7X4G

CD-NTase ClCdnE in complex with substrate UTP

7X4G の概要

• エントリーDOI: 10.2210/pdb7x4g/pdb
• 関連するPDBエントリー: 7X4A 7X4C 7X4F
• 分子名称: ClCdnE, URIDINE 5'-TRIPHOSPHATE, MAGNESIUM ION, ... (4 entities in total)
• 機能のキーワード: cd-ntase, cgas, cyclic dinucleotide, transferase
• 由来する生物種: Cecembia lonarensis
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 36904.56

構造登録者

Chen, Y.,Ko, T.P.,Yang, C.S.,Wang, Y.C.,Hou, M.H. (登録日: 2022-03-02, 公開日: 2023-03-08, 最終更新日: 2023-11-29)

主引用文献

Yang, C.S.,Ko, T.P.,Chen, C.J.,Hou, M.H.,Wang, Y.C.,Chen, Y.
Crystal structure and functional implications of cyclic di-pyrimidine-synthesizing cGAS/DncV-like nucleotidyltransferases.
Nat Commun, 14:5078-5078, 2023

PubMed Abstract: Purine-containing nucleotide second messengers regulate diverse cellular activities. Cyclic di-pyrimidines mediate anti-phage functions in bacteria; however, the synthesis mechanism remains elusive. Here, we determine the high-resolution structures of cyclic di-pyrimidine-synthesizing cGAS/DncV-like nucleotidyltransferases (CD-NTases) in clade E (CdnE) in its apo, substrate-, and intermediate-bound states. A conserved (R/Q)xW motif controlling the pyrimidine specificity of donor nucleotide is identified. Mutation of Trp or Arg from the (R/Q)xW motif to Ala rewires its specificity to purine nucleotides, producing mixed purine-pyrimidine cyclic dinucleotides (CDNs). Preferential binding of uracil over cytosine bases explains the product specificity of cyclic di-pyrimidine-synthesizing CdnE to cyclic di-UMP (cUU). Based on the intermediate-bound structures, a synthetic pathway for cUU containing a unique 2'3'-phosphodiester linkage through intermediate pppU[3'-5']pU is deduced. Our results provide a framework for pyrimidine selection and establish the importance of conserved residues at the C-terminal loop for the specificity determination of CD-NTases.

PubMed: 37604815
DOI: 10.1038/s41467-023-40787-9

実験手法

X-RAY DIFFRACTION (2.6 Å)