4ZF8

Cytochrome P450 pentamutant from BM3 with bound Metyrapone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.766 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Effect of Mutation and Substrate Binding on the Stability of Cytochrome P450BM3 Variants.

Geronimo, I.Denning, C.A.Rogers, W.E.Othman, T.Huxford, T.Heidary, D.K.Glazer, E.C.Payne, C.M.

(2016) Biochemistry 55: 3594-3606

  • DOI: 10.1021/acs.biochem.6b00183
  • Primary Citation of Related Structures:  4ZF6, 4ZFA, 4ZFB

  • PubMed Abstract: 
  • Cytochrome P450BM3 is a heme-containing enzyme from Bacillus megaterium that exhibits high monooxygenase activity and has a self-sufficient electron transfer system in the full-length enzyme. Its potential synthetic applications drive protein enginee ...

    Cytochrome P450BM3 is a heme-containing enzyme from Bacillus megaterium that exhibits high monooxygenase activity and has a self-sufficient electron transfer system in the full-length enzyme. Its potential synthetic applications drive protein engineering efforts to produce variants capable of oxidizing nonnative substrates such as pharmaceuticals and aromatic pollutants. However, promiscuous P450BM3 mutants often exhibit lower stability, thereby hindering their industrial application. This study demonstrated that the heme domain R47L/F87V/L188Q/E267V/F81I pentuple mutant (PM) is destabilized because of the disruption of hydrophobic contacts and salt bridge interactions. This was directly observed from crystal structures of PM in the presence and absence of ligands (palmitic acid and metyrapone). The instability of the tertiary structure and heme environment of substrate-free PM was confirmed by pulse proteolysis and circular dichroism, respectively. Binding of the inhibitor, metyrapone, significantly stabilized PM, but the presence of the native substrate, palmitic acid, had no effect. On the basis of high-temperature molecular dynamics simulations, the lid domain, β-sheet 1, and Cys ligand loop (a β-bulge segment connected to the heme) are the most labile regions and, thus, potential sites for stabilizing mutations. Possible approaches to stabilization include improvement of hydrophobic packing interactions in the lid domain and introduction of new salt bridges into β-sheet 1 and the heme region. An understanding of the molecular factors behind the loss of stability of P450BM3 variants therefore expedites site-directed mutagenesis studies aimed at developing thermostability.


    Organizational Affiliation

    Department of Chemical and Materials Engineering, University of Kentucky , Lexington, Kentucky 40506-0046, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bifunctional P-450/NADPH-P450 reductase
A
468Bacillus megateriumGene Names: cyp102A1 (cyp102)
EC: 1.14.14.1, 1.6.2.4
Find proteins for P14779 (Bacillus megaterium)
Go to UniProtKB:  P14779
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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
MYT
Query on MYT

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Download CCD File 
A
METYRAPONE
C14 H14 N2 O
FJLBFSROUSIWMA-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

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Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.766 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.215 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 55.899α = 90.00
b = 55.899β = 90.00
c = 711.033γ = 120.00
Software Package:
Software NamePurpose
XDSdata scaling
PHENIXrefinement
Cootmodel building
PHENIXphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-07-13
    Type: Initial release