9KGP | pdb_00009kgp

The structure of natural P450BM3-H derived from Bacillus megaterium for catalyzing the steroid DHEA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 
    0.227 (Depositor), 0.227 (DCC) 
  • R-Value Work: 
    0.221 (Depositor), 0.221 (DCC) 
  • R-Value Observed: 
    0.225 (Depositor) 

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This is version 1.1 of the entry. See complete history


Literature

Rationally designing P450BM3-H to excavate a novel channel for product exit and enhance overall performance.

Deng, Q.Lu, Z.M.Yuan, Z.Feng, Y.Zhang, L.Shi, J.Xu, Z.Kofas, M.A.G.Li, H.

(2025) Int J Biol Macromol 307: 142162-142162

  • DOI: https://doi.org/10.1016/j.ijbiomac.2025.142162
  • Primary Citation of Related Structures:  
    9KGP

  • PubMed Abstract: 

    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 (k cat /K m , 42.32-fold), electron transfer rate (k ET , 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.


  • Organizational Affiliation
    • School of Biotechnology, Jiangnan University, Wuxi, People's Republic of China. Electronic address: 7210201002@stu.jiangnan.edu.cn.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bifunctional cytochrome P450/NADPH--P450 reductase
A, B
455Priestia megaterium NBRC 15308 = ATCC 14581Mutation(s): 0 
Gene Names: cyp102A1cyp102BG04_163
EC: 1.14.14.1 (PDB Primary Data), 1.6.2.4 (PDB Primary Data)
UniProt
Find proteins for P14779 (Priestia megaterium (strain ATCC 14581 / DSM 32 / CCUG 1817 / JCM 2506 / NBRC 15308 / NCIMB 9376 / NCTC 10342 / NRRL B-14308 / VKM B-512 / Ford 19))
Explore P14779 
Go to UniProtKB:  P14779
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14779
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free:  0.227 (Depositor), 0.227 (DCC) 
  • R-Value Work:  0.221 (Depositor), 0.221 (DCC) 
  • R-Value Observed: 0.225 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.914α = 90
b = 145.713β = 97.513
c = 63.233γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China22078126

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-07
    Type: Initial release
  • Version 1.1: 2025-05-21
    Changes: Database references