8ABS

Crystal structure of CYP109A2 from Bacillus megaterium bound with testosterone and putative ligand 4,6-dimethyloctanoic acid

Summary for 8ABS

• Entry DOI: 10.2210/pdb8abs/pdb
• Descriptor: Cytochrome P450, HEME B/C, (4~{S},6~{S})-4,6-dimethyloctanoic acid, ... (6 entities in total)
• Functional Keywords: cytochrome p450, testosterone, fatty acid, steroid, complex, oxidoreductase
• Biological source: Priestia megaterium DSM 319
• Total number of polymer chains: 1
• Total formula weight: 48641.96

Authors

Jozwik, I.K.,Rozeboom, H.J.,Thunnissen, A.-M.W.H. (deposition date: 2022-07-04, release date: 2023-07-12, Last modification date: 2024-02-07)

Primary citation

Jozwik, I.K.,Bombino, E.,Abdulmughni, A.,Hartz, P.,Rozeboom, H.J.,Wijma, H.J.,Kappl, R.,Janssen, D.B.,Bernhardt, R.,Thunnissen, A.W.H.
Regio- and stereoselective steroid hydroxylation by CYP109A2 from Bacillus megaterium explored by X-ray crystallography and computational modeling.
Febs J., 290:5016-5035, 2023

PubMed Abstract: The P450 monooxygenase CYP109A2 from Bacillus megaterium DSM319 was previously found to convert vitamin D3 (VD3) to 25-hydroxyvitamin D3. Here, we show that this enzyme is also able to convert testosterone in a highly regio- and stereoselective manner to 16β-hydroxytestosterone. To reveal the structural determinants governing the regio- and stereoselective steroid hydroxylation reactions catalyzed by CYP109A2, two crystal structures of CYP109A2 were solved in similar closed conformations, one revealing a bound testosterone in the active site pocket, albeit at a nonproductive site away from the heme-iron. To examine whether the closed crystal structures nevertheless correspond to a reactive conformation of CYP109A2, docking and molecular dynamics (MD) simulations were performed with testosterone and vitamin D3 (VD3) present in the active site. These MD simulations were analyzed for catalytically productive conformations, the relative occurrences of which were in agreement with the experimentally determined stereoselectivities if the predicted stability of each carbon-hydrogen bond was taken into account. Overall, the first-time determination and analysis of the catalytically relevant 3D conformation of CYP109A2 will allow for future small molecule ligand screening in silico, as well as enabling site-directed mutagenesis toward improved enzymatic properties of this enzyme.

PubMed: 37453052
DOI: 10.1111/febs.16906

Experimental method

X-RAY DIFFRACTION (1.75 Å)