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

* Residue conservation analysis

PDB id:

2nnh

Name:

Oxidoreductase,electron transport

Title:

Cyp2c8dh complexed with 2 molecules of 9-cis retinoic acid

Structure:

Cytochrome p450 2c8. Chain: a, b. Synonym: cypiic8. P450 form 1. P450 mp-12/mp-20. P450 iic2. S- mephenytoin 4-hydroxylase. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: cyp2c8. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.60Å R-factor: 0.244 R-free: 0.290

Authors:

G.A.Schoch,J.K.Yano,C.D.Stout,E.F.Johnson

Key ref:

G.A.Schoch et al. (2008). Determinants of cytochrome P450 2C8 substrate binding: structures of complexes with montelukast, troglitazone, felodipine, and 9-cis-retinoic acid. J Biol Chem, 283, 17227-17237. PubMed id: 18413310 DOI: 10.1074/jbc.M802180200

Date:

24-Oct-06 Release date: 23-Oct-07

Protein chains

P10632  (CP2C8_HUMAN) -  Cytochrome P450 2C8 from Homo sapiens

Seq: 490 a.a.

Struc: 463 a.a.

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.M802180200

J Biol Chem 283:17227-17237 (2008)

PubMed id: 18413310

Determinants of cytochrome P450 2C8 substrate binding: structures of complexes with montelukast, troglitazone, felodipine, and 9-cis-retinoic acid.

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

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.

Selected figure(s)

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.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2008, 283, 17227-17237) copyright 2008.

Figures were selected by the author.