Complex formation of Streptomyces griseolus CYP105A1 with statins by room-temperature crystal data collection
Teisuke Takita, Sachiyo Yoneda, Kaori Yasuda, Kimihiko Mizutani, Kiyoshi Yasukawa, Toshiyuki Sakaki and Bunzo Mikami [1]
Molecular Tour
The collection of room temperature data using the capillary method may prevent the release of statins from the active site of CYP105A1. The release of mevastatin and simvastatin from the frozen crystals occurred due to cell shrinkage, particularly along the c-axis. In the CYP105A1/MEV and Cyp105A1/SIM crystals collected at room temperature, the Pro142-Thr143 peptide located in the D-E loop is fixed in the cis conformation due to interactions with the side chain of Trp406. In the cryo-crystals of the CYP105A1/MEV and SIM complexes, Pro83, Thr184, and Asp185 in the symmetry 3 molecule approach and interact with Pro142 in the trans conformation. The conformational changes of Pro83, Thr184, and Asp185 influence the conformational changes of Val88 and Val181, which are critical for the binding of MEV and SIM. Thus, it is suggested that the release of MEV from the cryo-crystal is attributed to the shrinkage of the c-axis. In the cryo-crystals, the extent of shrinkage in the c-axis varies among different crystals. Table 4 illustrates the relationship between the length of the c-axis and the cis/trans conformation of the peptide between Pro142 and Thr143 for the CYP105A1 structures deposited in PDB to date. The length of the c-axis ranges from 138.80 to 142.52 Å in the cryo-crystals, in contrast to 141.08 to 144.69 Å in the room temperature crystals. Even among the cryo-crystals, those with a c-axis longer than 139.44 Å exhibit a cis-peptide conformation between Pro142 and Thr143, with the exception of PDB 3CV9, which has a trans peptide conformation with a c-axis of 140.61 Å.
This study clearly demonstrates that the freezing of protein crystals can sometimes lead to the release of ligands due to increased symmetry interactions resulting from cell shrinkage.
References
- ↑ Takita T, Yoneda S, Yasuda K, Mizutani K, Yasukawa K, Sakaki T, Mikami B. Room-temperature X-ray data collection enabled the structural determination of statin-bound CYP105A1. Acta Crystallogr D Struct Biol. 2025 Oct 1;81(Pt 10):573-583. PMID:40965121 doi:10.1107/S2059798325007673
