Table 3. Comparison of the properties of the haloalkane dehalogenase DpcA with those of its closest structural homologs.
| Enzyme | DpcA | DhlA | DccA | DppA | DmrA |
|---|---|---|---|---|---|
| PDB code | 6f9o | 1b6g | 5esr | 2xt0 | 4mj3 |
| Resolution (Å) | 1.05 | 1.15 | 1.5 | 1.95 | 1.7 |
| Catalytic pentad | Asp123, Trp124, Trp164, Asp250, His280 | Asp124, Trp125, Trp175, Asp260, His289 | Asp123, Trp124, Trp163, Asp249, His279 | Asp123, Trp124, Trp163, Asp249, His278 | Asp123, Trp124, Trp164, Asp250, His280 |
| Sequence identity to DpcA (%) | — | 40 | 58 | 43 | 57 |
| R.m.s.d. for superposition with DpcA (Å)/No. of aligned Cα atoms | — | 1.6/294 | 1.3/304 | 1.5/293 | 0.7/303 |
| Substrate preference | C3–C6 | C2–C3 | C3–C6 | C3–C5 | C4–C5 |
| Monosubstituted, disubstituted, brominated | Terminally substituted, chlorinated, brominated | Monosubstituted, disubstituted, brominated, chlorinated | Monosubstituted, brominated | Monosubstituted, disubstituted, brominated | |
| Drienovska et al. (2012 ▸) | Janssen et al. (1985 ▸, 1989 ▸) | Carlucci et al. (2016 ▸) | Hesseler et al. (2011 ▸) | Fung et al. (2015 ▸) | |
| Active-site cavity volume† (Å3) | 435 | 363 | 869 | 441 | 1063 |
| Main tunnel radius/length‡ (Å) | 1.7/8.0 | 0.7/15.4 | 1.5/10.8 | 1.3/9.8 | 1.9/9.1 |
| Slot tunnel radius/length‡ (Å) | 0.9/7.9 | 0.9/16 | 1.5/12.3 | 1.2/9.1 | 1.9/11.6 |
†
Active-site volumes were calculated with CASTp (Dundas et al., 2006 ▸) using a 1.4 Å radius probe; the calculation of cavity volumes with opening to the solvent is approximate and is dependent on the termination of the calculation at the protein surface.
‡
Average bottleneck radius and average tunnel length were determined using CAVER (Pavelka et al., 2016 ▸).