Table 1.
Different domain family proteins and their domain architectures.
| No | Superfamily Proteins | Domain Motifs | Architecture of DNA-Binding Domains | Representative PROTEIN |
|---|---|---|---|---|
| 1 | Winged HTH proteins | Helix-turn-helix | mainly α | hRFX1 |
| 2 | GCM domain | β-sheet | mixed α/β | WRKY transcription factor |
| 3 | Zinc-coordinating proteins | Zinc finger | mixed α/β | SIP1, FOG, Msn2p, A20, Klf4 |
| 4 | ββα Zinc-finger family | Zinc finger | mixed α/β | Egr-1 |
| 5 | Loop-sheet-helix family | Helix-turn-helix | mainly α | p53 |
| 6 | Leucine zipper family | Helix-loop-helix | mainly α | Jun, Fos |
| 7 | POU domain | Helix-turn-helix | mainly α | Oct1, Oct2, Oct4 |
| 8 | Copper-fist | Zinc finger | mixed α/β | Mac1 |
| 9 | Histone-fold | NA | mainly α | TBP, TAF proteins, HuCHRAC |
| 10 | ETS domain | Helix-turn-helix | mainly α | pointed-P2 |
| 11 | Bet v1-like | NA | mixed α/β | VASt |
| 12 | P-loop domain | NA | multidomain, mixed α/β | ARTS |
| 13 | TEA domain | NA | NA | Simian virus 40 (SV40), enhancer factor TEF-1 |
| 14 | LytTR domain | NA | NA | AlgR/AgrA/LytR family of transcription factors |
| 15 | Steroid receptor | Zinc finger | mixed α/β | NA |
| 16 | p53-like transcription factors, E-set domains, and Runt domain proteins | Immunoglobulin-like β-sandwich motif | mainly β | NF-κB and Rel |
| 17 | TATA-box binding protein-like | TBP (TATA-binding protein) β-sheet | mainly β | HMGB1, HMGB2 |
| 18 | DNA/RNA polymerases | NA | multidomain, mixed α/β | RNA polymerase I, II, III, IV and V |
| 19 | Ribbon-helix-helix | Ribbon-helix-helix | mixed α/β | CopG, NikR, ParG |
| 20 | HMG-box | Helix-turn-helix | mainly α | TCF-1, SRY |
| 21 | IHF-like DNA-binding proteins | NA | mixed α/β | HBsu |
| 22 | RNase A-like | NA | mixed α/β | Train A |
| 23 | TrpR-like | Helix-turn-helix | mainly α | TrpR like proteins |
| 24 | T4 endonuclease V | Helix-turn-helix | mainly α | RuvC protein |
| 25 | ARID-like | Helix-turn-helix | mainly α | SWI-SNF complex protein p270 |
The superfamily proteins were taken from the structural classification of proteins (SCOP) database and the information was retrieved and updated from Rohs’s work [13]. NA: Not available.