2HI4

Crystal Structure of Human Microsomal P450 1A2 in complex with alpha-naphthoflavone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Adaptations for the oxidation of polycyclic aromatic hydrocarbons exhibited by the structure of human P450 1A2.

Sansen, S.Yano, J.K.Reynald, R.L.Schoch, G.A.Griffin, K.J.Stout, C.D.Johnson, E.F.

(2007) J.Biol.Chem. 282: 14348-14355

  • DOI: 10.1074/jbc.M611692200

  • PubMed Abstract: 
  • Microsomal cytochrome P450 family 1 enzymes play prominent roles in xenobiotic detoxication and procarcinogen activation. P450 1A2 is the principal cytochrome P450 family 1 enzyme expressed in human liver and participates extensively in drug oxidatio ...

    Microsomal cytochrome P450 family 1 enzymes play prominent roles in xenobiotic detoxication and procarcinogen activation. P450 1A2 is the principal cytochrome P450 family 1 enzyme expressed in human liver and participates extensively in drug oxidations. This enzyme is also of great importance in the bioactivation of mutagens, including the N-hydroxylation of arylamines. P450-catalyzed reactions involve a wide range of substrates, and this versatility is reflected in a structural diversity evident in the active sites of available P450 structures. Here, we present the structure of human P450 1A2 in complex with the inhibitor alpha-naphthoflavone, determined to a resolution of 1.95 A. alpha-Naphthoflavone is bound in the active site above the distal surface of the heme prosthetic group. The structure reveals a compact, closed active site cavity that is highly adapted for the positioning and oxidation of relatively large, planar substrates. This unique topology is clearly distinct from known active site architectures of P450 family 2 and 3 enzymes and demonstrates how P450 family 1 enzymes have evolved to catalyze efficiently polycyclic aromatic hydrocarbon oxidation. This report provides the first structure of a microsomal P450 from family 1 and offers a template to study further structure-function relationships of alternative substrates and other cytochrome P450 family 1 members.


    Organizational Affiliation

    Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome P450 1A2
A
495Homo sapiensMutation(s): 0 
Gene Names: CYP1A2
EC: 1.14.14.1
Find proteins for P05177 (Homo sapiens)
Go to Gene View: CYP1A2
Go to UniProtKB:  P05177
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BHF
Query on BHF

Download SDF File 
Download CCD File 
A
2-PHENYL-4H-BENZO[H]CHROMEN-4-ONE
7,8-BENZOFLAVONE; ALPHA-NAPHTHOFLAVONE
C19 H12 O2
VFMMPHCGEFXGIP-UHFFFAOYSA-N
 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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BHFKi: 20 nM (100) BINDINGDB
BHFIC50: 3.8 - 32600 nM (100) BINDINGDB
BHFKi: 25 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.226 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 79.630α = 90.00
b = 80.820β = 90.00
c = 175.820γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
MOSFLMdata reduction
PDB_EXTRACTdata extraction
CCP4data scaling
SCALAdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-02-20
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description