Fig. 5: The structural determinants for donor nucleotide specificity of cyclic di-pyrimidine-synthesizing CdnE. | Nature Communications

Fig. 5: The structural determinants for donor nucleotide specificity of cyclic di-pyrimidine-synthesizing CdnE.

From: Crystal structure and functional implications of cyclic di-pyrimidine-synthesizing cGAS/DncV-like nucleotidyltransferases

Fig. 5

A–C The conserved Trp residue in (A) ClCdnE-UTP, (B) LpCdnE-UTP, (C) LpCdnE-UMPnPP that makes direct contact with the uracil base of donor nucleotide. The ligand and sidechain of Trp are shown in spheres. D The sequence logo of the identified lid 3 of cyclic di-pyrimidine-synthesizing CdnE. The residue number is based on ClCdnE. The determinants for pyrimidine specificity are indicated by black arrows. E–H The complex structures of ClCdnE, RmCdnE (PDB 6E0L) and EmCdnE (PDB 6E0N) are superimposed while focusing on the donor nucleotides. In (E) and (F) the side-chains of Glu263 and Arg275 of ClCdnE form a salt bridge (yellow dashed line) that restrict the space for nucleobase. Uracil (and probably cytosine) fits snugly (E) but adenine and guanine can cause significant clashes (F). In RmCdnE the corresponding residues of Cys252 and Glu265 are well separated, making a more open space for adenine base (G). Similarly, the side-chains of Glu259 and Ser271 in EmCdnE are not associated, allowing the binding of guanine base (H).

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