Protein structural families are groups of homologous proteins defined by the organization of secondary structure elements (SSEs). Nowadays, many families contain vast numbers of structures, and the SSEs can help to orient within them. Communities around specific protein families have even developed specialized SSE annotations, always assigning the same name to the equivalent SSEs in homologous proteins. A detailed analysis of the groups of equivalent SSEs provides an overview of the studied family and enriches the analysis of any particular protein at hand. We developed a workflow for the analysis of the secondary structure anatomy of a protein family. We applied this analysis to the model family of cytochromes P450 (CYPs)-a family of important biotransformation enzymes with a community-wide used SSE annotation. We report the occurrence, typical length and amino acid sequence for the equivalent SSE groups, the conservation/variability of these properties and relationship to the substrate recognition sites. We also suggest a generic residue numbering scheme for the CYP family. Comparing the bacterial and eukaryotic part of the family highlights the significant differences and reveals a well-known anomalous group of bacterial CYPs with some typically eukaryotic features. Our workflow for SSE annotation for CYP and other families can be freely used at address https://sestra.ncbr.muni.cz .

CEITEC Central European Institute of Technology Masaryk University Brno 625 00 Czech Republic

Department of Physical Chemistry Faculty of Science Palacký University Olomouc 771 46 Czech Republic

National Centre for Biomolecular Research Faculty of Science Masaryk University Brno 625 00 Czech Republic

Zobrazit více v PubMed

Pauling L, Corey RB, Branson HR. The structure of proteins: two hydrogen-bonded helical configurations of the polypeptide chain. Proc. Natl. Acad. Sci. 1951;37:205–211. doi: 10.1073/pnas.37.4.205. PubMed DOI PMC

Pauling L, Corey RB. Configurations of polypeptide chains with favored orientations around single bonds: two new pleated sheets. Proc. Natl. Acad. Sci. U. S. A. 1951;37:729–740. doi: 10.1073/pnas.37.11.729. PubMed DOI PMC

Sillitoe I, et al. CATH: increased structural coverage of functional space. Nucleic Acids Res. 2021;49:D266–D273. doi: 10.1093/nar/gkaa1079. PubMed DOI PMC

Fox NK, Brenner SE, Chandonia J-M. SCOPe: Structural Classification of Proteins-extended, integrating SCOP and ASTRAL data and classification of new structures. Nucleic Acids Res. 2014;42:D304–309. doi: 10.1093/nar/gkt1240. PubMed DOI PMC

Thornton JM, Todd AE, Milburn D, Borkakoti N, Orengo CA. From structure to function: approaches and limitations. Nat. Struct. Biol. 2000;7(Suppl):991–994. doi: 10.1038/80784. PubMed DOI

Krejci E, Duval N, Chatonnet A, Vincens P, Massoulié J. Cholinesterase-like domains in enzymes and structural proteins: functional and evolutionary relationships and identification of a catalytically essential aspartic acid. Proc. Natl. Acad. Sci. U. S. A. 1991;88:6647–6651. doi: 10.1073/pnas.88.15.6647. PubMed DOI PMC

Lenfant N, et al. ESTHER, the database of the α/β-hydrolase fold superfamily of proteins: tools to explore diversity of functions. Nucleic Acids Res. 2013;41:D423–429. doi: 10.1093/nar/gks1154. PubMed DOI PMC

Isberg V, et al. Generic GPCR residue numbers—aligning topology maps while minding the gaps. Trends Pharmacol. Sci. 2015;36:22–31. doi: 10.1016/j.tips.2014.11.001. PubMed DOI PMC

Ehrenmann F, Kaas Q, Lefranc M-P. IMGT/3Dstructure-DB and IMGT/DomainGapAlign: a database and a tool for immunoglobulins or antibodies, T cell receptors, MHC, IgSF and MhcSF. Nucleic Acids Res. 2010;38:D301–307. doi: 10.1093/nar/gkp946. PubMed DOI PMC

Rowland P, et al. Crystal structure of human cytochrome P450 2D6. J. Biol. Chem. 2006;281:7614–7622. doi: 10.1074/jbc.M511232200. PubMed DOI

Cojocaru V, Winn PJ, Wade RC. The ins and outs of cytochrome P450s. Biochim. Biophys. Acta. 2007;1770:390–401. doi: 10.1016/j.bbagen.2006.07.005. PubMed DOI

Hendrychova T, Berka K, Navratilova V, Anzenbacher P, Otyepka M. Dynamics and hydration of the active sites of mammalian cytochromes P450 probed by molecular dynamics simulations. Curr. Drug Metab. 2012;13:177–189. doi: 10.2174/138920012798918408. PubMed DOI

Yu X, Cojocaru V, Wade RC. Conformational diversity and ligand tunnels of mammalian cytochrome P450s. Biotechnol. Appl. Biochem. 2013;60:134–145. doi: 10.1002/bab.1074. PubMed DOI

Otyepka M, Skopalík J, Anzenbacherová E, Anzenbacher P. What common structural features and variations of mammalian P450s are known to date? Biochim. Biophys. Acta. 2007;1770:376–389. doi: 10.1016/j.bbagen.2006.09.013. PubMed DOI

Otyepka M, Berka K, Anzenbacher P. Is there a relationship between the substrate preferences and structural flexibility of cytochromes P450? Curr. Drug Metab. 2012;13:130–142. doi: 10.2174/138920012798918372. PubMed DOI

Urban, P., Lautier, T., Pompon, D. & Truan, G. Ligand access channels in cytochrome P450 enzymes: a review. Int. J. Mol. Sci.19, 1617 (2018). PubMed PMC

Gotoh O. Substrate recognition sites in cytochrome P450 family 2 (CYP2) proteins inferred from comparative analyses of amino acid and coding nucleotide sequences. J. Biol. Chem. 1992;267:83–90. doi: 10.1016/S0021-9258(18)48462-1. PubMed DOI

Zawaira A, Ching LY, Coulson L, Blackburn J, Wei YC. An expanded, unified substrate recognition site map for mammalian cytochrome P450s: analysis of molecular interactions between 15 mammalian CYP450 isoforms and 868 substrates. Curr. Drug Metab. 2011;12:684–700. doi: 10.2174/138920011796504554. PubMed DOI

Schrödinger, LLC. The PyMOL Molecular Graphics System, Version 2.3. (2015).

Dunbar J, Deane CM. ANARCI: antigen receptor numbering and receptor classification. Bioinformatics. 2016;32:298–300. PubMed PMC

Midlik A, et al. Automated family-wide annotation of secondary structure elements. Methods Mol. Biol. 2019;1958:47–71. doi: 10.1007/978-1-4939-9161-7_3. PubMed DOI

Peterson JA, Graham SE. A close family resemblance: the importance of structure in understanding cytochromes P450. Structure. 1998;6:1079–1085. doi: 10.1016/S0969-2126(98)00109-9. PubMed DOI

Johnson EF, Stout CD. Structural diversity of eukaryotic membrane cytochrome p450s. J. Biol. Chem. 2013;288:17082–17090. doi: 10.1074/jbc.R113.452805. PubMed DOI PMC

Poulos TL, Finzel BC, Gunsalus IC, Wagner GC, Kraut J. The 2.6-A crystal structure of Pseudomonas putida cytochrome P-450. J. Biol. Chem. 1985;260:16122–16130. doi: 10.1016/S0021-9258(17)36209-9. PubMed DOI

Poulos TL, Finzel BC, Howard AJ. High-resolution crystal structure of cytochrome P450cam. J. Mol. Biol. 1987;195:687–700. doi: 10.1016/0022-2836(87)90190-2. PubMed DOI

Ravichandran KG, Boddupalli SS, Hasermann CA, Peterson JA, Deisenhofer J. Crystal structure of hemoprotein domain of P450BM-3, a prototype for microsomal P450’s. Science. 1993;261:731–736. doi: 10.1126/science.8342039. PubMed DOI

Hasemann CA, Ravichandran KG, Peterson JA, Deisenhofer J. Crystal structure and refinement of cytochrome P450terp at 2.3 A resolution. J. Mol. Biol. 1994;236:1169–1185. doi: 10.1016/0022-2836(94)90019-1. PubMed DOI

Park SY, et al. Crystal structure of nitric oxide reductase from denitrifying fungus Fusarium oxysporum. Nat. Struct. Biol. 1997;4:827–832. doi: 10.1038/nsb1097-827. PubMed DOI

Scott EE, et al. An open conformation of mammalian cytochrome P450 2B4 at 1.6-A resolution. Proc. Natl. Acad. Sci. U. S. A. 2003;100:13196–13201. doi: 10.1073/pnas.2133986100. PubMed DOI PMC

Wester MR, et al. Structure of a substrate complex of mammalian cytochrome P450 2C5 at 2.3 A resolution: evidence for multiple substrate binding modes. Biochemistry. 2003;42:6370–6379. doi: 10.1021/bi0273922. PubMed DOI

Ouellet H, Podust LM, de Montellano PRO. Mycobacterium tuberculosis CYP130: crystal structure, biophysical characterization, and interactions with antifungal azole drugs. J. Biol. Chem. 2008;283:5069–5080. doi: 10.1074/jbc.M708734200. PubMed DOI PMC

Hasemann CA, Kurumbail RG, Boddupalli SS, Peterson JA, Deisenhofer J. Structure and function of cytochromes P450:a comparative analysis of three crystal structures. Structure. 1995;3:41–62. doi: 10.1016/S0969-2126(01)00134-4. PubMed DOI

Pylypenko O, Vitali F, Zerbe K, Robinson JA, Schlichting I. Crystal structure of OxyC, a cytochrome P450 implicated in an oxidative C-C coupling reaction during vancomycin biosynthesis. J. Biol. Chem. 2003;278:46727–46733. doi: 10.1074/jbc.M306486200. PubMed DOI

Williams PA, et al. Crystal structures of human cytochrome P450 3A4 bound to metyrapone and progesterone. Science. 2004;305:683–686. doi: 10.1126/science.1099736. PubMed DOI

Berka K, Paloncýová M, Anzenbacher P, Otyepka M. Behavior of human cytochromes P450 on lipid membranes. J. Phys. Chem. B. 2013;117:11556–11564. doi: 10.1021/jp4059559. PubMed DOI

Agresti A, Coull BA. Approximate is better than “exact” for interval estimation of binomial proportions. Am. Stat. 1998;52:119–126.

Pándy-Szekeres G, et al. GPCRdb in 2018: adding GPCR structure models and ligands. Nucleic Acids Res. 2018;46:D440–D446. doi: 10.1093/nar/gkx1109. PubMed DOI PMC

Mistry J, et al. Pfam: The protein families database in 2021. Nucleic Acids Res. 2021;49:D412–D419. doi: 10.1093/nar/gkaa913. PubMed DOI PMC

Sevrioukova IF, Li H, Zhang H, Peterson JA, Poulos TL. Structure of a cytochrome P450-redox partner electron-transfer complex. Proc. Natl. Acad. Sci. U. S. A. 1999;96:1863–1868. doi: 10.1073/pnas.96.5.1863. PubMed DOI PMC

Strushkevich N, et al. Structural basis for pregnenolone biosynthesis by the mitochondrial monooxygenase system. Proc. Natl. Acad. Sci. U. S. A. 2011;108:10139–10143. doi: 10.1073/pnas.1019441108. PubMed DOI PMC

Bellamine A, Mangla AT, Nes WD, Waterman MR. Characterization and catalytic properties of the sterol 14α-demethylase from Mycobacterium tuberculosis. Proc. Natl. Acad. Sci. 1999;96:8937–8942. doi: 10.1073/pnas.96.16.8937. PubMed DOI PMC

Zhao B, et al. Biosynthesis of the sesquiterpene antibiotic albaflavenone in Streptomyces coelicolor A3(2) J. Biol. Chem. 2008;283:8183–8189. doi: 10.1074/jbc.M710421200. PubMed DOI PMC

Jackson CJ, et al. A novel sterol 14alpha-demethylase/ferredoxin fusion protein (MCCYP51FX) from Methylococcus capsulatus represents a new class of the cytochrome P450 superfamily. J. Biol. Chem. 2002;277:46959–46965. doi: 10.1074/jbc.M203523200. PubMed DOI

Dana JM, et al. SIFTS: updated structure integration with function, taxonomy and sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins. Nucleic Acids Res. 2019;47:D482–D489. doi: 10.1093/nar/gky1114. PubMed DOI PMC

Sayers EW, et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2009;37:D5–15. doi: 10.1093/nar/gkn741. PubMed DOI PMC

Midlik, A. et al. Annotation and analysis of the secondary structure elements in the Cytochrome P450 protein family. Zenodo (2020). 10.5281/zenodo.3939133.

Krissinel E, Henrick K. Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr. D Biol. Crystallogr. 2004;60:2256–2268. doi: 10.1107/S0907444904026460. PubMed DOI

Tareen A, Kinney JB. Logomaker: beautiful sequence logos in Python. Bioinformatics. 2020;36:2272–2274. doi: 10.1093/bioinformatics/btz921. PubMed DOI PMC

Schneider TD, Stephens RM. Sequence logos: a new way to display consensus sequences. Nucleic Acids Res. 1990;18:6097–6100. doi: 10.1093/nar/18.20.6097. PubMed DOI PMC

AlphaFind: discover structure similarity across the proteome in AlphaFold DB

2DProts: database of family-wide protein secondary structure diagrams