8HYK

CD-NTase EfCdnE in complex with intermediate pppU[2'-5']p

Summary for 8HYK

• Entry DOI: 10.2210/pdb8hyk/pdb
• Descriptor: EfCdnE, [[(2R,3R,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-4-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate, MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: cd-ntase, cgas, cyclic dinucleotide, transferase
• Biological source: Enterococcus faecalis EnGen0062
• Total number of polymer chains: 1
• Total formula weight: 36339.89

Authors

Ko, T.-P.,Wang, Y.-C.,Yang, C.-S.,Hou, M.-H.,Chen, Y. (deposition date: 2023-01-06, release date: 2023-07-05, Last modification date: 2023-09-13)

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 (2.021 Å)