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

J 2021

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

DVOŘÁK, Pavel, Carlos ALVAREZ-CARREÑO, Sergio CIORDIA, Alberto PARADELA, Víctor DE LORENZO et. al.

Základní údaje

Originální název

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

Autoři

DVOŘÁK, Pavel (203 Česká republika, domácí), Carlos ALVAREZ-CARREÑO, Sergio CIORDIA, Alberto PARADELA a Víctor DE LORENZO (garant)

Vydání

Environmental Microbiology, Wiley, 2021, 1462-2912

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

20902 Bioprocessing technologies biocatalysis, fermentation

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Odkazy

URL

Impakt faktor

Impact factor: 5.476

Kód RIV

RIV/00216224:14310/21:00119016

Organizační jednotka

Přírodovědecká fakulta

DOI

http://dx.doi.org/10.1111/1462-2920.15628

UT WoS

000662027200001

Klíčová slova anglicky

ENHANCER-BINDING PROTEINS; SIGNAL RECEPTOR DOMAIN; TRANSCRIPTIONAL REGULATORS; PU PROMOTER; NTRC FAMILY; LA-CARTE; ACTIVATOR; XYIR; SPECIFICITIES; PATHWAY

Štítky

rivok

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 8. 11. 2021 13:21, Mgr. Marie Šípková, DiS.

Anotace

V originále

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.

Návaznosti

GJ19-06511Y, projekt VaV

Název: Ortogonalizace metabolismu sacharidů v bakteriálním šasi Pseudomonas putida EM42 pro ko-utilizaci cukrů z rostlinné biomasy

Investor: Grantová agentura ČR, Ortogonalizace metabolismu sacharidů v bakteriálním šasi Pseudomonas putida EM42 pro ko-utilizaci cukrů z rostlinné biomasy

Citovat

DVOŘÁK, Pavel, Carlos ALVAREZ-CARREÑO, Sergio CIORDIA, Alberto PARADELA a Víctor DE LORENZO. An updated structural model of the A domain of the Pseudomonas putida XylR regulator poses an atypical interplay with aromatic effectors. Environmental Microbiology. Wiley, 2021, roč. 23, č. 8, s. 4418-4433. ISSN 1462-2912. Dostupné z: https://dx.doi.org/10.1111/1462-2920.15628.

@article{1776638,
   author = {Dvořák, Pavel and AlvarezandCarreño, Carlos and Ciordia, Sergio and Paradela, Alberto and de Lorenzo, Víctor},
   article_number = {8},
   doi = {http://dx.doi.org/10.1111/1462-2920.15628},
   keywords = {ENHANCER-BINDING PROTEINS; SIGNAL RECEPTOR DOMAIN; TRANSCRIPTIONAL REGULATORS; PU PROMOTER; NTRC FAMILY; LA-CARTE; ACTIVATOR; XYIR; SPECIFICITIES; PATHWAY},
   language = {eng},
   issn = {1462-2912},
   journal = {Environmental Microbiology},
   title = {An updated structural model of the A domain of the Pseudomonas putida XylR regulator poses an atypical interplay with aromatic effectors},
   url = {https://doi.org/10.1111/1462-2920.15628},
   volume = {23},
   year = {2021}
}

TY  - JOUR
ID  - 1776638
AU  - Dvořák, Pavel - Alvarez-Carreño, Carlos - Ciordia, Sergio - Paradela, Alberto - de Lorenzo, Víctor
PY  - 2021
TI  - An updated structural model of the A domain of the Pseudomonas putida XylR regulator poses an atypical interplay with aromatic effectors
JF  - Environmental Microbiology
VL  - 23
IS  - 8
SP  - 4418-4433
EP  - 4418-4433
PB  - Wiley
SN  - 14622912
KW  - ENHANCER-BINDING PROTEINS
KW  - SIGNAL RECEPTOR DOMAIN
KW  - TRANSCRIPTIONAL REGULATORS
KW  - PU PROMOTER
KW  - NTRC FAMILY
KW  - LA-CARTE
KW  - ACTIVATOR
KW  - XYIR
KW  - SPECIFICITIES
KW  - PATHWAY
UR  - https://doi.org/10.1111/1462-2920.15628
N2  - 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.
ER  -

DVOŘÁK, Pavel, Carlos ALVAREZ-CARREÑO, Sergio CIORDIA, Alberto PARADELA a Víctor DE LORENZO. An updated structural model of the A domain of the Pseudomonas putida XylR regulator poses an atypical interplay with aromatic effectors. \textit{Environmental Microbiology}. Wiley, 2021, roč.~23, č.~8, s.~4418-4433. ISSN~1462-2912. Dostupné z: https://dx.doi.org/10.1111/1462-2920.15628.

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