TABLE 1.
Comparision of key amino acid residues in the catalytic domain of the ornithine cyclodeaminase PpOCD (1X7D) (Goodman et al., 2004), and the lysine cyclodeaminase PipASp (5QZJ) (Ying, 2016), as well as the models of PipAf, model of FkbL and the crystal structure of PipAf (this work).
| Enzyme | Pp OCD | LCD PipAsp | LCD PipA, (model) | LCD FkbL | LCD pipm (structure) |
|---|---|---|---|---|---|
| PDBentry | 1X7D | 5Q13 | none | none | this work |
| 13-barrel | Phe4 | Va15 | Leu5 | 11e5 | — |
| 13-barrel | Tyr66 | Trp64 | Pro63/His65 | Phe64 | Trp61/Pro63/Glu60/Met62 |
| 13-barrel | Phe68 | Leu76 | Leu73 | Met76 | Lys74 |
| 13-barrel | Tyr70 | Thr78 | Leu75 | Thr78 | Tyr78 |
| 13-barrel | Phe88 | Thr97 | Thr94 | Thr97 | 11e91/Tyr98 |
| 13-barrel | Tyr98 | Ala107 | His104 | Ser107 | — |
| 13-barrel | Pro99 | Leu108 | Leu105 | Leu108 | Arg118 |
| 13-barrel | Trp325 | His333 | Leu330 | Thr333 | — |
| substrate carboxyl group side chains | Arg45 | Arg49 | Pro44/Pro45 | Arg49 | Arg46/Phe49 |
| substrate carboxyl group side chains | Lys69 | Lys77 | Lys74 | Lys77 | — |
| substrate carboxyl group side chains | Arg112 | Arg121 | Arg118 | Arg121 | — |
| Ammonia leaving group side chains | Asp228 | A1a235 | Asp233 | Ala235 | As p233 |