Evaluation and classification of RING-finger domains encoded by the Arabidopsis genome - PubMed (original) (raw)

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

Peter Kosarev et al. Genome Biol. 2002.

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 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.

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Figures

Figure 1

Figure 1

Schematic presentation of the structure of prototypical RING, PHD and LIM domains. The metal-ligand residues, either cysteine (C) or histidine (H), are shown as numbered spheres. Two pairs of metal ligands coordinate one zinc ion (hexagon). The numbers next to the loops connecting the metal-ligand residues indicate the minimum and maximum number of loop residues. (a) The structure of a RING domain (RING-HC type). The metal-ligand pairs 1 and 3 coordinate one zinc ion, while pairs 2 and 4 coordinate the second one in a so-called cross-brace arrangement. (b) The structure of a PHD domain reveals a cross-brace arrangement similar to the RING domain. (c) The LIM domain structure is distinct in its consecutive zinc ligation scheme: the first zinc ion is coordinated by the metal-ligand pairs 1 and 2, while the second ion is coordinated by pairs 3 and 4.

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