8HGC | pdb_00008hgc

Crystal structure of the CYP199A4 mutant F182T in complex with 4-methoxybenzoic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 
    0.177 (Depositor), 0.179 (DCC) 
  • R-Value Work: 
    0.156 (Depositor), 0.158 (DCC) 
  • R-Value Observed: 
    0.158 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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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 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.

Macromolecule Content 

  • Total Structure Weight: 46.84 kDa 
  • Atom Count: 3,517 
  • Modeled Residue Count: 393 
  • Deposited Residue Count: 420 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome P450420Rhodopseudomonas palustris HaA2Mutation(s): 1 
Gene Names: RPB_3613
UniProt
Find proteins for Q2IU02 (Rhodopseudomonas palustris (strain HaA2))
Explore Q2IU02 
Go to UniProtKB:  Q2IU02
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2IU02
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 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
ANN
(Subject of Investigation/LOI)

Query on ANN



Download:Ideal Coordinates CCD File
C [auth A]4-METHOXYBENZOIC ACID
C8 H8 O3
ZEYHEAKUIGZSGI-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
G [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free:  0.177 (Depositor), 0.179 (DCC) 
  • R-Value Work:  0.156 (Depositor), 0.158 (DCC) 
  • R-Value Observed: 0.158 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.326α = 90
b = 51.672β = 92.55
c = 79.158γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata 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
  • Version 1.1: 2026-03-04
    Changes: Refinement description, Structure summary