Uncovering of cytochrome P450 anatomy by SecStrAnnotator

Abstract 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 d...

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Autores principales:	Adam Midlik, Veronika Navrátilová, Taraka Ramji Moturu, Jaroslav Koča, Radka Svobodová, Karel Berka
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/fa34aa4ea88b4f8c86eb1023bbd26b74
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spelling	oai:doaj.org-article:fa34aa4ea88b4f8c86eb1023bbd26b742021-12-02T17:47:04ZUncovering of cytochrome P450 anatomy by SecStrAnnotator10.1038/s41598-021-91494-82045-2322https://doaj.org/article/fa34aa4ea88b4f8c86eb1023bbd26b742021-06-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-91494-8https://doaj.org/toc/2045-2322Abstract 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 .Adam MidlikVeronika NavrátilováTaraka Ramji MoturuJaroslav KočaRadka SvobodováKarel BerkaNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Adam Midlik Veronika Navrátilová Taraka Ramji Moturu Jaroslav Koča Radka Svobodová Karel Berka Uncovering of cytochrome P450 anatomy by SecStrAnnotator
description	Abstract 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 .
format	article
author	Adam Midlik Veronika Navrátilová Taraka Ramji Moturu Jaroslav Koča Radka Svobodová Karel Berka
author_facet	Adam Midlik Veronika Navrátilová Taraka Ramji Moturu Jaroslav Koča Radka Svobodová Karel Berka
author_sort	Adam Midlik
title	Uncovering of cytochrome P450 anatomy by SecStrAnnotator
title_short	Uncovering of cytochrome P450 anatomy by SecStrAnnotator
title_full	Uncovering of cytochrome P450 anatomy by SecStrAnnotator
title_fullStr	Uncovering of cytochrome P450 anatomy by SecStrAnnotator
title_full_unstemmed	Uncovering of cytochrome P450 anatomy by SecStrAnnotator
title_sort	uncovering of cytochrome p450 anatomy by secstrannotator
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/fa34aa4ea88b4f8c86eb1023bbd26b74
work_keys_str_mv	AT adammidlik uncoveringofcytochromep450anatomybysecstrannotator AT veronikanavratilova uncoveringofcytochromep450anatomybysecstrannotator AT tarakaramjimoturu uncoveringofcytochromep450anatomybysecstrannotator AT jaroslavkoca uncoveringofcytochromep450anatomybysecstrannotator AT radkasvobodova uncoveringofcytochromep450anatomybysecstrannotator AT karelberka uncoveringofcytochromep450anatomybysecstrannotator
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Uncovering of cytochrome P450 anatomy by SecStrAnnotator

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