Annotation and analysis of the secondary structure elements in the Cytochrome P450 protein family

We collected all currently available structures for proteins in the Cytochrome P450 family and annotated their secondary structure elements using SecStrAnnotator software (https://webchem.ncbr.muni.cz/Wiki/SecStrAnnotator). We used 2nnjA as the template domain for the annotation. Based on these annotations, we analysed the occurrence, length distribution, amino acid sequence, and presence of structural irregularities (β-bulges, 310-helices, π-helices) of each secondary structure element class. We also statistically compared the bacterial vs eukaryotic structures. For the secondary structure element classes with sufficient sequence conservation, the most conserved residue is annotated as the reference residue.

Main files:

set_ALL.json - Set-ALL: list of 1012 protein domains belonging to the Cytochrome P450 family (CATH accession 1.10.630.10 + Pfam accession PF00067, accessed on 7 July 2020, one domain per PDB entry)

set_NR.json - Set-NR: non-redundant list of 183 domains (one domain per UniProt ID)

domain_lists_table.tsv - Overview of Set-ALL and Set-NR and separation into subsets Set-NR-Bact (bacterial), Set-NR-Euka (eukaryotic), Set-NR-Arch (archaeal), Set-NR-Viru (viral)

structures/template_2NNJ-template.sses.json - Manually prepared annotation template (domain 2nnjA)

structures/template_2NNJ.cif - Structure of the template domain (2nnjA)

annotations_with_reference_residues_ALL.json, annotations_with_reference_residues_ALL.tsv - Annotation of secondary structure elements for Set-ALL

annotations_with_reference_residues_NR.json, annotations_with_reference_residues_NR.tsv - Annotation of secondary structure elements for Set-NR

aligments_NR - Multiple sequence alignments for each SSE class (Set-NR)

logos_NR - Sequence logos for each SSE class (Set-NR)

plots - Plots of SSE occurrence, length distribution, contained helix types and beta-bulge occurrence (Set-NR), some plots show the comparison between Set-NR-Bact and Set-NR-Euka

statistical_tests.ods - Comparison of SSE occurrence between Set-NR-Bact and Set-NR-Euka by the test of equal proportions and the Fisher test, comparision of the SSE length by the Kolmogorov-Smirnov test and the two-sample Wilcoxon test