# The World of Cyclic Dinucleotides in Bacterial Behavior
## 3 Cyclic Dinucleotide Receptors  
Different classes of CDN receptors have been described and are involved in the regulation of a broad range of bacterial behaviors, while, in eukaryotic cells, they are associated with the activation of innate immune response through interactions with STING proteins. In order to analyze the residues involved in CDN ligand and to compare the ligand structure inside of the protein pocket, we focused on the CDN receptors with three-dimensional structures solved and deposited in the Protein Data Bank (PDB) (Table 1). C-di-GMP receptors are the most studied CDN receptors, probably because it was the first CDN identified as a second bacterial messenger. Therefore, most of the receptors with the structure solved in complex with the ligand analyzed in this review are c-di-GMP receptors. Examples of these are STING proteins and proteins containing PilZ domains, degenerate EAL domains, allosteric site of DGC enzymes containing GGDEF domains, and RNA structures such as c-di-GMP I and c-di-GMP II riboswitches. Other examples of c-di-GMP receptors are the C-terminal domain of the master regulator of _Streptomyces_ cell development BldD, REC domain of the transcriptional regulator VspT protein, N-terminal domain of the ATPase of the Type II secretion system MshE protein (T2 SSE_N domain), MerR domain of BrIR protein, AAA+ ATPase domain (Sigma54_activat, PF00158) of the transcriptional regulator FleQ protein, and CA domain (HATPase_c, PF02518) of the cell cycle kinase CckA protein (Table 1). Different classes of c-di-AMP receptors have also been described, such as proteins containing STING domains, Aldo-keto reductase domain of oxidoreductase RECON proteins, cyclic-di-AMP receptor domain of PII-like signal transduction protein (PtsA), pyruvate carboxylase domain (HMGL-like domain, PF00682) of _L. monocytogenes_ pyruvate carboxylase (LmPC) or _Lactococcus lactis_ pyruvate carboxylase (Lipc), TrkA_C domain of potassium transporter A (KtrA), CBS domain of OpuC carnitine transporter, and RNA structures such as ydaO-yuaA riboswitches (Table 1). For cGAMP, the receptors analyzed in this review are only STING proteins and c-di-GMP I riboswitches. The function of each CDN receptor, as well as the residues involved in ligand binding, are described in more detail in Table 1. It is notable that most of CDN receptors are specific to their ligands, with the exception of receptors involved in mammalian cell innate immunity, such as STING that interact with different CDNs such as c-di-GMP, c-di-AMP and 3'-5' and 2'-3' cGAMP molecules (Figure 7B). Interestingly, even though the CDNs are chemically different, the STING binding pockets for each kind of CDN are very similar and the residues involved in ligand binding for each CDN are almost the same (Figure 7A,C). This suggests that STING adjusts the ligand binding site for each CDN by placing or removing water or magnesium molecules. STING proteins are localized on the endoplasmic reticulum membrane of eukaryotic cells and are CDN sensors that, when bound, regulate the induction of type I interferons (IFN-\(\alpha\) and IFN-\(\beta\)), thus eliciting the intracellular signals of the invasion by bacteria and/or viruses, and activating the innate immune response to attack the pathogen. STING proteins can directly sense the pathogen invasion by interaction with bacterial CDNs (3'-5' c-di-GMP, 3'-5' c-di-AMP or 3'-5' cGAMP) or indirectly by binding to eukaryotic 2'-3' cGAMP through its C-terminal domain ( TMEM173, PF15009). It is controversial whether STING binds 2'-5' cGAMP preferentially in relation to other CDNs, or binds all of them with the same affinity [114]. Figure 7: Some CDN receptors: STING, PILZ, and degenerate EAL domains. (**A**) multiple sequence alignment of STING proteins in complex with different CDNs: monomeric 3’-5’ c-di-GMP (PDBID: 4F5D), 2’-3’ cGAMP (PDBID: 6A06), 3’-5’ c-di-AMP (PDBID: 6A03), and 3’-5’ cGAMP (PDBID: 5 CFM).