A residue of motif III positions the helicase domains of motor
subunit HsdR in restriction-modification enzyme EcoR124I

J 2018

A residue of motif III positions the helicase domains of motor subunit HsdR in restriction-modification enzyme EcoR124I

SINHA, Dhiraj, Vitali BIALEVICH, Katsiaryna SHAMAYEVA, Alena GUZANOVA, Alexandra SISÁKOVÁ et. al.

Základní údaje

Originální název

A residue of motif III positions the helicase domains of motor subunit HsdR in restriction-modification enzyme EcoR124I

Autoři

SINHA, Dhiraj (203 Česká republika), Vitali BIALEVICH (203 Česká republika), Katsiaryna SHAMAYEVA (203 Česká republika), Alena GUZANOVA (203 Česká republika), Alexandra SISÁKOVÁ (703 Slovensko, domácí), Eva CSEFALVAY (203 Česká republika), David REHA (203 Česká republika), Lumír KREJČÍ (203 Česká republika, domácí), Jannette CAREY (840 Spojené státy), Marie WEISEROVA (203 Česká republika) a Rüdiger ETTRICH (840 Spojené státy)

Vydání

JOURNAL OF MOLECULAR MODELING, New York, Springer, 2018, 1610-2940

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

10608 Biochemistry and molecular biology

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Impakt faktor

Impact factor: 1.335

Kód RIV

RIV/00216224:14110/18:00105889

Organizační jednotka

Lékařská fakulta

DOI

http://dx.doi.org/10.1007/s00894-018-3722-8

UT WoS

000436486600002

Klíčová slova anglicky

DNA restriction enzymes; Molecular mechanics; Molecular modeling; Principal components analysis; Multisubunit enzyme complex; Domain interactions

Štítky

14110513, podil, rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 26. 3. 2019 10:42, Soňa Böhmová

Anotace

V originále

Type I restriction-modification enzymes differ significantly from the type II enzymes commonly used as molecular biology reagents. On hemi-methylated DNAs type I enzymes like the EcoR124I restriction-modification complex act as conventional adenine methylases at their specific target sequences, but unmethylated targets induce them to translocate thousands of base pairs through the stationary enzyme before cleaving distant sites nonspecifically. EcoR124I is a superfamily 2 DEAD-box helicase like eukaryotic double-strand DNA translocase Rad54, with two RecA-like helicase domains and seven characteristic sequence motifs that are implicated in translocation. In Rad54 a so-called extended region adjacent to motif III is involved in ATPase activity. Although the EcoR124I extended region bears sequence and structural similarities with Rad54, it does not influence ATPase or restriction activity as shown in this work, but mutagenesis of the conserved glycine residue of its motif III does alter ATPase and DNA cleavage activity. Through the lens of molecular dynamics, a full model of HsdR of EcoR124I based on available crystal structures allowed interpretation of functional effects of mutants in motif III and its extended region. The results indicate that the conserved glycine residue of motif III has a role in positioning the two helicase domains.

Návaznosti

LM2015055, projekt VaV

Název: Centrum pro systémovou biologii (Akronym: C4SYS)

Investor: Ministerstvo školství, mládeže a tělovýchovy ČR, The national infrastructure C4SYS - Centre for Systems Biology

Citovat

SINHA, Dhiraj, Vitali BIALEVICH, Katsiaryna SHAMAYEVA, Alena GUZANOVA, Alexandra SISÁKOVÁ, Eva CSEFALVAY, David REHA, Lumír KREJČÍ, Jannette CAREY, Marie WEISEROVA a Rüdiger ETTRICH. A residue of motif III positions the helicase domains of motor subunit HsdR in restriction-modification enzyme EcoR124I. JOURNAL OF MOLECULAR MODELING. New York: Springer, 2018, roč. 24, č. 7, s. 1-11. ISSN 1610-2940. Dostupné z: https://dx.doi.org/10.1007/s00894-018-3722-8.

@article{1490539,
   author = {Sinha, Dhiraj and Bialevich, Vitali and Shamayeva, Katsiaryna and Guzanova, Alena and Sisáková, Alexandra and Csefalvay, Eva and Reha, David and Krejčí, Lumír and Carey, Jannette and Weiserova, Marie and Ettrich, Rüdiger},
   article_location = {New York},
   article_number = {7},
   doi = {http://dx.doi.org/10.1007/s00894-018-3722-8},
   keywords = {DNA restriction enzymes; Molecular mechanics; Molecular modeling; Principal components analysis; Multisubunit enzyme complex; Domain interactions},
   language = {eng},
   issn = {1610-2940},
   journal = {JOURNAL OF MOLECULAR MODELING},
   title = {A residue of motif III positions the helicase domains of motor subunit HsdR in restriction-modification enzyme EcoR124I},
   volume = {24},
   year = {2018}
}

TY  - JOUR
ID  - 1490539
AU  - Sinha, Dhiraj - Bialevich, Vitali - Shamayeva, Katsiaryna - Guzanova, Alena - Sisáková, Alexandra - Csefalvay, Eva - Reha, David - Krejčí, Lumír - Carey, Jannette - Weiserova, Marie - Ettrich, Rüdiger
PY  - 2018
TI  - A residue of motif III positions the helicase domains of motor subunit HsdR in restriction-modification enzyme EcoR124I
JF  - JOURNAL OF MOLECULAR MODELING
VL  - 24
IS  - 7
SP  - 1-11
EP  - 1-11
PB  - Springer
SN  - 16102940
KW  - DNA restriction enzymes
KW  - Molecular mechanics
KW  - Molecular modeling
KW  - Principal components analysis
KW  - Multisubunit enzyme complex
KW  - Domain interactions
N2  - Type I restriction-modification enzymes differ significantly from the type II enzymes commonly used as molecular biology reagents. On hemi-methylated DNAs type I enzymes like the EcoR124I restriction-modification complex act as conventional adenine methylases at their specific target sequences, but unmethylated targets induce them to translocate thousands of base pairs through the stationary enzyme before cleaving distant sites nonspecifically. EcoR124I is a superfamily 2 DEAD-box helicase like eukaryotic double-strand DNA translocase Rad54, with two RecA-like helicase domains and seven characteristic sequence motifs that are implicated in translocation. In Rad54 a so-called extended region adjacent to motif III is involved in ATPase activity. Although the EcoR124I extended region bears sequence and structural similarities with Rad54, it does not influence ATPase or restriction activity as shown in this work, but mutagenesis of the conserved glycine residue of its motif III does alter ATPase and DNA cleavage activity. Through the lens of molecular dynamics, a full model of HsdR of EcoR124I based on available crystal structures allowed interpretation of functional effects of mutants in motif III and its extended region. The results indicate that the conserved glycine residue of motif III has a role in positioning the two helicase domains.
ER  -

SINHA, Dhiraj, Vitali BIALEVICH, Katsiaryna SHAMAYEVA, Alena GUZANOVA, Alexandra SISÁKOVÁ, Eva CSEFALVAY, David REHA, Lumír KREJČÍ, Jannette CAREY, Marie WEISEROVA a Rüdiger ETTRICH. A residue of motif III positions the helicase domains of motor subunit HsdR in restriction-modification enzyme EcoR124I. \textit{JOURNAL OF MOLECULAR MODELING}. New York: Springer, 2018, roč.~24, č.~7, s.~1-11. ISSN~1610-2940. Dostupné z: https://dx.doi.org/10.1007/s00894-018-3722-8.

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