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
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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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