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

Details

Serval ID
serval:BIB_E620AD512BEB
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Evaluation and classification of RING-finger domains encoded by the Arabidopsis genome
Journal
Genome Biology
Author(s)
Kosarev  P., Mayer  K. F., Hardtke  C. S.
ISSN
1465-6914 (Electronic)
Publication state
Published
Issued date
2002
Volume
3
Number
4
Pages
RESEARCH0016
Notes
Journal Article
Research Support, Non-U.S. Gov't
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.
Keywords
Amino Acid Motifs Arabidopsis/genetics Arabidopsis Proteins/*chemistry/classification Computational Biology Genome, Plant Molecular Sequence Data Protein Structure, Tertiary Proteome/analysis Sequence Analysis, Protein
Pubmed
Create date
24/01/2008 19:51
Last modification date
20/08/2019 16:09
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