1PQ2

Crystal Structure of Human Drug Metabolizing Cytochrome P450 2C8

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.248 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Structure of human microsomal cytochrome P450 2C8. Evidence for a peripheral fatty acid binding site

Schoch, G.A., Yano, J.K., Wester, M.R., Griffin, K.J., Stout, C.D., Johnson, E.F.

(2004) J Biol Chem 279: 9497-9503

  • DOI: 10.1074/jbc.M312516200
  • Primary Citation of Related Structures:  
    1PQ2

  • PubMed Abstract: 

    • A 2.7-Angstrom molecular structure of human microsomal cytochrome P450 2C8 (CYP2C8) was determined by x-ray crystallography. The membrane protein was modified for crystallization by replacement of the hydrophobic N-terminal transmembrane domain with a short hydrophilic sequence before residue 28 ...

    A 2.7-Angstrom molecular structure of human microsomal cytochrome P450 2C8 (CYP2C8) was determined by x-ray crystallography. The membrane protein was modified for crystallization by replacement of the hydrophobic N-terminal transmembrane domain with a short hydrophilic sequence before residue 28. The structure of the native sequence is complete from residue 28 to the beginning of a C-terminal histidine tag used for purification. CYP2C8 is one of the principal hepatic drug-metabolizing enzymes that oxidizes therapeutic drugs such as taxol and cerivastatin and endobiotics such as retinoic acid and arachidonic acid. Consistent with the relatively large size of its preferred substrates, the active site volume is twice that observed for the structure of CYP2C5. The extended active site cavity is bounded by the beta1 sheet and helix F' that have not previously been implicated in substrate recognition by mammalian P450s. CYP2C8 crystallized as a symmetric dimer formed by the interaction of helices F, F', G', and G. Two molecules of palmitic acid are bound in the dimer interface. The dimer is observed in solution, and mass spectrometry confirmed the association of palmitic acid with the enzyme. This novel finding identifies a peripheral binding site in P450s that may contribute to drug-drug interactions in P450 metabolism.

    Organizational Affiliation: 

    Department of Molecular and Experimental Medicine.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome P450 2C8A, B476Homo sapiensMutation(s): 9 
Gene Names: CYP2C8
EC: 1.14.14.1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P10632 (Homo sapiens)
Explore P10632 
Go to UniProtKB:  P10632
PHAROS:  P10632
GTEx:  ENSG00000138115
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM
Download Ideal Coordinates CCD File 
 D [auth A], G [auth B]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L		 Ligand Interaction
PLM
Query on PLM
Download Ideal Coordinates CCD File 
 E [auth A], F [auth B]PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N		 Ligand Interaction
PO4
Query on PO4
Download Ideal Coordinates CCD File 
 C [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.248 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.988α = 90
b = 137.405β = 112.51
c = 97.322γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4data scaling
CNSphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-01-13
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance