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Figure 1 | BMC Plant Biology

Figure 1

From: Correlation between amino acid residues converted by RNA editing and functional residues in protein three-dimensional structures in plant organelles

Figure 1

Amino acid residues converted by RNA editing in the RuBisCO large subunit. (A) Multiple sequence alignment of RuBisCO large subunit derived from chloroplast genes of Lycopodium digitatum (L. digit), Bazzania trilobata (B. trilo), Sphagnum palustre (S. palus), Anthoceros formosae (A. formo), Osmunda cinnamomea var. fokiensis (O. cinna) and Chlamydomonas reinhardtii (C. rei(3D)). Data regarding RNA editing sites were gathered from [10]. Amino acid sequence of C. reinhardtii RuBisCO was aligned to the other sequences to assign 3D positions of residues given in Protein Data Bank (ID: 1UW9[26]). Amino acid residues converted by RNA editing are colored as follows: Red indicates that the first nucleotide of the codon is edited, green the second, and cyan the second and the third. A red box below each alignment row indicates a residue in a helix structure; a blue box indicates a residue in a strand structure. A black dot below the row indicates a residue in a structural core; a triangle over the row indicates a residue in the interface for the small subunits or the other large subunits. A green triangle indicates a binding site of an intermediate analogue (2-carboxyarabinitol-1,5- diphosphate). Conversion pattern of amino acid residue by RNA editing is described in the box. (B) Three-dimensional structure of RuBisCO large subunit in a supramolecule form. Colored molecule in the center is the large subunit in focus, light grey molecules are RuBisCO small subunits, and deep grey molecules are RuBisCO large subunits. On the molecule in the center, residues in red form the structural core, and residues in white are ones converted by RNA editing. Numbers on white residue correspond to the numbers in (A). (C) A cross-section of (B) to depict the structural cores. The slice plane is parallel to the figure page. (D) A cross-section of (B). The slice plane is parallel to the figure page and deeper than (C).

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