7D4O

cyclic trinucleotide synthase CdnD in complex with ATP and ADP

Summary for 7D4O

• Entry DOI: 10.2210/pdb7d4o/pdb
• Related: 7D48 7D4J 7D4S 7D4U
• Descriptor: Cyclic AMP-AMP-GMP synthase, ADENOSINE-5'-TRIPHOSPHATE, ADENOSINE-5'-DIPHOSPHATE, ... (6 entities in total)
• Functional Keywords: cyclic trinucleotide synthesis nucleotidyl transferase, transferase
• Biological source: Enterobacter cloacae
• Total number of polymer chains: 2
• Total formula weight: 91508.63

Authors

Yang, C.-S.,Hou, M.-H.,Tsai, C.-L.,Wang, Y.-C.,Ko, T.-P.,Chen, Y. (deposition date: 2020-09-24, release date: 2021-03-17, Last modification date: 2023-11-29)

Primary citation

Ko, T.P.,Wang, Y.C.,Tsai, C.L.,Yang, C.S.,Hou, M.H.,Chen, Y.
Crystal structure and functional implication of a bacterial cyclic AMP-AMP-GMP synthetase.
Nucleic Acids Res., 49:4725-4737, 2021

PubMed Abstract: Mammalian cyclic GMP-AMP synthase (cGAS) and its homologue dinucleotide cyclase in Vibrio cholerae (VcDncV) produce cyclic dinucleotides (CDNs) that participate in the defense against viral infection. Recently, scores of new cGAS/DncV-like nucleotidyltransferases (CD-NTases) were discovered, which produce various CDNs and cyclic trinucleotides (CTNs) as second messengers. Here, we present the crystal structures of EcCdnD, a CD-NTase from Enterobacter cloacae that produces cyclic AMP-AMP-GMP, in its apo-form and in complex with ATP, ADP and AMPcPP, an ATP analogue. Despite the similar overall architecture, the protein shows significant structural variations from other CD-NTases. Adjacent to the donor substrate, another nucleotide is bound to the acceptor binding site by a non-productive mode. Isothermal titration calorimetry results also suggest the presence of two ATP binding sites. GTP alone does not bind to EcCdnD, which however binds to pppApG, a possible intermediate. The enzyme is active on ATP or a mixture of ATP and GTP, and the best metal cofactor is Mg2+. The conserved residues Asp69 and Asp71 are essential for catalysis, as indicated by the loss of activity in the mutants. Based on structural analysis and comparison with VcDncV and RNA polymerase, a tentative catalytic pathway for the CTN-producing EcCdnD is proposed.

PubMed: 33836064
DOI: 10.1093/nar/gkab165

Experimental method

X-RAY DIFFRACTION (1.87 Å)