PDBsum entry 2bdm

Oxidoreductase

PDB id: 2bdm

Contents

Protein chain

465 a.a. *

Ligands

HEM-TMI

TMI ×2

CM5 ×4

Waters ×131

* Residue conservation analysis

PDB id:

2bdm

Name:

Oxidoreductase

Title:

Structure of cytochrome p450 2b4 with bound bifonazole

Structure:

Cytochrome p450 2b4. Chain: a. Fragment: residues 28-491. Synonym: cypiib4, p450-lm2, isozyme 2, p450 types b0 and b1. Engineered: yes

Source:

Oryctolagus cuniculus. Rabbit. Organism_taxid: 9986. Gene: cyp2b4. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

2.30Å R-factor: 0.196 R-free: 0.215

Authors:

Y.Zhao,M.A.White,B.K.Muralidhara,L.Sun,J.R.Halpert,C.D.Stout

Key ref:

Y.Zhao et al. (2006). 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. PubMed id: 16373351 DOI: 10.1074/jbc.M511464200

Date:

20-Oct-05 Release date: 27-Dec-05

Protein chain

P00178  (CP2B4_RABIT) -  Cytochrome P450 2B4 from Oryctolagus cuniculus

Seq: 491 a.a.

Struc: 465 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.1.14.14.1 - unspecific monooxygenase.
• Reaction: an organic molecule + reduced [NADPH--hemoprotein reductase] + O2 = an alcohol + oxidized [NADPH--hemoprotein reductase] + H2O + H⁺
• Cofactor: Heme-thiolate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1074/jbc.M511464200

J Biol Chem 281:5973-5981 (2006)

PubMed id: 16373351

Structure of microsomal cytochrome P450 2B4 complexed with the antifungal drug bifonazole: insight into P450 conformational plasticity and membrane interaction.

Y.Zhao, M.A.White, B.K.Muralidhara, L.Sun, J.R.Halpert, C.D.Stout.

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.

Selected figure(s)

Figure 1.
A, structure of ligand-free 2B4. B, structure of 2B4-CPI. The chemical formula of CPI is shown below the protein structure. C, structure of 2B4-bifonazole. The chemical formula of bifonazole is shown below the protein structure. The three structures are shown in the same orientation by aligning the most conserved tertiary structure (residues 61-98 and 306-465). Four regions around the active site (residues 100-140, 203-262, 276-290, and 474-479) are colored green in A, orange in B, and yellow in C, respectively, with the major helices labeled. Other parts of the protein are colored gray in all three structures. Heme, CPI, and bifonazole are shown as red, cyan, and forest green sticks, respectively. Images were generated using PyMol (www.pymol.org) unless otherwise credited.

Figure 2.
A, divergent stereo view of the 2B4-bifonazole monomer. Helices and strands are colored yellow and blue, respectively. The termini and major helices are labeled. Heme, bifonazole, and Cymal-5 molecules are shown as red, forest green, and cyan sticks, respectively. B, the dimer interface of 2B4-bifonazole is stabilized by interdigitating β-strands, and extra copies of detergent and substrate that associate with exposed hydrophobic regions. For clarity, only residues 98-117 and 204-230 are shown. Molecules A and B are colored yellow and gray, respectively. Heme is shown as red sticks. Bifonazole and Cymal-5 of molecule A are shown as forest green and cyan sticks, respectively. Bifonazole and Cymal-5 of molecule B are shown as green and pale cyan sticks, respectively. Helix F′ and β-strands 6-1, 7-1, 7-2, and 7-3 are labeled. The chemical formula of Cymal-5 is shown.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 5973-5981) copyright 2006.

Figures were selected by an automated process.