Table 1.
Comparison of type I topoisomerases
| Properties | Type |
||
|---|---|---|---|
| IA | IB | IC | |
| Phylogenetic distribution | Archaea, Prokarya, and Eukarya (3) | Prokarya, Eukarya, and some eukaryotic viruses (3) | Archaea* (3) |
| Cleavage polarity | 5′ (25) | 3′ (3) | 3′ (1) |
| Substrate DNA | Negatively supercoiled DNA† (25) | Positively and negatively supercoiled DNA (3) | Positively and negatively supercoiled DNA (1) |
| Mg2+ dependence | Yes (25) | No (3) | No (1) |
| Change in linking number | Strictly in steps of +1 (9) | In steps of n (〈ΔLk〉 ≈19 at zero force) (11) | In steps of n (〈ΔLk〉 ≈12 at zero angular velocity in 40% glycerol) |
| Force dependence on linking number change | No (9, 26) | Yes (11) | Yes |
| Relaxation velocity | 0.0023‡ μm/sec (26) | 4.1§–6.7¶ μm/sec (11) | 3.0 μm/sec‖ |
| Structural properties | Toroidal shape; binds ssDNA along a groove and accepts passing strand in central hole (6, 27); structural and mechanistic similarities to type II enzymes (22) | Concave shape; surrounds DNA in a clamp-like manner; structural similarities to tyrosine recombinases suggest a common ancestor (21, 28) | Unique fold that includes a large positively charged groove containing a helix–turn–helix motif; some of the active site residues are found in the helix–turn–helix motif (5) |
| Mechanism | Enzyme-bridged strand passage (7–9) | Swiveling or ″controlled rotation″ (10, 11) | Constrained swiveling |