4EJI

Human Cytochrome P450 2A13 in complex with two molecules of 4-(methylnitrosamino)-1-(3-puridyl)-1-butanone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Nicotine and 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone binding and access channel in human cytochrome P450 2A6 and 2A13 enzymes.

DeVore, N.M.Scott, E.E.

(2012) J.Biol.Chem. 287: 26576-26585

  • DOI: 10.1074/jbc.M112.372813
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cytochromes P450 (CYP) from the 2A subfamily are known for their roles in the metabolism of nicotine, the addictive agent in tobacco, and activation of the tobacco procarcinogen 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK). Although both the ...

    Cytochromes P450 (CYP) from the 2A subfamily are known for their roles in the metabolism of nicotine, the addictive agent in tobacco, and activation of the tobacco procarcinogen 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK). Although both the hepatic CYP2A6 and respiratory CYP2A13 enzymes metabolize these compounds, CYP2A13 does so with much higher catalytic efficiency, but the structural basis for this has been unclear. X-ray structures of nicotine complexes with CYP2A13 (2.5 Å) and CYP2A6 (2.3 Å) yield a structural rationale for the preferential binding of nicotine to CYP2A13. Additional structures of CYP2A13 with NNK reveal either a single NNK molecule in the active site with orientations corresponding to metabolites known to form DNA adducts and initiate lung cancer (2.35 Å) or with two molecules of NNK bound (2.1 Å): one in the active site and one in a more distal staging site. Finally, in contrast to prior CYP2A structures with enclosed active sites, CYP2A13 conformations were solved that adopt both open and intermediate conformations resulting from an ∼2.5 Å movement of the F to G helices. This channel occurs in the same region where the second, distal NNK molecule is bound, suggesting that the channel may be used for ligand entry and/or exit from the active site. Altogether these structures provide multiple new snapshots of CYP2A13 conformations that assist in understanding the binding and activation of an important human carcinogen, as well as critical comparisons in the binding of nicotine, one of the most widely used and highly addictive drugs in human use.


    Organizational Affiliation

    Department of Medicinal Chemistry, The University of Kansas, Lawrence, Kansas 66045, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytochrome P450 2A13
A
476Homo sapiensMutation(s): 0 
Gene Names: CYP2A13
EC: 1.14.14.1
Find proteins for Q16696 (Homo sapiens)
Go to Gene View: CYP2A13
Go to UniProtKB:  Q16696
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0QA
Query on 0QA

Download SDF File 
Download CCD File 
A
4-[methyl(nitroso)amino]-1-(pyridin-3-yl)butan-1-one
C10 H13 N3 O2
FLAQQSHRLBFIEZ-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 %)
0QAKd: 4400 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.201 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 122.807α = 90.00
b = 122.807β = 90.00
c = 194.213γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
SCALAdata scaling
MOSFLMdata reduction
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-06-06
    Type: Initial release
  • Version 1.1: 2013-01-02
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description