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.

Základní údaje

Originální název

Uncovering of cytochrome P450 anatomy by SecStrAnnotator

Autoři

MIDLIK, Adam (703 Slovensko, domácí), Veronika NAVRÁTILOVÁ (203 Česká republika), Tarakaramji MOTURU (356 Indie, domácí), Jaroslav KOČA (203 Česká republika, domácí), Radka SVOBODOVÁ (203 Česká republika, garant, domácí) a K. BERKA

Vydání

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

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10608 Biochemistry and molecular biology

Stát vydavatele

Německo

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 4.996

Kód RIV

RIV/00216224:14740/21:00122561

Organizační jednotka

Středoevropský technologický institut

DOI

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

UT WoS

000663777900001

Klíčová slova anglicky

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

Štítky

CF BioData, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 18. 5. 2022 13:21, Mgr. Pavla Foltynová, Ph.D.

Anotace

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.

Návaznosti

EF16_013/0001777, projekt VaV

Název: ELIXIR-CZ: Budování kapacit

LM2018131, projekt VaV

Název: Česká národní infrastruktura pro biologická data (Akronym: ELIXIR-CZ)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, Česká národní infrastruktura pro biologická data

LQ1601, projekt VaV

Název: CEITEC 2020 (Akronym: CEITEC2020)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, CEITEC 2020

Citovat

MIDLIK, Adam, Veronika NAVRÁTILOVÁ, Tarakaramji MOTURU, Jaroslav KOČA, Radka SVOBODOVÁ a K. BERKA. Uncovering of cytochrome P450 anatomy by SecStrAnnotator. Nature Scientific Reports. London: NATURE RESEARCH, 2021, roč. 11, č. 1, s. 12345-12356. ISSN 2045-2322. Dostupné z: 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 a K. BERKA. Uncovering of cytochrome P450 anatomy by SecStrAnnotator. \textit{Nature Scientific Reports}. London: NATURE RESEARCH, 2021, roč.~11, č.~1, s.~12345-12356. ISSN~2045-2322. Dostupné z: https://dx.doi.org/10.1038/s41598-021-91494-8.

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