update: 30th, Aug., 2009

Correspondence of RNA editing sites to protein 3D structures

This page is built on continuous collaborative efforts to show that the locations of amino acid residues coded by codons converted by RNA editing is significantly skewed to a protein structural core and the amino acid conversion pattern is basically from hydrophilic to hydrophobic, both of which suggest that RNA editing should regulate protein function through protein folding.

Conversion type of RNA editing is often found in organelles (mitochondria and chloroplasts) of land plants. The majority of conversion editing events occurs within protein-coding regions of mRNAs, and involves cytidine-to-uridine (C-U) and sometimes uridine-to-cytidine (U-C) conversion.

RNA editing often increases the percent identity of the encoded amino acid sequence to the homologous sequences, implying an important role for RNA editing in the function of encoded proteins.

It was found that the location of amino acid residues converted by RNA editing is significantly biased to protein structural core (Yura and Go, 2008) based on the data available at that time. Since then, the amount and types of data for conversion type RNA editing has increased and still increasing.

To show the consistency of our analysis, we start to follow the RNA editing data and launched this database. RNA editing data mapped onto amino acid sequence data with human curation is available from the download page. Based on these data, amino acid conversion pattern and correspondence to the protein 3D structure data are automatically generated and are stored in this database. The significance of skwed distribution of editing residues to protein structural core is automatically checked based on these data.

Reference:

• Yura, K., Go, M. (2008) Correlation between amino acid residues converted by RNA editing and functional residues in protein three-dimensional structures in plant organelles. BMC Plant Biology, 8, 79 (open access).
• Yura, K., Sulaiman, S., Hatta, Y., Shionyu, M., Go, M. RESOPS: A database for analyzing the correspondence of RNA editing sites to protein three-dimensional structures, Plant and Cell Physiology, in press.

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