Evaluation and classification of RING-finger domains encoded by the Arabidopsis genome.
BACKGROUND
In computational analysis, the RING-finger domain is one of the most frequently detected domains in the Arabidopsis proteome. In fact, it is more abundant in Arabidopsis than in other eukaryotic genomes. However, computational analysis might classify ambiguous domains of the closely related PHD and LIM motifs as RING domains by mistake. Thus, we set out to define an ordered set of Arabidopsis RING domains by evaluating predicted domains on the basis of recent structural data.


RESULTS
Inspection of the proteome with a current InterPro release predicts 446 RING domains. We evaluated each detected domain and as a result eliminated 59 false positives. The remaining 387 domains were grouped by cluster analysis and according to their metal-ligand arrangement. We further defined novel patterns for additional computational analyses of the proteome. They were based on recent structural data that enable discrimination between the related RING, PHD and LIM domains. These patterns allow us to predict with different degrees of certainty whether a particular domain is indeed likely to form a RING finger.


CONCLUSIONS
In summary, 387 domains have a significant potential to form a RING-type cross-brace structure. Many of these RING domains overlap with predicted PHD domains; however, the RING domain signature mostly prevails. Thus, the abundance of PHD domains in Arabidopsis has been significantly overestimated. Cluster analysis of the RING domains defines groups of proteins, which frequently show significant similarity outside the RING domain. These groups document a common evolutionary origin of their members and potentially represent genes of overlapping functionality.
Kosarev
Peter
P
Department of Biology, McGill University, Montréal, Québec H3A 1B1, Canada. christian.hardtke@mcgill.ca
Mayer
Klaus F X
KF
Hardtke
Christian S
CS
D020816:Amino Acid Motifs; D017360:Arabidopsis / Q000235:genetics; D029681:Arabidopsis Proteins / Q000737:chemistry* / Q000145:classification; D019295:Computational Biology; D018745:Genome, Plant; D008969:Molecular Sequence Data; D017434:Protein Structure, Tertiary; D020543:Proteome / Q000032:analysis; D020539:Sequence Analysis, Protein
D029681:Arabidopsis Proteins; D020543:Proteome