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.

Basic information

Original name

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

Authors

SINHA, Dhiraj (203 Czech Republic), Vitali BIALEVICH (203 Czech Republic), Katsiaryna SHAMAYEVA (203 Czech Republic), Alena GUZANOVA (203 Czech Republic), Alexandra SISÁKOVÁ (703 Slovakia, belonging to the institution), Eva CSEFALVAY (203 Czech Republic), David REHA (203 Czech Republic), Lumír KREJČÍ (203 Czech Republic, belonging to the institution), Jannette CAREY (840 United States of America), Marie WEISEROVA (203 Czech Republic) and Rüdiger ETTRICH (840 United States of America)

Edition

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

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10608 Biochemistry and molecular biology

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

Impact factor

Impact factor: 1.335

RIV identification code

RIV/00216224:14110/18:00105889

Organization unit

Faculty of Medicine

DOI

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

UT WoS

000436486600002

Keywords in English

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

Abstract

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.

Links

LM2015055, research and development project

Name: Centrum pro systémovou biologii (Acronym: C4SYS)

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

Citovat

SINHA, Dhiraj, Vitali BIALEVICH, Katsiaryna SHAMAYEVA, Alena GUZANOVA, Alexandra SISÁKOVÁ, Eva CSEFALVAY, David REHA, Lumír KREJČÍ, Jannette CAREY, Marie WEISEROVA and 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, vol. 24, No 7, p. 1-11. ISSN 1610-2940. Available from: 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 and 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, vol.~24, No~7, p.~1-11. ISSN~1610-2940. Available from: https://dx.doi.org/10.1007/s00894-018-3722-8.

Detailed Information on Publication Record