8VL0 | pdb_00008vl0

The crystal structure of wild-type CYP199A4 bound to 4-(2-oxopropyl)benzoic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 
    0.222 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.183 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.185 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Selective alpha -Hydroxyketone Formation and Subsequent C-C Bond Cleavage by Cytochrome P450 Monooxygenase Enzymes.

Lee, J.H.Z.Coleman, T.Mclean, M.A.Podgorski, M.N.Hayball, E.F.Stone, I.S.J.Bruning, J.B.Whelan, F.Voss, J.J.Sligar, S.G.Bell, S.G.

(2024) ACS Catal 14: 8958-8971

  • DOI: https://doi.org/10.1021/acscatal.4c01766
  • Primary Citation of Related Structures:  
    8VKF, 8VL0

  • PubMed Abstract: 

    The heme enzymes of the cytochrome P450 superfamily (CYPs) catalyze oxidation reactions with a high level of selectivity. Here, the CYP199A4 enzyme from the bacterium Rhodopseudomonas palustris HaA2 is used to catalyze the hydroxylation of carbonyl-containing compounds to generate α -hydroxyketones. Both 4-propionyl- and 4-(2-oxopropyl)-benzoic acids were regioselectively hydroxylated by this enzyme to generate α -hydroxyketone metabolites, 4-(2-hydroxypropanoyl)benzoic acid and 4-(1-hydroxy-2-oxopropyl)benzoic acid, respectively, with high stereoselectivity. Co-crystallization of CYP199A4 with each substrate allowed high-resolution X-ray crystal structures of the enzyme bound with both to be determined. These provide a rationale for biochemical observations related to substrate binding and activity. As these versatile enzymes have a demonstrated ability to support carbon-carbon (C-C) bond cleavage (lyase) reactions on α -hydroxyketones, we assessed if this activity would be catalyzed by wild-type (WT) CYP199A4. Molecular dynamics (MD) simulations predicted the regioselective hydroxylation of each substrate but indicated that the WT enzyme would not be a good catalyst for lyase activity, in agreement with the experimental observations. The MD simulations also suggested the F182L mutant of CYP199A4 would permit closer approach of the substrate to the ferric-peroxo intermediate, enabling the formation of the lyase transition state. Indeed, this variant was observed to catalyze the cleavage reaction. Furthermore, the F182A variant of CYP199A4 was used to catalyze both the hydroxylation and C-C bond cleavage reactions with both 4-propionyl- and 4-(2-oxopropyl)-benzoic acids using hydrogen peroxide as the oxidant. This dual CYP activity is analogous to that supported by the mammalian CYP17A1 enzyme in steroid biosynthesis.


  • Organizational Affiliation
    • Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome P450410Rhodopseudomonas palustris HaA2Mutation(s): 0 
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free:  0.222 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.183 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.185 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.179α = 90
b = 51.407β = 92.01
c = 79.296γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)Australia--

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-08
    Type: Initial release
  • Version 1.1: 2024-07-31
    Changes: Database references
  • Version 1.2: 2025-02-19
    Changes: Database references, Structure summary