3MVR

Crystal Structure of cytochrome P450 2B4-H226Y in a closed conformation

Summary for 3MVR

• Entry DOI: 10.2210/pdb3mvr/pdb
• Related: 1PO5 1SUO 2BDM 2Q6N 3G5N
• Descriptor: Cytochrome P450 2B4, PROTOPORPHYRIN IX CONTAINING FE, 5-CYCLOHEXYL-1-PENTYL-BETA-D-MALTOSIDE, ... (4 entities in total)
• Functional Keywords: ligand free closed conformation, p450, cytochrome p450 2b4, monooxygenase, oxidoreductase, membrane protein, cyp 2b4.
• Biological source: Oryctolagus cuniculus (rabbit)
• Cellular location: Endoplasmic reticulum membrane; Peripheral membrane protein: P00178
• Total number of polymer chains: 2
• Total formula weight: 111549.43

Authors

Shah, M.B.,Stout, C.D.,Halpert, J.R. (deposition date: 2010-05-04, release date: 2010-09-29, Last modification date: 2023-09-06)

Primary citation

Wilderman, P.R.,Shah, M.B.,Liu, T.,Li, S.,Hsu, S.,Roberts, A.G.,Goodlett, D.R.,Zhang, Q.,Woods, V.L.,Stout, C.D.,Halpert, J.R.
Plasticity of Cytochrome P450 2B4 as Investigated by Hydrogen-Deuterium Exchange Mass Spectrometry and X-ray Crystallography.
J.Biol.Chem., 285:38602-38611, 2010

PubMed Abstract: Crystal structures of the xenobiotic metabolizing cytochrome P450 2B4 have demonstrated markedly different conformations in the presence of imidazole inhibitors or in the absence of ligand. However, knowledge of the plasticity of the enzyme in solution has remained scant. Thus, hydrogen-deuterium exchange mass spectrometry (DXMS) was utilized to probe the conformations of ligand-free P450 2B4 and the complex with 4-(4-chlorophenyl)imidazole (4-CPI) or 1-biphenyl-4-methyl-1H-imidazole (1-PBI). The results of DXMS indicate that the binding of 4-CPI slowed the hydrogen-deuterium exchange rate over the B'- and C-helices and portions of the F-G-helix cassette compared with P450 2B4 in the absence of ligands. In contrast, there was little difference between the ligand-free and 1-PBI-bound exchange sets. In addition, DXMS suggests that the ligand-free P450 2B4 is predominantly open in solution. Interestingly, a new high resolution structure of ligand-free P450 2B4 was obtained in a closed conformation very similar to the 4-CPI complex. Molecular dynamics simulations performed with the closed ligand-free structure as the starting point were used to probe the energetically accessible conformations of P450 2B4. The simulations were found to equilibrate to a conformation resembling the 1-PBI-bound P450 2B4 crystal structure. The results indicate that conformational changes observed in available crystal structures of the promiscuous xenobiotic metabolizing cytochrome P450 2B4 are consistent with its solution structural behavior.

PubMed: 20880847
DOI: 10.1074/jbc.M110.180646

Experimental method

X-RAY DIFFRACTION (1.76 Å)