Definition of the chi (χ) torsion angle for pseudouridine

In nucleic acid structures, the chi (χ) torsion angle is about the glycosidic bond (N-C1′) that connects the sugar and the A/C/G/T/U bases (or their modified variants). Specifically, for pyrimidines (C, T and U), χ is defined by O4′-C1′-N1-C2; and for purines (A and G) by O4′-C1′-N9-C4 (see figure below).

Pseudouridine (5-ribosyluracil, PSU) was the first identified modified nucleoside in RNA and is the most abundant. PSU is unique in that it has a C-glycosidic bond (C-C1′) instead of the N-glycosidic bond common to all other nucleosides, canonical or modified. It thus poses a problem as to how to calculate the χ torsion angle: should it be O4′-C1′-C5-C4, reflecting the actual glycosidic bond connection, or should the conventional definition O4′-C1′-N1-C2 still be applied literally? As a concrete example, the figure below shows the (slightly) different numerical values (–162.7° vs. –163.9°), as given by the two definitions, for PSU 6 on chain A of the PDB entry 3cgp (based on the 2009 Biochemistry article by Lin & Kielkopf titled X-ray structures of U2 snRNA-branchpoint duplexes containing conserved pseudouridines).

Needless to say, the specific definition of the χ torsion angle for PSU in RNA structures is a very subtle point, and I am not aware of any discussion on this issue in literature. In 3DNA, PSU is identified explicitly, and χ is defined by O4′-C1′-C5-C4. In NDB and a couple of other tools I am familiar with, χ for PSU is defined by O4′-C1′-N1-C2. Again using 3cgp (figure below) as an example, 3DNA gives –162.7°, whilst NDB gives –163.9°. Additionally, this distinction in N-C1′ vs. C-C1′ connection also comes into play when calculating the perpendicular distance from the 3′ phosphorus atom to the glycosidic bond, as per Richardson et al.





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