A preliminary 3D model for cytochrome P450 2D6 constructed by homology model building

Koymans, Lucien M. H.; Vermeulen, Nico; Baarslag, Allard; Kelder, Gabriëlle M. Donné-Op den

doi:10.1007/bf00125503

Cited by 62 publications

(55 citation statements)

References 28 publications

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“…As early as 1993, Koymans et al (12) published a preliminary model based on the crystal structure of P450 101. This model only contained the active site regions but was the first to implicate Asp-301 as a residue necessary for catalytic activity (12). Since then, numerous other models have appeared, based both on bacterial enzymes (10 -18) and more recently on the mammalian 2C5 isoform (19 -24).…”

Section: Resultsmentioning

confidence: 99%

Crystal Structure of Human Cytochrome P450 2D6

Rowland¹,

Blaney²,

Smyth

et al. 2006

Journal of Biological Chemistry

413

381

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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 3.0 Å 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, ␤ sheet 4, and part of ␤ 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. The cytochromes P4504 constitute a superfamily of heme-containing enzymes that catalyze the metabolism of a wide variety of endogenous and xenobiotic compounds. This is accomplished through the activation of molecular oxygen by the heme group, a process that involves the delivery of two electrons to the P450 system followed by cleavage of the dioxygen bond, yielding water and an activated iron-oxygen species (Compound 1), which reacts with substrates through a variety of mechanisms (1). In eukaryotic species, the electron source is a single flavoprotein, the FAD/FMN-containing cytochrome P450 reductase, which binds to the largely basic proximal face of the cytochrome through a number of salt bridges. Of the known human isoforms, cytochrome P450 2D6 is responsible for the metabolism of at least 20% of known drugs (2), with only 3A4 being responsible for a higher (50%) percentage.The cDNA encoding human P450 2D6 has been characterized (3) and subsequently localized to chromosome 22 in the q13.1 region (4). A relatively large number of genetic polymorphisms have been described for 2D6, some of which can either result in rapid or very poor metabolism. 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). It results in the defective metabolism of a number of important drug molecules, including debrisoquine, from which the condition got its name. The inability of patients to turn over compounds such as debrisoquine eventually leads to toxic levels of the drug in t...

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Section: Resultsmentioning

confidence: 99%

Crystal Structure of Human Cytochrome P450 2D6

Rowland¹,

Blaney²,

Smyth

et al. 2006

Journal of Biological Chemistry

413

381

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“…The Zimbabwean Shona population belongs to the Bantu people (black Africans populating the region phobic Ile. This change takes place in a region (b∞-helix) which is shown to be conserved in alignment studies from Cameroon to Central and Eastern Africa, and most of Southern Africa) who are genetically closely between CYP2D6 and CYP101 [25 ]. This amino acid change may therefore disturb the structure of CYP2D6.…”

Section: Primers For Amplificationmentioning

confidence: 99%

A novel mutant variant of the CYP2D6 gene (CYP2D617) common in a black African population: association with diminished debrisoquine hydroxylase activity

Masimirembwa

Persson

Bertilsson

et al. 1996

Brit J Clinical Pharma

175

112

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1The debrisoquine hydroxylase (CYP2D6) is polymorphically distributed. Not only are there differences in the proportions of extensive metabolisers to poor metabolisers in various ethnic groups, but there are also pronounced variations in the metabolic capacity among those classified as extensive metabolisers. 2The mean debrisoquine metabolic ratio of Caucasian extensive metabolisers is lower than that for a number of African populations. In the present study, we have searched for novel CYP2D6 mutations to explain the diminished enzyme activity in African populations. 3Three Zimbabwean Shona subjects with EM phenotypes (metabolic ratios for debrisoquine of 0.4, 1.5 and 10.5 respectively) were selected and the open reading frame of the CYP2D6 gene of each was sequenced. 4The subject with metabolic ratio of 10.5 was found to be homozygous for an allele with a nucleotide exchange in exon 2, 1111C→T causing a 107Thr→Ile amino acid exchange in a conserved region of the enzyme. In addition, he was homozygous for the 2938C→T and 4268G→C mutations causing 296Arg→Ser and 486Ser→Thr amino acid substitution found in the CYP2D6*2 allele. 5Seventy‐six Zimbabwean Shona subjects were subsequently genotyped for the 1111C→T mutation and for the intron 1 gene conversion present in the CYP2D6*2 gene. The 1111C→T mutation was found at an allele frequency of 34% and was only present in alleles carrying the gene conversion in intron 1 indicative for the CYP2D6*2 gene. 6This allele (CYP2D6*17), containing the 1111C→T, 2938C→T and 4268G→C mutations, was found to be strongly associated with lower capacity for debrisoquine hydroxylation. We therefore postulate that the CYP2D6*17 allele might contribute to the molecular basis of the previously established diminished debrisoquine hydroxylase activity in African Bantu populations.

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Section: Discussionmentioning

confidence: 99%

“…Numerous 3D models for CYP2D6 have been developed and are being continually refined (Koymans et al, 1993;Ellis et al, 1996;Modi et al, 1996;Lewis et al, 1997;deGroot et al, 1999). In the CYP2D6 models, small molecules such as amphetamine are believed to orient through interaction of the protonated amine with Asp301 in the CYP2D6 binding site (Koymans et al, 1993;Ellis et al, 1995;Lewis et al, 1997;deGroot et al, 1999). Additional common characteristics for many CYP2D6 compounds that bind or are substrates requires the presence of one basic nitrogen, a distance of 5 to 7 Å between the basic nitrogen and a potential site of oxidation and a flat hydrophobic area near the site of oxidation (Islam et al, 1991;Koymans et al, 1993;Strobl et al, 1993;deGroot et al, 1997).…”

Section: Discussionmentioning

confidence: 99%