8HGT

Crystal structure of the CYP153A mutant V456A from Marinobacter aquaeolei


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 

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Literature

Enabling Peroxygenase Activity in Cytochrome P450 Monooxygenases by Engineering Hydrogen Peroxide Tunnels.

Zhao, P.Kong, F.Jiang, Y.Qin, X.Tian, X.Cong, Z.

(2023) J Am Chem Soc 145: 5506-5511

  • DOI: https://doi.org/10.1021/jacs.3c00195
  • Primary Citation of Related Structures:  
    8HGC, 8HGT

  • PubMed Abstract: 

    Given prominent physicochemical similarities between H 2 O 2 and water, we report a new strategy for promoting the peroxygenase activity of P450 enzymes by engineering their water tunnels to facilitate H 2 O 2 access to the heme center buried therein. Specifically, the H 2 O 2 -driven activities of two native NADH-dependent P450 enzymes (CYP199A4 and CYP153A M.aq ) increase significantly (by >183-fold and >15-fold, respectively). Additionally, the amount of H 2 O 2 required for an artificial P450 peroxygenase facilitated by a dual-functional small molecule to obtain the desired product is reduced by 95%-97.5% (with ∼95% coupling efficiency). Structural analysis suggests that mutating the residue at the bottleneck of the water tunnel may open a second pathway for H 2 O 2 to flow to the heme center (in addition to the natural substrate tunnel). This study highlights a promising, generalizable strategy whereby P450 monooxygenases can be modified to adopt peroxygenase activity through H 2 O 2 tunnel engineering, thus broadening the application scope of P450s in synthetic chemistry and synthetic biology.


  • Organizational Affiliation

    CAS Key Laboratory of Biofuels and Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome P450480Marinobacter nauticusMutation(s): 1 
Gene Names: DET51_1164
UniProt
Find proteins for A0A368UNN3 (Marinobacter nauticus)
Explore A0A368UNN3 
Go to UniProtKB:  A0A368UNN3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A368UNN3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.204 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.12α = 90
b = 103.312β = 112.49
c = 52.377γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data scaling
HKL-3000data reduction
PHENIXphasing
PDB_EXTRACTdata extraction

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)China21977104

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-16
    Type: Initial release