6H1T

Structure of the BM3 heme domain in complex with clotrimazole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Novel insights into P450 BM3 interactions with FDA-approved antifungal azole drugs.

Jeffreys, L.N.Poddar, H.Golovanova, M.Levy, C.W.Girvan, H.M.McLean, K.J.Voice, M.W.Leys, D.Munro, A.W.

(2019) Sci Rep 9: 1577-1577

  • DOI: 10.1038/s41598-018-37330-y
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Flavocytochrome P450 BM3 is a natural fusion protein constructed of cytochrome P450 and NADPH-cytochrome P450 reductase domains. P450 BM3 binds and oxidizes several mid- to long-chain fatty acids, typically hydroxylating these lipids at the ω-1, ω-2 ...

    Flavocytochrome P450 BM3 is a natural fusion protein constructed of cytochrome P450 and NADPH-cytochrome P450 reductase domains. P450 BM3 binds and oxidizes several mid- to long-chain fatty acids, typically hydroxylating these lipids at the ω-1, ω-2 and ω-3 positions. However, protein engineering has led to variants of this enzyme that are able to bind and oxidize diverse compounds, including steroids, terpenes and various human drugs. The wild-type P450 BM3 enzyme binds inefficiently to many azole antifungal drugs. However, we show that the BM3 A82F/F87V double mutant (DM) variant binds substantially tighter to numerous azole drugs than does the wild-type BM3, and that their binding occurs with more extensive heme spectral shifts indicative of complete binding of several azoles to the BM3 DM heme iron. We report here the first crystal structures of P450 BM3 bound to azole antifungal drugs - with the BM3 DM heme domain bound to the imidazole drugs clotrimazole and tioconazole, and to the triazole drugs fluconazole and voriconazole. This is the first report of any protein structure bound to the azole drug tioconazole, as well as the first example of voriconazole heme iron ligation through a pyrimidine nitrogen from its 5-fluoropyrimidine ring.


    Organizational Affiliation

    Centre for Synthetic Biology of Fine and Specialty Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bifunctional cytochrome P450/NADPH--P450 reductase
A, B, C, D
458Bacillus megateriumMutation(s): 2 
Find proteins for A0A1Q8UP87 (Bacillus megaterium)
Go to UniProtKB:  A0A1Q8UP87
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MPO
Query on MPO

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B, D
3[N-MORPHOLINO]PROPANE SULFONIC ACID
C7 H15 N O4 S
DVLFYONBTKHTER-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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A, B, C, D
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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Download CCD File 
A, B, C, D
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
PGE
Query on PGE

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Download CCD File 
B, C
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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D
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
CL6
Query on CL6

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Download CCD File 
A, B, C, D
1-[(2-CHLOROPHENYL)(DIPHENYL)METHYL]-1H-IMIDAZOLE
CLOTRIMAZOLE
C22 H17 Cl N2
VNFPBHJOKIVQEB-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

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Download CCD File 
A, B, C, D
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.167 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 79.408α = 90.00
b = 70.747β = 95.31
c = 209.644γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
PHASERphasing
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/K001884/1

Revision History 

  • Version 1.0: 2019-02-20
    Type: Initial release