7X4P

CD-NTase EfCdnE in complex with intermediate pppUpU

Summary for 7X4P

• Entry DOI: 10.2210/pdb7x4p/pdb
• Related: 7X4A 7X4C 7X4F 7X4G
• Descriptor: EfCdnE, URIDINE 5'-TRIPHOSPHATE, URIDINE-5'-MONOPHOSPHATE, ... (5 entities in total)
• Functional Keywords: cd-ntase, cgas, cyclic dinucleotide, intermediate complex, transferase
• Biological source: Enterococcus faecalis
• Total number of polymer chains: 1
• Total formula weight: 36584.09

Authors

Chen, Y.,Ko, T.P.,Yang, C.S.,Wang, Y.C.,Hou, M.H. (deposition date: 2022-03-03, release date: 2023-03-08, Last modification date: 2024-05-29)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (1.6 Å)