PDBsum entry 2nnh

Oxidoreductase,electron transport

PDB id

2nnh

Contents

			Protein chain

					463 a.a.

			Ligands

					SO4 ×2


					HEM ×2


					9CR ×4


					PLM ×2

			Waters ×88

References listed in PDB file

Key reference

Title

Determinants of cytochrome p450 2c8 substrate binding: structures of complexes with montelukast, Troglitazone, Felodipine, And 9-Cis-Retinoic acid.

Authors

G.A.Schoch, J.K.Yano, S.Sansen, P.M.Dansette, C.D.Stout, E.F.Johnson.

Ref.

J Biol Chem, 2008, 283, 17227-17237. [DOI no: 10.1074/jbc.M802180200]

PubMed id

18413310

Abstract

Although a crystal structure and a pharmacophore model are available for cytochrome P450 2C8, the role of protein flexibility and specific ligand-protein interactions that govern substrate binding are poorly understood. X-ray crystal structures of P450 2C8 complexed with montelukast (2.8 A), troglitazone (2.7 A), felodipine (2.3 A), and 9-cis-retinoic acid (2.6 A) were determined to examine ligand-protein interactions for these chemically diverse compounds. Montelukast is a relatively large anionic inhibitor that exhibits a tripartite structure and complements the size and shape of the active-site cavity. The inhibitor troglitazone occupies the upper portion of the active-site cavity, leaving a substantial part of the cavity unoccupied. The smaller neutral felodipine molecule is sequestered with its dichlorophenyl group positioned close to the heme iron, and water molecules fill the distal portion of the cavity. The structure of the 9-cis-retinoic acid complex reveals that two substrate molecules bind simultaneously in the active site of P450 2C8. A second molecule of 9-cis-retinoic acid is located above the proximal molecule and can restrain the position of the latter for more efficient oxygenation. Solution binding studies do not discriminate between cooperative and noncooperative models for multiple substrate binding. The complexes with structurally distinct ligands further demonstrate the conformational adaptability of active site-constituting residues, especially Arg-241, that can reorient in the active-site cavity to stabilize a negatively charged functional group and define two spatially distinct binding sites for anionic moieties of substrates.



	Figure 2. FIGURE 2. Views of the ligand-binding site of P450 2C8 illustrating interactions of R-montelukast (A and B) or 2R,5R-troglitazone (C and D) with the protein. The heme prosthetic group is rendered as a red stick figure, with the central iron atom shown as a sphere. Portions of the secondary structure of the protein are rendered as a cyan ribbon, with side chains shown as stick figures with carbons colored cyan. In some cases, portions of the substrate-free structure (Protein Data Bank code 1pq2) are shown as a gray ribbon, with side chains shown as stick figures with carbons colored gray. The nitrogen, carbon, and oxygen atoms of the backbone are shown in some cases to illustrate hydrogen bonding interactions (black dashed lines). The distances between each ligand and the heme iron are indicated and identified by black dashed lines. Side chains making close contacts (<4 Å) are depicted and labeled if visible. The substrates are depicted as stick figures with carbon atoms colored orange. Other atoms are colored red for oxygen, blue for nitrogen, yellow for sulfur, and green for chlorine. The oxygen atoms of several water molecules that occupy the cavity are rendered as spheres.A gold mesh is used to render 2\|F[o]\| - \|F[c]\| [A]-weighted ligand omit maps contoured at 1 around the ligands. A black mesh is used to depict the solvent-accessible surface of the active-site cavity. The views differ between panels to clearly depict different features of the structures. The transparent solid surface in D illustrates the solvent-accessible surface of the volume that is left unoccupied upon troglitazone binding. The figures were rendered by ray tracing using PyMOL (DeLano Scientific, Palo Alto, CA).		Figure 3. FIGURE 3. Views of the ligand-binding site of P450 2C8 illustrating interactions of (R)-felodipine (A and B) or 9-cis-retinoic acid (C and D) with the protein. The proximal molecule of retinoic acid is designated as RA1, and the distal molecule is labeled as RA2. The atom color code is the same as described in the legend of Fig. 2.

PROCHECK

	Headers