Table 1. The occurrence of carboxylate-ribose interactions in all known protein structures with ribose-containing ligands.
| Bidentate Asp/Glu Interactions | Other Interactions | |||
|---|---|---|---|---|
| Canonical | Noncanonical | Monodentate Asp/Glu Interactions | No Glu/Asp Interaction | |
| Rossmann fold (n = 484) | 263 (54%) | 38 (8%) | 66 (14%) | 117 (24%) |
| P-loop nucleoside triphosphatases (NTPases) (n = 210) | 0 (0%) | 2 (1%) | 17 (8%) | 191 (91%) |
| Non-Rossmann folds (n = 901) 1 | 27 15(1.7%) 1 | 52 (6%) | 179 (20%) | 643 (71%) |
| No assigned fold (n = 1,354) 2 | 279 (20%) | 150 (11%) | 249 (18.4%) | 676 (50%) |
| Total (n = 2,949) | 578 | 233 | 511 | 1,627 |
| Methyltransferases 3 (n = 55) | 50 (91%) | n.d. | 0 (0%) | 5 (9%) 4 |
| NAD/FAD-utilizing enzymes 3 (n = 315) | 228 (73%) | n.d. | 22 (7%) | 65 (20%) |
The analysis includes all deposited nonredundant PDB structures circa July 2014, with <2.5 Å resolution and with a ligand containing a ribose with unmodified 2ʹ and 3ʹ hydroxyls (n = 2,739). Fold categories are defined in the Methods.
1 Initially, 27 non-Rossmann PDB structures were identified by the computational search as having a canonical motif. These were manually examined, and consequently eight structures that are clearly Rossmann or Rossmannoids (1DJN, 1GTE, 1PS9, 1I8T, 2C31, 2E5W, 3C6K, and 2DHP) were excluded. It appears that their CATH/SCOP non-Rossmann annotations were derived primarily from additional domains in these structures.
2 Structures for which neither a SCOP nor a CATH category is specified in the PDB (SCOP v.1.75 and CATH_v3.5.0, version date: 20.09.2013 used for this analysis).
3 Superfamily specific statistics for methyltransferases (SCOP families c.66.1 structures bound to SAM) and of NAD/FAD dehydrogenases (SCOP families c.2.1 and c.3.1.5). n.d. = not determined.
4 A profound change in the SAM-binding site was observed in these five structures, whereby a long loop extending from β2 interacts with the ribose hydroxyls.