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Utility of a Phylogenetic Perspective in Structural Analysis of CYP72A Enzymes from Flowering Plants

View Article: PubMed Central - PubMed

ABSTRACT

Plant adaptation to external pressures depends on functional diversity in cytochrome P450 (CYP) enzymes. CYPs contain structural domains necessary for the characteristic P450 fold that allows monooxygenation, but they also have great variation in substrate binding affinity. Plant genomes typically contain hundreds of CYPs that contribute to essential functions and species-specific metabolism. The CYP72A subfamily is conserved in angiosperms but its contribution to physiological functions is largely unknown. With genomic information available for many plants, a focused analysis of CYP subfamily diversity is important to understand the contributions of these enzymes to plant evolution. This study examines the extent to which independent gene duplication and evolution have contributed to structural diversification of CYP72A enzymes in different plant lineages. CYP72A genes are prevalent across angiosperms, but the number of genes within each genome varies greatly. The prevalence of CYP72As suggest that the last common ancestor of flowering plants contained a CYP72A sequence, but gene duplication and retention has varied greatly for this CYP subfamily. Sequence comparisons show that CYP72As are involved in species-specific metabolic functions in some plants while there is likely functional conservation between closely related species. Analysis of structural and functional domains within groups of CYP72As reveals clade-specific residues that contribute to functional constraints within subsets of CYP72As. This study provides a phylogenetic framework that allows comparisons of structural features within subsets of the CYP72A subfamily. We examined a large number of sequences from a broad collection of plant species to detect patterns of functional conservation across the subfamily. The evolutionary relationships between CYPs in plant genomes are an important component in understanding the evolution of biochemical diversity in plants.

No MeSH data available.


Homology model of CYP72A13 with the predicted substrate binding region highlighted with spheres above the heme cofactor.(A) Cartoon structure model showing typical CYP helices folded around the heme and an internal binding pocket. (B) Oxygen activation domain. (C) PERF domain. (D) SRS1. (E) SRS5.
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pone.0163024.g008: Homology model of CYP72A13 with the predicted substrate binding region highlighted with spheres above the heme cofactor.(A) Cartoon structure model showing typical CYP helices folded around the heme and an internal binding pocket. (B) Oxygen activation domain. (C) PERF domain. (D) SRS1. (E) SRS5.

Mentions: Since primary sequence alone cannot reveal the extent to which an amino acid difference will impact function, it was important to visualize the position of each amino acid within the folded structure of the protein. There is no crystal structure available for a CYP72A enzyme, so homology modeling was used to predict the structure of CYP72A13 from Arabidopsis thaliana. CYP72A13 was chosen from the model plant, Arabidopsis, to aid in functional analysis of the subfamily in the Brassicales clade. CYP72A13 is similar to other subfamily members in Arabidopsis thaliana and it is orthologous to CYP72A485 from Capsella rubella. The CYP72A13 structure was modeled from the crystal structure of human CYP3A4, which was 24.6% identical (Fig 8A). The structural coordinates for the CYP72A13 model for viewing in a PDB viewer are provided in S7 Fig. This model had a template modeling score of 0.72 and an RMSD of 7.29Å, indicating a good global folding to the template [25]. Small spheres were placed in the predicted binding pocket to highlight the substrate binding region above the heme cofactor. Amino acid positions identified in Table 2 were located in the CYP72A13 sequence for assessing the impact of the property changes on the function of the encoded enzyme. Amino acid numbering in Fig 8 is consistent with the consensus sequence used to number the amino acids in Figs 6 and 7.


Utility of a Phylogenetic Perspective in Structural Analysis of CYP72A Enzymes from Flowering Plants
Homology model of CYP72A13 with the predicted substrate binding region highlighted with spheres above the heme cofactor.(A) Cartoon structure model showing typical CYP helices folded around the heme and an internal binding pocket. (B) Oxygen activation domain. (C) PERF domain. (D) SRS1. (E) SRS5.
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Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC5036807&req=5

pone.0163024.g008: Homology model of CYP72A13 with the predicted substrate binding region highlighted with spheres above the heme cofactor.(A) Cartoon structure model showing typical CYP helices folded around the heme and an internal binding pocket. (B) Oxygen activation domain. (C) PERF domain. (D) SRS1. (E) SRS5.
Mentions: Since primary sequence alone cannot reveal the extent to which an amino acid difference will impact function, it was important to visualize the position of each amino acid within the folded structure of the protein. There is no crystal structure available for a CYP72A enzyme, so homology modeling was used to predict the structure of CYP72A13 from Arabidopsis thaliana. CYP72A13 was chosen from the model plant, Arabidopsis, to aid in functional analysis of the subfamily in the Brassicales clade. CYP72A13 is similar to other subfamily members in Arabidopsis thaliana and it is orthologous to CYP72A485 from Capsella rubella. The CYP72A13 structure was modeled from the crystal structure of human CYP3A4, which was 24.6% identical (Fig 8A). The structural coordinates for the CYP72A13 model for viewing in a PDB viewer are provided in S7 Fig. This model had a template modeling score of 0.72 and an RMSD of 7.29Å, indicating a good global folding to the template [25]. Small spheres were placed in the predicted binding pocket to highlight the substrate binding region above the heme cofactor. Amino acid positions identified in Table 2 were located in the CYP72A13 sequence for assessing the impact of the property changes on the function of the encoded enzyme. Amino acid numbering in Fig 8 is consistent with the consensus sequence used to number the amino acids in Figs 6 and 7.

View Article: PubMed Central - PubMed

ABSTRACT

Plant adaptation to external pressures depends on functional diversity in cytochrome P450 (CYP) enzymes. CYPs contain structural domains necessary for the characteristic P450 fold that allows monooxygenation, but they also have great variation in substrate binding affinity. Plant genomes typically contain hundreds of CYPs that contribute to essential functions and species-specific metabolism. The CYP72A subfamily is conserved in angiosperms but its contribution to physiological functions is largely unknown. With genomic information available for many plants, a focused analysis of CYP subfamily diversity is important to understand the contributions of these enzymes to plant evolution. This study examines the extent to which independent gene duplication and evolution have contributed to structural diversification of CYP72A enzymes in different plant lineages. CYP72A genes are prevalent across angiosperms, but the number of genes within each genome varies greatly. The prevalence of CYP72As suggest that the last common ancestor of flowering plants contained a CYP72A sequence, but gene duplication and retention has varied greatly for this CYP subfamily. Sequence comparisons show that CYP72As are involved in species-specific metabolic functions in some plants while there is likely functional conservation between closely related species. Analysis of structural and functional domains within groups of CYP72As reveals clade-specific residues that contribute to functional constraints within subsets of CYP72As. This study provides a phylogenetic framework that allows comparisons of structural features within subsets of the CYP72A subfamily. We examined a large number of sequences from a broad collection of plant species to detect patterns of functional conservation across the subfamily. The evolutionary relationships between CYPs in plant genomes are an important component in understanding the evolution of biochemical diversity in plants.

No MeSH data available.