variations include ancient folds such as the TIM-barrel and Rossmann folds. Most of these domains are observed to show structural loss that does not affect their functional sites.


CONCLUSIONS
Our analysis has significantly increased the known cases of domain atrophy. We discuss specific instances of domain atrophy and see that there has often been a compensatory mechanism that helps to maintain the stability of the partial domain. Our study indicates that although domain atrophy is an extremely rare phenomenon, protein domains under certain circumstances can tolerate extreme mutations giving rise to partial, but functional, domains.
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK. ananth@ebi.ac.uk.
Ananth
A
Prakash
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK. agb@ebi.ac.uk.
Alex
A
Bateman
D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism; D057508:Burkholderia cenocepacia / Q000201:enzymology / Q000235:genetics; D002352:Carrier Proteins / Q000235:genetics / Q000378:metabolism; D003454:Cryptococcus / Q000201:enzymology / Q000235:genetics; D004926:Escherichia coli / Q000201:enzymology / Q000235:genetics; D019143:Evolution, Molecular; D017353:Gene Deletion; D005798:Genes, Bacterial; D006801:Humans; D007778:Lactobacillus / Q000201:enzymology / Q000235:genetics; D008156:Luciferases / Q000235:genetics* / Q000378:metabolism; D008958:Models, Molecular; D010088:Oxidoreductases / Q000235:genetics* / Q000378:metabolism; D010776:Photobacterium / Q000201:enzymology / Q000235:genetics; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D020027:Pyrococcus furiosus / Q000201:enzymology / Q000235:genetics; D013211:Staphylococcus aureus / Q000201:enzymology / Q000235:genetics
D001426:Bacterial Proteins; D002352:Carrier Proteins; D010088:Oxidoreductases; C063122:luxG protein, Bacteria; D008156:Luciferases