Structural Insights into Nonspecific Binding of DNA by TrmBL2, an Archaeal Chromatin Protein

Ahmad, Misbha Ud Din; Waege, Ingrid; Hausner, Winfried; Thomm, Michael; Boos, Winfried; Diederichs, Kay; Welte, Wolfram

Structural Insights into Nonspecific Binding of DNA by TrmBL2, an Archaeal Chromatin Protein

Dateien

Ahmad_0-300504.pdfGröße: 1.98 MBDownloads: 298

Datum

2015

Autor:innen

Ahmad, Misbha Ud Din

Waege, Ingrid

Hausner, Winfried

Thomm, Michael

Boos, Winfried

Diederichs, Kay

Welte, Wolfram

Publikationstyp

Zeitschriftenartikel

unikn.publication.listelement.citation.prefix.version.undefined

Journal of Molecular Biology. 2015, 427(20), pp. 3216-3229. ISSN 0022-2836. eISSN 1089-8638. Available under: doi: 10.1016/j.jmb.2015.08.012

Zusammenfassung

The crystal structure of TrmBL2 from the archaeon Pyrococcus furiosus shows an association of two pseudosymmetric dimers. The dimers follow the prototypical design of known bacterial repressors with two helix–turn–helix (HTH) domains binding to successive major grooves of the DNA. However, in TrmBL2, the two dimers are arranged at a mutual displacement of approximately 2 bp so that they associate with the DNA along the double-helical axis at an angle of approximately 80°.

While the deoxyribose phosphate groups of the double-stranded DNA (dsDNA) used for co-crystallization are clearly seen in the electron density map, most of the nucleobases are averaged out. Refinement required to assume a superposition of at least three mutually displaced dsDNAs. The HTH domains interact primarily with the deoxyribose phosphate groups and polar interactions with the nucleobases are almost absent.

This hitherto unseen mode of DNA binding by TrmBL2 seems to arise from nonoptimal protein–DNA contacts made by its four HTH domains resulting in a low-affinity, nonspecific binding to DNA.

Fachgebiet (DDC)

570 Biowissenschaften, Biologie

Schlagwörter

TrmBL2, nonspecific DNA binding, chromatin protein, protein–DNA complex, Archaea

Zitieren

ISO 690

AHMAD, Misbha Ud Din, Ingrid WAEGE, Winfried HAUSNER, Michael THOMM, Winfried BOOS, Kay DIEDERICHS, Wolfram WELTE, 2015. Structural Insights into Nonspecific Binding of DNA by TrmBL2, an Archaeal Chromatin Protein. In: Journal of Molecular Biology. 2015, 427(20), pp. 3216-3229. ISSN 0022-2836. eISSN 1089-8638. Available under: doi: 10.1016/j.jmb.2015.08.012

BibTex

@article{Ahmad2015-10-09Struc-31791,
  year={2015},
  doi={10.1016/j.jmb.2015.08.012},
  title={Structural Insights into Nonspecific Binding of DNA by TrmBL2, an Archaeal Chromatin Protein},
  number={20},
  volume={427},
  issn={0022-2836},
  journal={Journal of Molecular Biology},
  pages={3216--3229},
  author={Ahmad, Misbha Ud Din and Waege, Ingrid and Hausner, Winfried and Thomm, Michael and Boos, Winfried and Diederichs, Kay and Welte, Wolfram}
}

RDF

<rdf:RDF
    xmlns:dcterms="http://purl.org/dc/terms/"
    xmlns:dc="http://purl.org/dc/elements/1.1/"
    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
    xmlns:bibo="http://purl.org/ontology/bibo/"
    xmlns:dspace="http://digital-repositories.org/ontologies/dspace/0.1.0#"
    xmlns:foaf="http://xmlns.com/foaf/0.1/"
    xmlns:void="http://rdfs.org/ns/void#"
    xmlns:xsd="http://www.w3.org/2001/XMLSchema#" > 
  <rdf:Description rdf:about="https://kops.uni-konstanz.de/server/rdf/resource/123456789/31791">
    <dc:language>eng</dc:language>
    <dc:contributor>Ahmad, Misbha Ud Din</dc:contributor>
    <dc:creator>Thomm, Michael</dc:creator>
    <dc:contributor>Boos, Winfried</dc:contributor>
    <dspace:hasBitstream rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/31791/1/Ahmad_0-300504.pdf"/>
    <dc:contributor>Thomm, Michael</dc:contributor>
    <dc:contributor>Welte, Wolfram</dc:contributor>
    <dspace:isPartOfCollection rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/28"/>
    <dc:creator>Hausner, Winfried</dc:creator>
    <dc:creator>Waege, Ingrid</dc:creator>
    <dc:creator>Ahmad, Misbha Ud Din</dc:creator>
    <void:sparqlEndpoint rdf:resource="http://localhost/fuseki/dspace/sparql"/>
    <dc:contributor>Hausner, Winfried</dc:contributor>
    <dcterms:isPartOf rdf:resource="https://kops.uni-konstanz.de/server/rdf/resource/123456789/28"/>
    <dc:contributor>Diederichs, Kay</dc:contributor>
    <dcterms:abstract xml:lang="eng">The crystal structure of TrmBL2 from the archaeon Pyrococcus furiosus shows an association of two pseudosymmetric dimers. The dimers follow the prototypical design of known bacterial repressors with two helix–turn–helix (HTH) domains binding to successive major grooves of the DNA. However, in TrmBL2, the two dimers are arranged at a mutual displacement of approximately 2 bp so that they associate with the DNA along the double-helical axis at an angle of approximately 80°.&lt;br /&gt;&lt;br /&gt;While the deoxyribose phosphate groups of the double-stranded DNA (dsDNA) used for co-crystallization are clearly seen in the electron density map, most of the nucleobases are averaged out. Refinement required to assume a superposition of at least three mutually displaced dsDNAs. The HTH domains interact primarily with the deoxyribose phosphate groups and polar interactions with the nucleobases are almost absent.&lt;br /&gt;&lt;br /&gt;This hitherto unseen mode of DNA binding by TrmBL2 seems to arise from nonoptimal protein–DNA contacts made by its four HTH domains resulting in a low-affinity, nonspecific binding to DNA.</dcterms:abstract>
    <dcterms:rights rdf:resource="https://rightsstatements.org/page/InC/1.0/"/>
    <dcterms:title>Structural Insights into Nonspecific Binding of DNA by TrmBL2, an Archaeal Chromatin Protein</dcterms:title>
    <dc:rights>terms-of-use</dc:rights>
    <dc:creator>Diederichs, Kay</dc:creator>
    <dcterms:issued>2015-10-09</dcterms:issued>
    <foaf:homepage rdf:resource="http://localhost:8080/"/>
    <dcterms:available rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2015-09-21T11:38:47Z</dcterms:available>
    <dcterms:hasPart rdf:resource="https://kops.uni-konstanz.de/bitstream/123456789/31791/1/Ahmad_0-300504.pdf"/>
    <dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#dateTime">2015-09-21T11:38:47Z</dc:date>
    <dc:creator>Welte, Wolfram</dc:creator>
    <dc:contributor>Waege, Ingrid</dc:contributor>
    <dc:creator>Boos, Winfried</dc:creator>
    <bibo:uri rdf:resource="http://kops.uni-konstanz.de/handle/123456789/31791"/>
  </rdf:Description>
</rdf:RDF>

Universitätsbibliographie

Ja