Table 1.
Known Riboswitch Structures with Representative Ligand Bound and Free States
| Riboswitch | Ligand | Free- State |
Organism or Source | PDB Code and Select References |
||
|---|---|---|---|---|---|---|
| Purine Class | ||||||
| Guanine | Hypoxanthine | B. subtilis | 1U8D59 | |||
| Guanine | Guanine | B. subtilis | 1Y2760 | |||
| Adenine | Adenine | V. vulnificus | 1Y2660 | |||
| PreQ1 | PreQ0, PreQ1 | yes | T. tengcongensis | 3GCA61, 3Q50, 3Q5146 | ||
| PreQ1 | PreQ1 | B. subtilis | 3FU263, 2L1V62 | |||
| SAM Class | ||||||
| SAM-I | SAM | T. tengcongensis | 2GIS47, 3IQN45 | |||
| SAM-I (A94G) | - | yes | T. tengcongensis | 3IQP45 | ||
| SAM-I | SAM | B. Subtilis | 3NPB50 | |||
| SAM-II | SAM | Sargasso Sea metagenome | 2QWY51 | |||
| SAM-III | SAM | E. faecalis | 3E5C55 | |||
| Amino Acid Classes | ||||||
| Lysine | Lysine | yes | T. maritima | 3D0U, 3D0X23, 3DIL, 3DIS44 | ||
| Glycine (VCII) | Glycine | yes | V. cholerae | 3OWW, 3OXO43 | ||
| Others (Bound State Only) | ||||||
| glmS | GlcN6P | T. tengcongensis | 2Z75 | |||
| FMN | FMN | F. nucleatum | 3F2Q | |||
| M-box | Mg(II) | B. subtilis | 2QBZ | |||
| SAH | SAH | R. solanacearum | 3NPQ | |||
| TPP | TPP | A. thaliana | 2CKY | |||
| TPP | TPP | E. coli | 2GDI | |||
| c-di-GMP | c-di-GMP | V. cholerae | 3MXH | |||