6PQS

The crystal structure of 4-methylbenzoate-bound CYP199A4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 

wwPDB Validation   3D Report Full Report

Currently 6PQS does not have a validation slider image.


This is version 1.2 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: https://doi.org/10.1016/j.jinorgbio.2019.110913
  • Primary Citation of Related Structures:  
    6PQ6, 6PQD, 6PQS, 6PQW, 6PRR, 6PRS

  • 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 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.


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
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
4MA Binding MOAD:  6PQS Kd: 660 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.161 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.22α = 90
b = 51.31β = 92.12
c = 78.94γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Currently 6PQS does not have a validation slider image.



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaDP140103229 and ANSTO Australian Synchrotron grant MXCAP13667/14238

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-27
    Type: Initial release
  • Version 1.1: 2019-12-04
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description