9KGP image
Deposition Date 2024-11-08
Release Date 2025-05-07
Last Version Date 2025-05-21
Entry Detail
PDB ID:
9KGP
Keywords:
Title:
The structure of natural P450BM3-H derived from Bacillus megaterium for catalyzing the steroid DHEA
Biological Source:
Method Details:
Experimental Method:
Resolution:
1.52 Å
R-Value Free:
0.22
R-Value Work:
0.22
R-Value Observed:
0.22
Space Group:
P 1 21 1
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Bifunctional cytochrome P450/NADPH--P450 reductase
Gene (Uniprot):cyp102A1
Chain IDs:A, B
Chain Length:455
Number of Molecules:2
Biological Source:Priestia megaterium NBRC 15308 = ATCC 14581
Ligand Molecules
Primary Citation
Rationally designing P450BM3-H to excavate a novel channel for product exit and enhance overall performance.
Int.J.Biol.Macromol. 307 142162 142162 (2025)
PMID: 40107536 DOI: 10.1016/j.ijbiomac.2025.142162

Abstact

P450 dihydroxylase plays a crucial role in steroid drug synthesis by efficiently catalyzing two-step selective hydroxylation reactions. However, natural P450 dihydroxylases are scarce, with poor catalytic performance and intermediate accumulation limiting production. Here, we report a P450 dihydroxylase BM3-H that synthesizes 7α,15α-diOH-DHEA with 76 % selectivity. To enhance 7α,15α-diOH-DHEA synthesis, we engineered a novel exit channel for the intermediate by modifying key residues in the solvent channel. The triple mutant D182K/E143D/V178A exhibited significant improvements in product concentration (10.08-fold), enzymatic activity (2.16-fold), catalytic efficiency (kcat/Km, 42.32-fold), electron transfer rate (kET, 27.14-fold), and coupling efficiency (CE, 3.93-fold). Molecular dynamics simulations revealed that D182K/E143D/V178A created a novel exit channel for 7α-OH-DHEA, with channel length, polarity, and steric hindrance influencing enzyme performance. Our approach enhances the overall catalytic performance of P450BM3-H by excavating new intermediate product exit channels, providing theoretical guidance for the design of other enzyme molecules.

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Primary Citation of related structures