Table 1. Classification of common protein domains that interact with RNA.
The classification of ribonuclease domains is based on Anantharaman and Koonin17, of helicase domains on Fairman et al.25, and of methyltransferase domains on Motorin and Helm 134. The compilation of the RNA-binding protein domains is based on Gerstberger et. al. 1.
| Domain Class | Subclass (Superfamily) | Family |
|---|---|---|
| Nucleotidyl transferase | Poly(A) polymerases | Canonical PAPs |
| Non-canonical PAPs | ||
| Terminal UridylateTransferases | ||
| CCA-adding enzyme | ||
| Guanylyltransferase | ||
| RNA ligase | ||
| 2′5′ poly(A) polymerase (OAS) | ||
| RNA-dependent RNA polymerase | ||
| Ribonuclease | α/β | RNase A |
| RNase H | ||
| 3 → 5 exo | ||
| RNase II/R | ||
| RNase E | ||
| RNase PH | ||
| Metallolactamase | ||
| α + β | RNase T2 | |
| XRN1 | ||
| α | RNase III | |
| Decapping enzyme | ||
| RNA modifying enzymes | tRNAsynthetases | Class I |
| Class II | ||
| Deaminases | ADAR | |
| APOBEC | ||
| TadA | ||
| CDA | ||
| Pseudouridine Synthases | ||
| Methyltransferases | RMFTase | |
| SPOUT | ||
| Radical SAMTase | ||
| FAD/NAD(p) | ||
| Helicase | SF1 | Upf1-like |
| SF2 | Ski2-like | |
| RIG-I-like | ||
| DEAD-box | ||
| DEAH/RHA | ||
| Viral SF2 | ||
| Cas3 | ||
| SF3 | ||
| SF4 | ||
| SF5 | ||
| GTPase | EF-Tu/EF-G | |
| BMS1/SNU114 | ||
| RNA-binding domains | RRM | |
| KH | ||
| S1 | ||
| OB-fold | ||
| PUF | ||
| dsRBD | ||
| Zn-fingers | ||
| PAZ | ||
| PIWI | ||
| LSM | ||
| KOW | ||
| MIF4G | ||
| NTF2 | ||
| GAR (RGG) | ||
| HEAT repeat | ||
| Homeodomain | ||
| CSD | ||