# The World of Cyclic Dinucleotides in Bacterial Behavior
### SMODS Domain Structure and Catalysis
Human dsRNA-activated oligoadenylate synthase (OAS), which matches both NTP_tranf_2 and OAS1_C PFAM models, is a mammalian dsRNA sensor, which is increased during pathogen infections, and activates the synthesis of a second messenger 2'-5'-linked RNA molecules to cause RNA decay [109; 110]. TRF4 protein, which also contains a region most similar to the NTP_Tranf_2 model, makes part of a polyadenylation TRAMP complex that recognizes aberrant eukaryotic RNAs and target them for degradation [111]. Members of DNA polymerase family X, which have a \"palm\" subdomain, play essential roles in the base-excision repair mechanism, a process that repairs cell DNA base damage, being responsible for DNA synthesis and 5'-deoxyribose-phosphate (dRP) removal (dRP lyase activity). These enzymes can be also involved in other DNA repair processes such as non-homologous end-joining and lesion bypass [105; 112; 113]. Utp22, which has a Nrap_D2 domain, forms a complex with Rrp7 and they are present in early precursors of small ribosomal subunit. Utp22 is a structural building block and apparently lacks any enzymatic activity [97]. Among all described enzymes, cGAS enzymes are the only ones that share functional similarities with the prokaryotic DncV enzymes. While DncV synthesizes 3'-5' cGAMP molecules, cGAS enzymes synthesize 2'-3' cGAMP. Most of the other enzymes with structural similarity with the DncV SMODS domain have functions related to DNA or RNA processing. Active site of SMODS domains--DncV synthesizes preferentially cGAMP, but also produces c-di-AMP and c-di-GMP molecules. DncV regulates the expression of more than 80 genes in _Vibrio cholerae_ and its DGC activity is inhibited by folate-like molecules in vitro [5; 94; 114]. Orthologs of DncV are found in Gram-negative and Gram-positive bacterial species and the residues involved in ligand binding and to folate-like molecule binding are conserved among them [94] (Figure 5A). The active site is located in the interface between SMODS and AGS-C domains, while the folate-like molecule binds at the opposite of the substrate-binding pocket at the flat side of the protein (Figure 5A). The folate-like molecule binds mainly at the SMODS domain and makes few interactions with the linker between the two domains (Figure 5). The inhibitory site of the DncV, which binds folate-like molecules, such as 5-methyletrahydrofolate diglutamate (5 MTHGLU2), is formed by side chains of Arg36, Arg40, Arg44, Arg108, Trp110, Gln116, Tyr137, Phe204, and Asp260, by the main chain of Phe109, Thr111, and Leu240 and by a hydrophobic pocket formed mostly by the side chains of Leu240 and Val245 (Figure 5B). These residues are not conserved in members of SMODS (Figure 5A). The active site of DncV is built by nine residues: Ser114, Tyr117, Asp131, Asp133, Arg182, Ser259, Lys287, Ser301, and Asp348. Asp348 and Ser259 interact with the guanine and adenine bases of the substrate, respectively. Tyr117 and Asp133 are involved in the interaction with the ribose of the guanine and the adenine nucleotides, respectively. Arg182 binds the \(\beta\) and \(\gamma\) phosphate groups of the ATP. Tyr117, Ser114, Lys287, and Ser301 interact with the \(\beta\) and \(\gamma\) phosphate groups of GTP. The magnesium ion is coordinated by Asp131, Asp133, and the \(\alpha\), \(\beta\) and \(\gamma\)-groups of the GTP ligand (Figure 5B). These two aspartic residues belong to the Dh(D/E) motif conserved in members of NTS, as described above, and are key residues in (2'-5') oligoadenylate synthetase (OAS1) and poly(A) polymerase activities [115]. Figure 5: Conserved sequences within SMODS members and their substrate and inhibitor binding pockets. (**A**) residue frequency in SMODS proteins. Forty-five sequences were used from the Pfam database to create a multiple sequence alignment of the SMODS domain of different proteins using ClustalW [116], and the sequence logo was done using the WebLogo server [90].