6PRR

The crystal structure of 3-methylaminobenzoate-bound CYP199A4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.146 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Investigation of the requirements for efficient and selective cytochrome P450 monooxygenase catalysis across different reactions.

Podgorski, M.N.Coleman, T.Chao, R.R.De Voss, J.J.Bruning, J.B.Bell, S.G.

(2019) J.Inorg.Biochem. 203: 110913-110913

  • DOI: 10.1016/j.jinorgbio.2019.110913
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The cytochrome P450 metalloenzyme (CYP) CYP199A4 from Rhodopseudomonas palustris HaA2 catalyzes the highly efficient oxidation of para-substituted benzoic acids. Here we determined crystal structures of CYP199A4, and the binding and turnover paramete ...

    The cytochrome P450 metalloenzyme (CYP) CYP199A4 from Rhodopseudomonas palustris HaA2 catalyzes the highly efficient oxidation of para-substituted benzoic acids. Here we determined crystal structures of CYP199A4, and the binding and turnover parameters, with different meta-substituted benzoic acids in order to establish which criteria are important for efficient catalysis. When compared to the para isomers, the meta-substituted benzoic acids were less efficiently oxidized. For example, 3-formylbenzoic acid was oxidized with lower activity than the equivalent para isomer and 3-methoxybenzoic acid did not undergo O-demethylation by CYP199A4. The structural data highlighted that the meta-substituted benzoic acids bound in the enzyme active site in a modified position with incomplete loss of the distal water ligand of the heme moiety. However, for both sets of isomers the meta- or para-substituent pointed towards, and was in close proximity, to the heme iron. The absence of oxidation activity with 3-methoxybenzoic acid was assigned to the observation that the CH bonds of this molecule point away from the heme iron. In contrast, in the para isomer they are in an ideal location for abstraction. These findings were confirmed by using the bulkier 3-ethoxybenzoic acid as a substrate which removed the water ligand and reoriented the meta-substituent so that the methylene hydrogens pointed towards the heme, enabling more efficient oxidation. Overall we show relatively small changes in substrate structure and position in the active site can have a dramatic effect on the activity.


    Organizational Affiliation

    Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia.,School of Chemistry and Molecular Bioscience, University of Queensland, St Lucia, Qld 4072, Australia.,School of Biological Sciences, University of Adelaide, SA 5005, Australia.,Department of Chemistry, University of Adelaide, Adelaide, SA 5005, Australia. Electronic address: stephen.bell@adelaide.edu.au.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome P450
A
410Rhodopseudomonas palustris (strain HaA2)Mutation(s): 0 
Find proteins for Q2IU02 (Rhodopseudomonas palustris (strain HaA2))
Go to UniProtKB:  Q2IU02
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
OW4
Query on OW4

Download SDF File 
Download CCD File 
A
3-(methylamino)benzoic acid
C8 H9 N O2
ZCCNWBPFIBQFQX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.146 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 44.354α = 90.00
b = 51.430β = 92.13
c = 79.460γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaDP140103229 and ANSTO Australian Synchrotron Collaborative Access Program (CAP) grant MXCAP12393/13630

Revision History 

  • Version 1.0: 2019-11-27
    Type: Initial release
  • Version 1.1: 2019-12-04
    Type: Database references