Crystal Structure of Human Cytochrome P450 2D6

Paul Rowland,Frank E Blaney,Martin G Smyth,Jo J Jones,Vaughan R Leydon,Amanda K Oxbrow,Ceri J Lewis,Mike G Tennant,Sandeep Modi,Drake S Eggleston,Richard J Chenery,Angela M Bridges

doi:10.1074/jbc.m511232200

Paul Rowland, Frank E Blaney + Show 10 more

Open Access

https://doi.org/10.1074/jbc.m511232200

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Abstract

Cytochrome P450 2D6 is a heme-containing enzyme that is responsible for the metabolism of at least 20% of known drugs. Substrates of 2D6 typically contain a basic nitrogen and a planar aromatic ring. The crystal structure of human 2D6 has been solved and refined to 3.0A resolution. The structure shows the characteristic P450 fold as seen in other members of the family, with the lengths and orientations of the individual secondary structural elements being very similar to those seen in 2C9. There are, however, several important differences, the most notable involving the F helix, the F-G loop, the B'helix, beta sheet 4, and part of beta sheet 1, all of which are situated on the distal face of the protein. The 2D6 structure has a well defined active site cavity above the heme group, containing many important residues that have been implicated in substrate recognition and binding, including Asp-301, Glu-216, Phe-483, and Phe-120. The crystal structure helps to explain how Asp-301, Glu-216, and Phe-483 can act as substrate binding residues and suggests that the role of Phe-120 is to control the orientation of the aromatic ring found in most substrates with respect to the heme. The structure has been compared with published homology models and has been used to explain much of the reported site-directed mutagenesis data and help understand the metabolism of several compounds.

Highlights

The cDNA encoding human P450 2D6 has been characterized [3] and subsequently localized to chromosome 22 in the q13.1 region [4]
Whereas 3A4 exhibits a wide diversity in its substrate recognition, a fact that is often attributed to its large cavity size [8], 2D6 generally only recognizes substrates containing a basic nitrogen and a planar aromatic ring
E. coli if the extreme N terminus containing the putative membranespanning region is replaced with different signal sequences, the OmpA signal sequence [53], or the sequence used to express P450 17␣ in E. coli [54]

Summary

Introduction

The cDNA encoding human P450 2D6 has been characterized [3] and subsequently localized to chromosome 22 in the q13.1 region [4]. One well characterized allelic variant is responsible for a condition known as debrisoquine/sparteine type polymorphism [5, 6] This arises as a result of various genetic mutations and affects a significant percentage of the Caucasian population [7]. The availability of a crystal structure of 2D6 was anticipated to go a long way toward explaining the effects of polymorphism and the results of SDM studies and toward answering some of the questions raised by in silico modeling work Such improved information would in time help achieve the ultimate goals of predicting the metabolic fate of drug compounds or predicting which compounds would inhibit the cytochromes and eventually lead to improved therapeutic ligand design. This new structure has already proved to be valuable in understanding the metabolism of several compounds and the effects of many SDM studies

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