Pseudouridine (5-ribosyluracil, PSU) is the most abundant modified nucleotide in RNA. It is unique in that it has a C-glycosidic bond (C-C1′) instead of the N-glycosidic bond (N-C’) common to all other nucleotides, canonical or modified. In 3DNA, the one-letter code for PSU is assigned to the upper case ‘P’, reserving the lower case ‘p’ for its modified variants. Distinguishing PSU from standard U (or T) is important for deriving sensible base-pair parameters and the χ torsion angle.
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| PSU | 3TD |
Recently, I came across 3TD (see figure above) in PDB entry 5afi. 3TD is a modified variant of PSU, with a methyl group attached to N3. In 3DNA v2.1 v2.1-2015mar11, 3TD is abbreviated to ‘p’ to signify its connection to PSU.
In the list of recognized nucleotides (‘baselist.dat’) distributed with 3DNA, there are two other residues mapped to ‘p’: FHU and P2U (see figure below). As is often the case, it is the chemical structure, not the 3-letter PDB ligand identifier (or even full chemical name), that shows clearly to what 3DNA 1-letter abbreviation a residue matches.
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| FHU | P2U |
