# The World of Cyclic Dinucleotides in Bacterial Behavior
### SMODS Domain Structure and Catalysis  
SMODS structure and structural similarities with other protein domains. The _Vibrio cholerae_ dinucleotide cyclase (DncV, the gene product of VC0179) has two domains, a SMODS domain located at its N-terminus and an **A**denylyl/**G**uanylyl and sMODS C-terminal sensor domain (AGS-C) [4] at its C-terminus [94]. The first 23 residues of the protein are located in the AGS-C domain, which presents a mainly \(\alpha\)-helical structure. The SMODS domain has two \(\beta\)-sheets connected by one \(\beta\)-strand (\(\beta\)3). It also has six \(\alpha\)-helices that do not make part of the interface between the two domains. The two \(\beta\)-sheets are composed by the strands: \(\beta\)2-\(\beta\)3-\(\beta\)7-\(\beta\)8-\(\beta\)9 and \(\beta\)3-\(\beta\)6-\(\beta\)5-\(\beta\) (Figure 4A). The substrate binding site is located in the interface between the two domains, in which the SMODS \(\beta\)-sheets make close contacts with the substrate (Figure 5A). Proteins containing SMODS domains are also found associated with other domains (Figure 2B) and, in rare cases, can be found in proteins containing two enzymatic domains: a SMODS and a class III AC/GC catalytic domain, both domains related with synthesis of cyclic nucleotide second messengers. DncV have structural similarities with proteins belonging to the nucleotidyltransferase (NTase) fold, a highly diverse superfamily of proteins (Figure 4C,E) [95]. NTase fold structure is characterized by the presence of a minimal conserved core of a mixed \(\beta\)-sheet flanked by \(\alpha\)-helices (\(\alpha\)1-\(\beta\)1-\(\alpha\)2-\(\beta\)2-\(\alpha\)3-\(\beta\)3-\(\alpha\)4) that correspond to \(\alpha\)3-\(\beta\)2-\(\alpha\)8-\(\beta\)3-\(\alpha\)9-\(\beta\)6 in DncV protein, missing the \(\alpha\)4 element (Figure 4A,B). This common core is usually decorated by various additional structural elements depending on the family. The NTase fold core is present in the DncV SMODS domain and various insertions are observed (Figure 4A,B). Members of NTases superfamily contain three conserved motifs located at the active site: (i) hG[G/S] located at \(\alpha\)2; (ii) [D/E]h[D/E]h (h indicates a hydrophobic amino acid) located at \(\beta\)2, and (iii) h[D/E]h located at \(\beta\)3 [95]. These three conserved motifs in DncV protein correspond to: (i) G\({}_{113}\)-S\({}_{114}\) (located at \(\alpha\)8); (ii) D\({}_{131}\)-I\({}_{132}\)-D\({}_{133}\) (located at \(\beta\)3); and (iii) N\({}_{193}\) (located at \(\beta\)6). Two of these motifs are conserved in proteins containing SMODS domains, the hG[G/S] and [D/E]h[D/E]h motifs (Figure 4A). Figure 4: Structural similarities between the SMODS domain and other nucleotidyltransferase superfamily members. **(A)** the N-terminal domain SMODS (colored in red) and the C-terminal ACS_C  
(light pink) of the DncV protein structure are shown as cartoons (PDBID: 4U0M). The SMODS domain is involved in cGAMP synthesis and belongs to the nucleotidyltransferase superfamily (NTS). The NTS fold is characterized by the presence of a minimal conserved core of a mixed \(\beta\)-sheet flanked by \(\alpha\)-helices with \(\alpha\)1-\(\beta\)1-\(\alpha\)2-\(\beta\)2-\(\alpha\)3-\(\beta\)3-\(\alpha\)4 topology that correspond to \(\alpha\)3-\(\beta\)2-\(\alpha\)8-\(\beta\)3-\(\alpha\)9-\(\beta\)6 (colored in red), missing the \(\alpha\)4 element. Various insertions are observed and are colored in grey (right panel). Members of NTS contain three conserved motifs located at the active site: (i) G[G/S] located at \(\alpha\)8, (ii) [D/E]h[D/E] (h indicates a hydrophobic amino acid) located at \(\beta\)3, and (iii) [D/E] located at \(\beta\)6. Two of these motifs are conserved in proteins containing SMODS domains (see Figure 5A). (**B**) topology of DncV, showing the location of the NTS fold core (bold outlines). The secondary structure elements from SMODS are colored in red and the AGS-C domain in light pink. (**C**) dendrogram showing structures similar to DncV made with the Dali server [79] (query: DncV, PDBID: 4U03).