Uncovering of cytochrome P450 anatomy by SecStrAnnotator

J 2021

Uncovering of cytochrome P450 anatomy by SecStrAnnotator

MIDLIK, Adam, Veronika NAVRÁTILOVÁ, Tarakaramji MOTURU, Jaroslav KOČA, Radka SVOBODOVÁ et. al.

Basic information

Original name

Uncovering of cytochrome P450 anatomy by SecStrAnnotator

Authors

MIDLIK, Adam (703 Slovakia, belonging to the institution), Veronika NAVRÁTILOVÁ (203 Czech Republic), Tarakaramji MOTURU (356 India, belonging to the institution), Jaroslav KOČA (203 Czech Republic, belonging to the institution), Radka SVOBODOVÁ (203 Czech Republic, guarantor, belonging to the institution) and K. BERKA

Edition

Nature Scientific Reports, London, NATURE RESEARCH, 2021, 2045-2322

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10608 Biochemistry and molecular biology

Country of publisher

Germany

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 4.996

RIV identification code

RIV/00216224:14740/21:00122561

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1038/s41598-021-91494-8

UT WoS

000663777900001

Keywords in English

CRYSTAL-STRUCTURE; SEQUENCE LOGOS; PROTEINS; DIVERSITY; DATABASE; BIOSYNTHESIS; RESOLUTION; ENZYMES; SITES; P450S

Abstract

V originále

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.

Links

EF16_013/0001777, research and development project

Name: ELIXIR-CZ: Budování kapacit

LM2018131, research and development project

Name: Česká národní infrastruktura pro biologická data (Acronym: ELIXIR-CZ)

Investor: Ministry of Education, Youth and Sports of the CR, Czech National Infrastructure for Biological Data

LQ1601, research and development project

Name: CEITEC 2020 (Acronym: CEITEC2020)

Investor: Ministry of Education, Youth and Sports of the CR

Citovat

MIDLIK, Adam, Veronika NAVRÁTILOVÁ, Tarakaramji MOTURU, Jaroslav KOČA, Radka SVOBODOVÁ and K. BERKA. Uncovering of cytochrome P450 anatomy by SecStrAnnotator. Nature Scientific Reports. London: NATURE RESEARCH, 2021, vol. 11, No 1, p. 12345-12356. ISSN 2045-2322. Available from: https://dx.doi.org/10.1038/s41598-021-91494-8.

@article{1797277,
   author = {Midlik, Adam and Navrátilová, Veronika and Moturu, Tarakaramji and Koča, Jaroslav and Svobodová, Radka and Berka, K.},
   article_location = {London},
   article_number = {1},
   doi = {http://dx.doi.org/10.1038/s41598-021-91494-8},
   keywords = {CRYSTAL-STRUCTURE; SEQUENCE LOGOS; PROTEINS; DIVERSITY; DATABASE; BIOSYNTHESIS; RESOLUTION; ENZYMES; SITES; P450S},
   language = {eng},
   issn = {2045-2322},
   journal = {Nature Scientific Reports},
   title = {Uncovering of cytochrome P450 anatomy by SecStrAnnotator},
   url = {https://www.nature.com/articles/s41598-021-91494-8.pdf},
   volume = {11},
   year = {2021}
}

TY  - JOUR
ID  - 1797277
AU  - Midlik, Adam - Navrátilová, Veronika - Moturu, Tarakaramji - Koča, Jaroslav - Svobodová, Radka - Berka, K.
PY  - 2021
TI  - Uncovering of cytochrome P450 anatomy by SecStrAnnotator
JF  - Nature Scientific Reports
VL  - 11
IS  - 1
SP  - 12345
EP  - 12345
PB  - NATURE RESEARCH
SN  - 20452322
KW  - CRYSTAL-STRUCTURE
KW  - SEQUENCE LOGOS
KW  - PROTEINS
KW  - DIVERSITY
KW  - DATABASE
KW  - BIOSYNTHESIS
KW  - RESOLUTION
KW  - ENZYMES
KW  - SITES
KW  - P450S
UR  - https://www.nature.com/articles/s41598-021-91494-8.pdf
N2  - 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.
ER  -

MIDLIK, Adam, Veronika NAVRÁTILOVÁ, Tarakaramji MOTURU, Jaroslav KOČA, Radka SVOBODOVÁ and K. BERKA. Uncovering of cytochrome P450 anatomy by SecStrAnnotator. \textit{Nature Scientific Reports}. London: NATURE RESEARCH, 2021, vol.~11, No~1, p.~12345-12356. ISSN~2045-2322. Available from: https://dx.doi.org/10.1038/s41598-021-91494-8.

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