Unusual glycosidic bond in nucleic acid structures in the PDB/NDB

Glycosidic bond “is a type of covalent bond that joins a carbohydrate (sugar) molecule to another group, which may or may not be another carbohydrate.” In nucleic acid structures, the other group is a nucleobase, and the predominated type is the N-glycosidic bond where the purine (A/G) N9 or pyrimidine (C/T/U) N1 atom connects to the C1′ atom of the five-membered (deoxy) ribose sugar ring. Another well-known type is the C-glycosidic bond in pseudouridine, the most common modified base in RNA structures where the C5 atom instead of N1 is linked to the C1′ atom of the sugar ring.

N-glycosidic bond in U vs C-glycosidic bond in pesudoU

Recently, I performed a survey of all nucleic-acid-containing structures in the PDB/NDB database to see how many types of glycosidic bond are there. As always, I noticed some inconsistencies in the data: nucleotides with disconnected base/sugar, a base labeled as U but with pseudoU-type C-glycosidic bond. Shown below are a few unusual types of glycosidic bond in otherwise seemingly “normal” structures:

  • The residue GN7 (number 28 on chain A) in PDB entry 1gn7 contains a N7-glycosylated guanine.

N7-glycosylated guanine

  • The residue UPG (number 501 on chain A) in PDB entry 1y6f has sugar C1C (instead of C1′) atom connects to N1 of U.

C1C links to N1 of U

  • The residue XAE (number 11 on chain B) in PDB entry 2icz contains a benzo-homologous adenine.

xA in the benzo-homologous xDNA

  • The residue F5H (number 206 on chain B) in PDB entry 3v06 has N1 of U connects to C2′ of a six-membered sugar ring.

N1(U) connects to C2′

The unusual glycosidic bond has implications in 3DNA calculated parameters, for example the chi torsion angle. Identifying such cases would help refine 3DNA to provide sensible parameters and to avoid possible misinterpretations.



Thank you, your article helped me.

Eric Nitler · 2013-09-19 07:52 · #



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