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145 results for “Cytochrome P450”
EPR Characterization of the Heme Domain of a Self-Sufficient Cytochrome P450 (CYP116B5)
<p><strong>Description of the dataset: </strong></p> <ul> <li><strong>Data type</strong>: Experimental spectroscopic measurements, computer simulation.</li> <li>Files are with filename extensions: .<strong>DSC</strong>, .<strong>DAT</strong>, .<strong>m</strong></li> <li>Information on <strong>origin of the data</strong>:</li> </ul> <ul> <li>EPR spectroscopic measurements with filename extensions .<strong>DSC</strong>, .<strong>DTA.</strong></li> <li>EPR spectroscopic simulation with filename extension .<strong>m</strong>.</li> </ul> <ul> <li>CW and Pulse X-band experiments were performed on a Bruker Elexys E580 X-band spectrometer (microwave frequency 9.68 GHz) equipped with a cylindrical dielectric cavity and a helium gas-flow cryostat from Oxford Inc.</li> <li><strong>If the dataset includes multiple files that relate to each other:</strong> <ul> <li>Files in <strong>PARACAT_WP5_20220225_CW</strong> folder includes X-band CW-EPR spectroscopic measurements, original data are in DTA/DSC/txt.</li> <li>Files in <strong>PARACAT_WP5_20220225_HYSCORE</strong> folder includes HYSCORE spectroscopic measurements, data are in .DTA, .DSC, .txt formats.</li> <li>Files in <strong>PARACAT_WP5_20220225_MATLAB</strong> folder includes computer simulations/analyses of the EPR measurements, data are in .m formats.</li> </ul> </li> </ul>
Cytochrome P450 Genes Expressed in Phasmatodea Midguts
<p>In June 2021, representative sequences for insect cytochrome P450s were downloaded from NCBI, limiting the search to those in the UniProtKB database. The resulting 111 sequences were used as a query to mine the above transcriptomes using tblastn with an expect value threshold of e-10. These were manually annotated by removing truncated sequences, using the ExPASy online translation tool to obtain the complete amino acid sequences, removing duplicates using the sRNAtoolbox webserver, and confirming that the sequences were cytochrome P450s by identifying them using blastp against the NCBI database. The resulting sequences were combined with the representatives from NCBI, aligned using the Clustal W program built into the software MEGA version X. Any sequences missing the heme-binding domain FXXGXXXCXG/A, which is a signature motif for CYPs, were deleted. The sequences were also checked for the presence and absence of other four signature motifs from insect CYPs: helix C (WxxxR), helix I (GxE/DTT/S), helix K (ExLR), and PERF (PxxFxPE/DRE/F).</p>
Sequence Similarity Network (SSN) and Genome Neighbourhood Network (GNN) for Mycobacterium Cytochrome P450 enzymes
<p>This dataset was generated in the context of the Horizon 2020 MSCA IF action deCrYPtion (Grant 839116). The aim of this project is to use comparative genomics in order to propose and then test the function of uncharacterised Cytochrome P450 enzymes that are present among Mycobacterium species.</p> <p>More information about this project can be found at: https://cordis.europa.eu/project/id/839116.</p> <p>This dataset contains:</p> <p>- The FASTA sequences files obtained from the UniProt database, for members of the PF00067 protein family (CYP).</p> <p>- A set of reference FASTA sequences, matching the supplementary material from the following publication: Parvez, M. <em>et al.</em> (2016) ‘Molecular evolutionary dynamics of cytochrome P450 monooxygenases across kingdoms: Special focus on mycobacterial P450s’, <em>Scientific Reports</em>, 6(1), p. 33099. doi:<a href="https://doi.org/10.1038/srep33099">10.1038/srep33099</a>.</p> <p>- A combined FASTA files of both previously described, that was used for the generation of SSNs</p> <p>- A PNG image produced from the analysis of the Sequence Similarity Networks generated at AST78 (corresponding to 40% identity, defining CYP families)</p> <p>- A PNG image produced from the analysis of the Sequence Similarity Networks generated at AST141 (corresponding to 55% identity, defining CYP subfamilies)</p> <p>- A Cytoscape session for the Sequence Similarity Networks from the combined FASTA file generated using the Enzyme Function Initiative web tools (https://efi.igb.illinois.edu), at AST78</p> <p>- A Cytoscape session containing Sequence Similarity Networks and Genome Neighborhood Network from the combined FASTA file generated using the Enzyme Function Initiative web tools (https://efi.igb.illinois.edu), at AST141</p>
Fig. 7 in Differential analysis of the cytochrome p450 acaricide-resistance genes in Panonychus citri (Trombidiformes: Tetranychidae) strains
Fig. 7. Alignment of the predicted amino acid sequences of the CYP307A1 in Panonychus citri between the hexythiazox-resistant (RR) and susceptible (SS) strains. Mazarine shading indicates identities and different color shading represents mutations. "-" represents no sequence to compare. We detected a sense amino acid mutation (14-threonine to serine).. This figure is shown in color in a supplementary document online as Suppl. Fig. 7 in Florida Entomologist 98(1) (March 2015) at http://purl.fcla.edu/fcla/entomologist/browse.
Fig. 5 in Differential analysis of the cytochrome p450 acaricide-resistance genes in Panonychus citri (Trombidiformes: Tetranychidae) strains
Fig. 5. Alignment of the predicted amino acid sequences of CYP307A1 in Panonychus citribetween the hexythiazox-resistant (RR) and susceptible (SS) strains. Mazarine shading indicates identities and different color shading represents mutations. "-" represents no sequence to compare. Only one amino acid mutation (278-lysine to glutamine) was detected.. This figure is shown in color in a supplementary document online as Suppl. Fig. 5 in Florida Entomologist 98(1) (March 2015) at http://purl.fcla.edu/fcla/entomologist/browse.
Fig. 6 in Differential analysis of the cytochrome p450 acaricide-resistance genes in Panonychus citri (Trombidiformes: Tetranychidae) strains
Fig. 6. Nucleotide sequence comparison of CYP381A2 in Panonychus citri between the hexythiazox-resistant (RR) and susceptible (SS) strains. Mazarine shading indicates identities and different color shading represents mutations. "-" represents no sequence to compare. Just one SNP site was detected. The nucleotide transition of A to T was at position 40.. This figure is shown in color in a supplementary document online as Suppl. Fig. 6 in Florida Entomologist 98(1) (March 2015) at http://purl.fcla.edu/fcla/entomologist/browse.
Fig. 4 in Differential analysis of the cytochrome p450 acaricide-resistance genes in Panonychus citri (Trombidiformes: Tetranychidae) strains
Fig. 4. Nucleotide sequence comparison of the CYP307A1 in Panonychus citri between the hexythiazox-resistant (RR) and susceptible (SS) strains. Mazarine shading indicates identities and different color shading represents mutations. "-" represents no sequence to compare. Three SNP sites were detected in all. The first nucleotide mutation (A to C) is located at 841, the second mutation is 1395-T to C, and the final mutation is 1491-T to C.. This figure is shown in color in a supplementary document online as Suppl. Fig. 4 in Florida Entomologist 98(1) (March 2015) at http://purl.fcla.edu/fcla/entomologist/browse.
Fig. 3 in Differential analysis of the cytochrome p450 acaricide-resistance genes in Panonychus citri (Trombidiformes: Tetranychidae) strains
Fig. 3. Quantitative Real-time PCR analysis of CYPs in Panonychus citri between the hexythiazox-resistant (RR) and susceptible (SS) strains. The numbers of genes down-regulated and up-regulated in the RR relative to the SS are indicated above or below the X axis. The light or dark gray was susceptible strain and resistant strain, respectively.
Fig. 1 in Differential analysis of the cytochrome p450 acaricide-resistance genes in Panonychus citri (Trombidiformes: Tetranychidae) strains
Fig. 1. Number, family and clan distribution of cytochrome P450 genes in Panonychus citri. The number shown along each column represents the P450 family and the number in parenthesis is the number of individual genes in the corresponding family. The P450 gene sequence information generated is from the VectorBase of the P. citri transcriptome sequence.
Fig. 2 in Differential analysis of the cytochrome p450 acaricide-resistance genes in Panonychus citri (Trombidiformes: Tetranychidae) strains
Fig. 2. Neighbor-joining phylogenetic analysis of cytochrome P450 from Panonychus citri and Tetranychus urticae. 4clans were observed. There are species (P. citri and T. urticae) in the phylogenetic tree. Only 10 sequences belong to T. urticae; A (Pc) before the CYP name denotes P. citri, a (Tu) before the CYP name denotes T. urticae. Numbers at nodes are bootstrap values.
Hyper-specialized bamboo lemurs possess a reduced suite of xenobiotic-metabolizing cytochrome P450 genes
<p><span>Subfamilies of cytochrome P450 proteins have been strongly linked to the metabolism of physiologically disruptive compounds such as alkaloids, terpenoids, and other xenobiotics. Consistent with this function, these genes have adaptively evolved in response to environmental pressures exerted on animals, such as herbivores, that consume elevated amounts of toxic xenobiotics or plant secondary metabolites (PSMs). Theory on evolutionary tradeoffs predicts that highly specialized herbivores should exhibit a relatively narrow toolkit of adaptations to accommodate the concomitantly narrow arrays of PSMs in their diets. The bamboo lemurs of Madagascar (genera </span><em>Prolemur</em> and <em>Hapalemur</em>) represent an interesting test case for this theory because of their dietary hyper-specialization, as these lemurs consume bamboo and grasses at rates otherwise unseen in the order Primates. To test whether the hyper-specialized folivory of these primates is reflected in a similarly specialized and narrow P450 gene suite, we assembled a dataset of confidently assembled CYP1-3 genes for two species of bamboo lemur and 13 additional lemur species. With this dataset, we tested the predictions that bamboo lemurs would exhibit, first, greater rates of gene loss for xenobiotic-metabolizing P450s and, second, relaxed selection on xenobiotic-metabolizing P450 subfamilies relative to lemurs without such dietary hyper-specialization. We found support for the prediction of gene loss in the <em>CYP2B,</em> <em>CYP2C</em>, <em>CYP2D</em>, <em>CYP2J</em>, and <em>CYP3A</em> subfamilies, all of which encode xenobiotic metabolizers. We inferred relaxation of selection for the <em>CYP1A</em> and <em>CYP2D</em> subfamilies. The <em>CYP2F</em> subfamily exhibited a signal of significant intensification of selection in the bamboo-lemur lineage. The evolution of the P450 genes in bamboo lemurs provides support for the evolutionary tradeoff hypothesis, and we further hypothesize that, rather than adapting to a general array of PSMs, bamboo lemurs have instead adapted to the primary toxin in their diet, the highly potent poison cyanide.</p>
Data for: A computational pipeline to observe the flexibility and dynamics of (plant) cytochrome P450 binding sites
<p>Binding site flexibility and dynamics strongly affect the ability of proteins to accommodate substrates and inhibitors. The significance of these properties is particularly pronounced for proteins that are inherently flexible, such as cytochrome P450 enzymes (CYPs). While the research on human CYPs provides detailed knowledge on both structural and functional level, such analyses are still lacking for their plant counterparts. This study aims to bridge this gap. Firstly, we use molecular dynamics (MD) simulations to capture the full conformational ensemble for a certain plant CYP. Subsequently, we developed and applied a comprehensive methodology to analyse a number of binding site properties - size, flexibility, shape, hydrophobicity, and accessibility - using the fpocket and mdpocket packages on MD-generated trajectories. This led to a first categorization of 15 chosen plant CYPs based on their binding site's (dis)similarities. The workflow was tested and verified on human CYPs 1A2, 2A6, and 3A4 as their binding site characteristics are well known. In addition to confirming known binding site properties, we identified and named previously unseen binding site channels for CYPs 1A2 and 2A6. This study gives initial insights into the largely uncharted fields plant CYP substrate specificity and facilitates a more precise understanding of their largely unknown specific biological functions. It offers new insights into the structural and functional dynamics of plant CYPs, which may facilitate a more accurate understanding of the fate of agrochemicals or the biotechnological design and exploitation of enzymes with specific functions. Additionally, it serves as a reference for future structural-functional analyses of CYP enzymes across various biological kingdoms.</p>
Associated coordinate and mtz files for "Crystal structure of cytochrome P450 NysL and the structural basis for stereo- and regio- selective oxidation of antifungal macrolides"
<p>Coordinate and mtz files for the associated protein structures reported in "Crystal structure of cytochrome P450 NysL and the structural basis for stereo- and regio- selective oxidation of antifungal macrolides".</p>
Computational redesign of cytochrome P450 CYP102A1 for highly stereoselective omeprazole hydroxylation by UniDesign
<p>To make it consistent with our manuscript, in this version of Zenodo dataset, all "conformers" have been changed to "poses" in the file names and the contents of the Perl scripts (in Scripts.zip). </p>
Interactions Between Cannabinoids and Cytochrome P450-Metabolized Drugs
ClinicalTrials.gov study NCT04201197. IPD Sharing: YES. Countries: 1. Publications: 1.
The Effect of a Peroxisome Proliferator-activated Receptor (PPAR) Alpha Agonist on Cytochrome P450 (CYP) Monooxygenase Activity in Humans
ClinicalTrials.gov study NCT00872599. IPD Sharing: Not stated. Countries: 1. Publications: 2.
CYP19A1 (Cytochrome P450 Family 19 Subfamily A Member 1) Gene and Pharmacogenetics of Response to Testosterone Therapy
ClinicalTrials.gov study NCT01378299. IPD Sharing: YES. Countries: 1. Publications: 2.
Cytochrome P450 metabolic resistance (CYP6P9a) to pyrethroids imposes a fitness cost in the major African malaria vector Anopheles funestus
Open the record for dataset details and reuse information.
Hyper-specialized bamboo lemurs possess a reduced suite of xenobiotic-metabolizing cytochrome P450 genes
Open the record for dataset details and reuse information.
Data from: Cytochrome P450 diversification and hostplant utilization patterns in specialist and generalist moths: birth, death, and adaptation
Across insect genomes, the size of the cytochrome P450 monooxygenase (CYP) gene superfamily varies widely. CYPome size variation has been attributed to reciprocal adaptive radiations in insect detoxification genes in response to plant biosynthetic gene radiations driven by coevolution between herbivores and their chemically defended hostplants. Alternatively, variation in CYPome size may be due to random "birth and death" processes, whereby exponential increase via gene duplications is limited by random decay via gene death or transition via divergence. We examined CYPome diversification in the genomes of seven Lepidoptera species varying in host breadth from monophagous (Bombyx mori) to highly polyphagous (Amyelois transitella). CYPome size largely reflects the size of Clan 3, the clan associated with xenobiotic detoxification, and to some extent phylogenetic age. Consistently across genomes, families CYP6, CYP9, and CYP321 are most diverse and CYP6AB, CYP6AE, CYP6B, CYP9A, and CYP9G are most diverse among subfamilies. Higher gene number in subfamilies is due to duplications occurring primarily after speciation and specialization ("P450 blooms"), and the genes are arranged in clusters, indicative of active duplicating loci. In the parsnip webworm, Depressaria pastinacella, gene expression levels in large subfamilies are high relative to smaller subfamilies. Functional and phylogenetic data suggest a correlation between highly dynamic loci (reflective of extensive gene duplication, functionalization, and in some cases loss) and the ability of enzymes encoded by these genes to metabolize hostplant defenses, consistent with an adaptive, nonrandom process driven by ecological interactions.
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