2P85

Structure of Human Lung Cytochrome P450 2A13 with indole bound in two alternate conformations


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the human lung cytochrome P450 2A13.

Smith, B.D.Sanders, J.L.Porubsky, P.R.Lushington, G.H.Stout, C.D.Scott, E.E.

(2007) J Biol Chem 282: 17306-17313

  • DOI: 10.1074/jbc.M702361200
  • Primary Citation of Related Structures:  
    2P85

  • PubMed Abstract: 
  • The human lung cytochrome P450 2A13 (CYP2A13) activates the nicotine-derived procarcinogen 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) into DNA-altering compounds that cause lung cancer. Another cytochrome P450, CYP2A6, is also present in human lung, but at much lower levels ...

    The human lung cytochrome P450 2A13 (CYP2A13) activates the nicotine-derived procarcinogen 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) into DNA-altering compounds that cause lung cancer. Another cytochrome P450, CYP2A6, is also present in human lung, but at much lower levels. Although these two enzymes are 93.5% identical, CYP2A13 metabolizes NNK with much lower K(m) values than does CYP2A6. To investigate the structural differences between these two enzymes the structure of CYP2A13 was determined to 2.35A by x-ray crystallography and compared with structures of CYP2A6. As expected, the overall CYP2A13 and CYP2A6 structures are very similar with an average root mean square deviation of 0.5A for the Calpha atoms. Like CYP2A6, the CYP2A13 active site cavity is small and highly hydrophobic with a cluster of Phe residues composing the active site roof. Active site residue Asn(297) is positioned to hydrogen bond with an adventitious ligand, identified as indole. Amino acid differences between CYP2A6 and CYP2A13 at positions 117, 300, 301, and 208 relate to different orientations of the ligand plane in the two protein structures and may underlie the significant variations observed in binding and catalysis of many CYP2A ligands. In addition, docking studies suggest that residues 365 and 366 may also contribute to differences in NNK metabolism.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome P450 2A13A, B, C, D, E, F476Homo sapiensMutation(s): 7 
Gene Names: CYP2A13
EC: 1.14.14.1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q16696 (Homo sapiens)
Explore Q16696 
Go to UniProtKB:  Q16696
PHAROS:  Q16696
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
G [auth A], J [auth B], M [auth C], P [auth D], S [auth E], V [auth F]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
IND
Query on IND

Download Ideal Coordinates CCD File 
H [auth A] , I [auth A] , K [auth B] , L [auth B] , N [auth C] , O [auth C] , Q [auth D] , R [auth D] , 
H [auth A],  I [auth A],  K [auth B],  L [auth B],  N [auth C],  O [auth C],  Q [auth D],  R [auth D],  T [auth E],  U [auth E],  W [auth F],  X [auth F]
INDOLE
C8 H7 N
SIKJAQJRHWYJAI-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.219 
  • Space Group: P 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.32α = 90
b = 110.28β = 110.28
c = 142γ = 90
Software Package:
Software NamePurpose
CNSrefinement
Blu-Icedata collection
MOSFLMdata reduction
CCP4data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-04-10
    Type: Initial release
  • Version 1.1: 2007-10-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance