3IBD

Crystal structure of a cytochrome P450 2B6 genetic variant in complex with the inhibitor 4-(4-chlorophenyl)imidazole

Summary for 3IBD

• Entry DOI: 10.2210/pdb3ibd/pdb
• Descriptor: Cytochrome P450 2B6, PROTOPORPHYRIN IX CONTAINING FE, 4-(4-CHLOROPHENYL)IMIDAZOLE, ... (6 entities in total)
• Functional Keywords: p450, cytochrome p450 2b6, monooxygenase, oxidoreductase, membrane protein, cyp 2b6, endoplasmic reticulum, heme, iron, membrane, metal-binding, microsome, phosphoprotein, oxidoreductase-oxidoreductase inhibitor complex, oxidoreductase/oxidoreductase inhibitor
• Biological source: Homo sapiens (human)
• Cellular location: Endoplasmic reticulum membrane; Peripheral membrane protein: P20813
• Total number of polymer chains: 1
• Total formula weight: 56662.58

Authors

Gay, S.C.,Sun, L.,Talakad, J.C.,Shah, M.B.,Stout, D.C.,Halpert, J.R. (deposition date: 2009-07-15, release date: 2010-01-19, Last modification date: 2023-09-06)

Primary citation

Gay, S.C.,Shah, M.B.,Talakad, J.C.,Maekawa, K.,Roberts, A.G.,Wilderman, P.R.,Sun, L.,Yang, J.Y.,Huelga, S.C.,Hong, W.X.,Zhang, Q.,Stout, C.D.,Halpert, J.R.
Crystal structure of a cytochrome P450 2B6 genetic variant in complex with the inhibitor 4-(4-chlorophenyl)imidazole at 2.0-A resolution.
Mol.Pharmacol., 77:529-538, 2010

PubMed Abstract: The structure of the K262R genetic variant of human cytochrome P450 2B6 in complex with the inhibitor 4-(4-chlorophenyl)imidazole (4-CPI) has been determined using X-ray crystallography to 2.0-A resolution. Production of diffraction quality crystals was enabled through a combination of protein engineering, chaperone coexpression, modifications to the purification protocol, and the use of unique facial amphiphiles during crystallization. The 2B6-4-CPI complex is virtually identical to the rabbit 2B4 structure bound to the same inhibitor with respect to the arrangement of secondary structural elements and the placement of active site residues. The structure supports prior P450 2B6 homology models based on other mammalian cytochromes P450 and is consistent with the limited site-directed mutagenesis studies on 2B6 and extensive studies on P450 2B4 and 2B1. Although the K262R genetic variant shows unaltered binding of 4-CPI, altered binding affinity, kinetics, and/or product profiles have been previously shown with several other ligands. On the basis of new P450 2B6 crystal structure and previous 2B4 structures, substitutions at residue 262 affect a hydrogen-bonding network connecting the G and H helices, where subtle differences could be transduced to the active site. Docking experiments indicate that the closed protein conformation allows smaller ligands such as ticlopidine to bind to the 2B6 active site in the expected orientation. However, it is unknown whether 2B6 undergoes structural reorganization to accommodate bulkier molecules, as previously inferred from multiple P450 2B4 crystal structures.

PubMed: 20061448
DOI: 10.1124/mol.109.062570

Experimental method

X-RAY DIFFRACTION (2 Å)