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An updated structural model of the A domain of the Pseudomonas putida XylR regulator poses an atypical interplay with aromatic effectors

The result's identifiers

  • Result code in IS VaVaI

    <a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14310%2F21%3A00119016" target="_blank" >RIV/00216224:14310/21:00119016 - isvavai.cz</a>

  • Result on the web

    <a href="https://doi.org/10.1111/1462-2920.15628" target="_blank" >https://doi.org/10.1111/1462-2920.15628</a>

  • DOI - Digital Object Identifier

    <a href="http://dx.doi.org/10.1111/1462-2920.15628" target="_blank" >10.1111/1462-2920.15628</a>

Alternative languages

  • Result language

    angličtina

  • Original language name

    An updated structural model of the A domain of the Pseudomonas putida XylR regulator poses an atypical interplay with aromatic effectors

  • Original language description

    A revised model of the aromatic binding A domain of the σ54-dependent regulator XylR of Pseudomonas putida mt-2 was produced based on the known 3D structures of homologous regulators PoxR, MopR and DmpR. The resulting frame was instrumental for mapping a number of mutations known to alter effector specificity, which were then reinterpreted under a dependable spatial reference. Some of these changes involved the predicted aromatic binding pocket but others occurred in distant locations, including dimerization interfaces and putative zinc binding site. The effector pocket was buried within the protein structure and accessible from the outside only through a narrow tunnel. Yet, several loop regions of the A domain could provide the flexibility required for widening such a tunnel for passage of aromatic ligands. The model was experimentally validated by treating the cells in vivo and the purified protein in vitro with benzyl bromide, which reacts with accessible nucleophilic residues on the protein surface. Structural and proteomic analyses confirmed the predicted in/out distribution of residues but also supported two additional possible scenarios of interaction of the A domain with aromatic effectors: a dynamic interaction of the fully structured yet flexible protein with the aromatic partner and/or inducer-assisted folding of the A domain.

  • Czech name

  • Czech description

Classification

  • Type

    J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database

  • CEP classification

  • OECD FORD branch

    20902 - Bioprocessing technologies (industrial processes relying on biological agents to drive the process) biocatalysis, fermentation

Result continuities

  • Project

    <a href="/en/project/GJ19-06511Y" target="_blank" >GJ19-06511Y: Orthogonalisation of carbohydrate metabolism in bacterial chassis Pseudomonas putida EM42 for co-utilisation of lignocellulose-derived sugars</a><br>

  • Continuities

    P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Others

  • Publication year

    2021

  • Confidentiality

    S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Data specific for result type

  • Name of the periodical

    Environmental Microbiology

  • ISSN

    1462-2912

  • e-ISSN

    1462-2920

  • Volume of the periodical

    23

  • Issue of the periodical within the volume

    8

  • Country of publishing house

    US - UNITED STATES

  • Number of pages

    16

  • Pages from-to

    4418-4433

  • UT code for WoS article

    000662027200001

  • EID of the result in the Scopus database

    2-s2.0-85108016994