2BDM

Structure of Cytochrome P450 2B4 with Bound Bifonazole

Summary for 2BDM

• Entry DOI: 10.2210/pdb2bdm/pdb
• Related: 1PO5 1SUO
• Descriptor: Cytochrome P450 2B4, PROTOPORPHYRIN IX CONTAINING FE, 1-[PHENYL-(4-PHENYLPHENYL)-METHYL]IMIDAZOLE, ... (5 entities in total)
• Functional Keywords: p450, monooxygenase, oxidoreductase, membrane protein, cyp 2b4, cyp lm2
• Biological source: Oryctolagus cuniculus (rabbit)
• Cellular location: Endoplasmic reticulum membrane; Peripheral membrane protein: P00178
• Total number of polymer chains: 1
• Total formula weight: 57695.04

Authors

Zhao, Y.,White, M.A.,Muralidhara, B.K.,Sun, L.,Halpert, J.R.,Stout, C.D. (deposition date: 2005-10-20, release date: 2005-12-27, Last modification date: 2023-08-23)

Primary citation

Zhao, Y.,White, M.A.,Muralidhara, B.K.,Sun, L.,Halpert, J.R.,Stout, C.D.
Structure of microsomal cytochrome P450 2B4 complexed with the antifungal drug bifonazole: insight into P450 conformational plasticity and membrane interaction.
J.Biol.Chem., 281:5973-5981, 2006

PubMed Abstract: To better understand ligand-induced structural transitions in cytochrome P450 2B4, protein-ligand interactions were investigated using a bulky inhibitor. Bifonazole, a broad spectrum antifungal agent, inhibits monooxygenase activity and induces a type II binding spectrum in 2B4dH(H226Y), a modified enzyme previously crystallized in the presence of 4-(4-chlorophenyl)imidazole (CPI). Isothermal titration calorimetry and tryptophan fluorescence quenching indicate no significant burial of protein apolar surface nor altered accessibility of Trp-121 upon bifonazole binding, in contrast to recent results with CPI. A 2.3 A crystal structure of 2B4-bifonazole reveals a novel open conformation with ligand bound in the active site, which is significantly different from either the U-shaped cleft of ligand-free 2B4 or the small active site pocket of 2B4-CPI. The O-shaped active site cleft of 2B4-bifonazole is widely open in the middle but narrow at the top. A bifonazole molecule occupies the bottom of the active site cleft, where helix I is bent approximately 15 degrees to accommodate the bulky ligand. The structure also defines unanticipated interactions between helix C residues and bifonazole, suggesting an important role of helix C in azole recognition by mammalian P450s. Comparison of the ligand-free 2B4 structure, the 2B4-CPI structure, and the 2B4-bifonazole structure identifies structurally plastic regions that undergo correlated conformational changes in response to ligand binding. The most plastic regions are putative membrane-binding motifs involved in substrate access or substrate binding. The results allow us to model the membrane-associated state of P450 and provide insight into how lipophilic substrates access the buried active site.

PubMed: 16373351
DOI: 10.1074/jbc.M511464200

Experimental method

X-RAY DIFFRACTION (2.3 Å)