4MGJ

Crystal structure of cytochrome P450 2B4 F429H in complex with 4-CPI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural and Functional Characterization of a Cytochrome P450 2B4 F429H Mutant with an Axial Thiolate-Histidine Hydrogen Bond.

Yang, Y.Zhang, H.Usharani, D.Bu, W.Im, S.Tarasev, M.Rwere, F.Pearl, N.M.Meagher, J.Sun, C.Stuckey, J.Shaik, S.Waskell, L.

(2014) Biochemistry 53: 5080-5091

  • DOI: 10.1021/bi5003794

  • PubMed Abstract: 
  • The structural basis of the regulation of microsomal cytochrome P450 (P450) activity was investigated by mutating the highly conserved heme binding motif residue, Phe429, on the proximal side of cytochrome P450 2B4 to a histidine. Spectroscopic, pre- ...

    The structural basis of the regulation of microsomal cytochrome P450 (P450) activity was investigated by mutating the highly conserved heme binding motif residue, Phe429, on the proximal side of cytochrome P450 2B4 to a histidine. Spectroscopic, pre-steady-state and steady-state kinetic, thermodynamic, theoretical, and structural studies of the mutant demonstrate that formation of an H-bond between His429 and the unbonded electron pair of the Cys436 axial thiolate significantly alters the properties of the enzyme. The mutant lost >90% of its activity; its redox potential was increased by 87 mV, and the half-life of the oxyferrous mutant was increased ∼37-fold. Single-crystal electronic absorption and resonance Raman spectroscopy demonstrated that the mutant was reduced by a small dose of X-ray photons. The structure revealed that the δN atom of His429 forms an H-bond with the axial Cys436 thiolate whereas the εN atom forms an H-bond with the solvent and the side chain of Gln357. The amide of Gly438 forms the only other H-bond to the tetrahedral thiolate. Theoretical quantification of the histidine-thiolate interaction demonstrates a significant electron withdrawing effect on the heme iron. Comparisons of structures of class I-IV P450s demonstrate that either a phenylalanine or tryptophan is often found at the location corresponding to Phe429. Depending on the structure of the distal pocket heme, the residue at this location may or may not regulate the thermodynamic properties of the P450. Regardless, this residue appears to protect the thiolate from solvent, oxidation, protonations, and other deleterious reactions.


    Organizational Affiliation

    Department of Anesthesiology, University of Michigan and VA Medical Center , 2215 Fuller Road, Building 31, Room 225, Ann Arbor, Michigan 48105, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome P450 2B4
A
476Oryctolagus cuniculusMutation(s): 2 
Gene Names: CYP2B4
EC: 1.14.14.1
Find proteins for P00178 (Oryctolagus cuniculus)
Go to UniProtKB:  P00178
Small Molecules
Ligands 2 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
CPZ
Query on CPZ

Download SDF File 
Download CCD File 
A
4-(4-CHLOROPHENYL)IMIDAZOLE
C9 H7 Cl N2
DVKIFCXVRCGAEE-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.219 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 91.490α = 90.00
b = 91.490β = 90.00
c = 150.380γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
ADSCdata collection
HKL-2000data scaling
PHASERphasing
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-08-13
    Type: Initial release
  • Version 1.1: 2014-09-24
    Type: Database references