Evaluation and classification of RING-finger domains encoded by the Arabidopsis genome.docVIP

/2002/3/4/research/0016.1 Research Evaluation and classification of RING-finger domains encoded by theArabidopsis genome Peter Kosarev*, Klaus X Mayer* and Christian S Hardtke? Addresses: *MIPS/IBI, National Center for Environment and Health (GS), Ingolst?dter Landstrasse 1, 85758 Neuherberg, Germany. ?Department of Biology, McGill University, Montréal, Québec H3A 1B1, Canada. Correspondence: Christian S Hardtke. E-mail: christian.hardtke@mcgill.ca Published: 14 March 2002 Received: 24 January 2002 Revised: 19 February 2002 Accepted: 22 February 2002 GenomeBiology 2002, 3(4):research0016.1–0016.12 The electronic version of this article is the complete one and can be found online at /2002/3/4/research/0016 ? 2002 Kosarev et al., licensee BioMed Central Ltd (Print ISSN 1465-6906; Online ISSN 1465-6914) Abstract 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 d