Crystal structure of the C-terminal domain of Bacillus subtilis GabR reveals a closed conformation by γ-aminobutyric acid binding, inducing transcriptional activation

Park, Seong Ah; Park, Ye Song; Lee, Ki Seog

doi:10.1016/j.bbrc.2017.04.052

Cited by 12 publications

(39 citation statements)

References 16 publications

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“…PLP is initially bound in this sequence of chemical reactions by the side‐chain of Lys‐302 present in the carboxy‐terminal aminotransferase domain of EnuR (Schulz et al ., ). This scheme was adapted from data reported for the MocR/GabR‐type regulators GabR and DdlR that respond to the availability of GABA and a di‐peptide (D‐alanyl‐D‐alanine), respectively (Edayathumangalam et al ., ; Okuda et al ., ; Takenaka et al ., ; Park et al ., ; Wu et al ., ).…”

Section: Resultsmentioning

confidence: 99%

“…Instead, a partial aminotransferase reaction occurs that initially involves the covalent binding of a system‐specific low molecular mass effector molecule to the protein‐bound PLP co‐factor (the internal aldimine) and the subsequent formation of an external aldimine between PLP and the effector molecule. These chemical reactions are transduced into a conformational change of the entire regulatory protein, which then dictates the DNA‐binding and functional properties of MocR/GabR‐type proteins to function either as activators or repressors (or both) of gene transcription (Belitsky and Sonenshein, ; Wiethaus et al ., ; Edayathumangalam et al ., ; Okuda et al ., ; Takenaka et al ., ; Park et al ., ; Tramonti et al ., ; Wu et al ., ). EnuR possesses such a covalently bound PLP molecule, and Lys‐302 present in its carboxy‐terminal aminotransferase domain has been identified through in silico modelling and mutant studies as the residue to which the co‐factor is attached (Schulz et al ., ).…”

Section: Introductionmentioning

confidence: 98%

“…This latter domain is structurally related to aminotransferases of type-I fold (Edayathumangalam et al, 2013;Milano et al, 2015;Suvorova and Rodionov, 2016). It frequently contains a covalently bound pyridoxal-5'-phosphate (PLP) co-factor (attached to a Lys-residue) but MocR/GabR-type regulators do not perform a full aminotransferase enzyme reaction (Edayathumangalam et al, 2013;Okuda et al, 2015a,b;Takenaka et al, 2015;Park et al, 2017;Wu et al, 2017). Instead, a partial aminotransferase reaction occurs that initially involves the covalent binding of a system-specific low molecular mass effector molecule to the protein-bound PLP co-factor (the internal aldimine) and the subsequent formation of an external aldimine between PLP and the effector molecule.…”

Section: Introductionmentioning

confidence: 99%

“…All enzymes involved in ectoine and hydroxyectoine biosynthesis have been enzymatically studied (Ono et al, 1999;Bursy et al, 2007;St€ oveken et al, 2011), while EutD (DeoA) is the only enzyme from the catabolic route whose function has been experimentally assessed. The information on the generation of both N-(a)-ADABA and N-(g)-ADABA by the recombinant EutD (DoeA) enzyme from H. elongata is based on data reported by Schwibbert et al (Schwibbert et al, 2011). regulatory protein, which then dictates the DNA-binding and functional properties of MocR/GabR-type proteins to function either as activators or repressors (or both) of gene transcription (Belitsky and Sonenshein, 2002;Wiethaus et al, 2008;Edayathumangalam et al, 2013;Okuda et al, 2015a,b;Takenaka et al, 2015;Park et al, 2017;Tramonti et al, 2017;Wu et al, 2017). EnuR possesses such a covalently bound PLP molecule, and Lys-302 present in its carboxy-terminal aminotransferase domain has been identified through in silico modelling and mutant studies as the residue to which the co-factor is attached (Schulz et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Transcriptional regulation of ectoine catabolism in response to multiple metabolic and environmental cues

Schulz

Hermann

Freibert

et al. 2017

Environmental Microbiology

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Ectoine and hydroxyectoine are effective microbial osmostress protectants, but can also serve as versatile nutrients for bacteria. We have studied the genetic regulation of ectoine and hydroxyectoine import and catabolism in the marine Roseobacter species Ruegeria pomeroyi and identified three transcriptional regulators involved in these processes: the GabR/MocR-type repressor EnuR, the feast and famine-type regulator AsnC and the two-component system NtrYX. The corresponding genes are widely associated with ectoine and hydroxyectoine uptake and catabolic gene clusters (enuR, asnC), and with microorganisms predicted to consume ectoines (ntrYX). EnuR contains a covalently bound pyridoxal-5'-phosphate as a co-factor and the chemistry underlying the functioning of MocR/GabR-type regulators typically requires a system-specific low molecular mass effector molecule. Through ligand binding studies with purified EnuR, we identified N-(alpha)-L-acetyl-2,4-diaminobutyric acid and L-2,4-diaminobutyric acid as inducers for EnuR that are generated through ectoine catabolism. AsnC/Lrp-type proteins can wrap DNA into nucleosome-like structures, and we found that the asnC gene was essential for use of ectoines as nutrients. Furthermore, we discovered through transposon mutagenesis that the NtrYX two-component system is required for their catabolism. Database searches suggest that our findings have important ramifications for an understanding of the molecular biology of most microbial consumers of ectoines.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 98%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Transcriptional regulation of ectoine catabolism in response to multiple metabolic and environmental cues

Schulz

Hermann

Freibert

et al. 2017

Environmental Microbiology

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“…Superimposition of this structure to the crystal structure of the full length GabR protein (Fig. B) suggests that this conformational change could weaken the interactions between the AAT‐like and DB‐domains, by the loss of hydrogen bonds between residues Tyr17, Gln18 and Tyr21 of the DB‐domain with Asp290 of the AAT‐like domain, and may induce their dissociation . The entire crystallographic structure of the GabR homodimer has been taken in consideration in a very recent molecular dynamic work carried out with the aim to highlight the role of the conformational flexibility in the functional role of GabR .…”

Section: Cofactor and Effector Binding Properties Of Mocr‐tfsmentioning

confidence: 96%

The MocR‐like transcription factors: pyridoxal 5′‐phosphate‐dependent regulators of bacterial metabolism

et al. 2018

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Many biological functions played by current proteins were not created by evolution from scratch, rather they were obtained combining already available protein scaffolds. This is the case of MocR-like bacterial transcription factors (MocR-TFs), a subclass of GntR transcription regulators, whose structure is the outcome of the fusion between DNA-binding proteins and pyridoxal 5'-phosphate (PLP)-dependent enzymes. The resultant chimeras can count on the properties of both protein classes, i.e. the capability to recognize specific DNA sequences and to bind PLP and amino-compounds; it is the modulation of such binding properties to confer to MocR-TFs chimeras the ability to interact with effector molecules and DNA so as to regulate transcription. MocR-TFs control different metabolic processes involving vitamin B and amino acids, which are canonical ligands of PLP-dependent enzymes. However, MocR-TFs are also implicated in the metabolism of compounds that are not substrates of PLP-dependent enzymes, such as rhizopine and ectoine. Genomic analyses show that MocR-TFs are widespread among eubacteria, implying an essential role in their metabolism and highlighting the scarcity of our knowledge on these important players in microbial metabolism. Although MocR-TFs have been discovered 15 years ago, the research activity on these transcriptional regulators has only recently intensified, producing a wealth of information that needs to be brought back to general principles. This is the main task of this review, which reports and analyses the available information concerning MocR-TFs functional role, structural features, interaction with effector molecules and the characteristics of DNA transcriptional factor-binding sites of MocR-based regulatory systems.

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(S)‐4‐Amino‐5‐phenoxypentanoate designed as a potential selective agonist of the bacterial transcription factor GabR

et al. 2020

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Addressing molecular recognition in the context of evolution requires pursuing new molecular targets to enable the development of agonists or antagonists with new mechanisms of action. Disruption of transcriptional regulation through targeting transcription factors that regulate the expression of key enzymes in bacterial metabolism may provide a promising method for controlling the bacterial metabolic pathways. To this end, we have selectively targeted a bacterial transcription regulator through the design and synthesis of a series of γ‐aminobutyric acid (GABA) derivatives, including (S)‐4‐amino‐5‐phenoxypentanoate (4‐phenoxymethyl‐GABA), which are based on docking insights gained from a previously‐solved crystal structure of GabR from Bacillus subtilis. This target was selected because GabR strictly controls GABA metabolism by regulating the transcription of the gabT/D operon. These GabR transcription modulators are selective for the bacterial transcription factor GabR and are unable to bind to structural homologs of GabR due to distinct steric constraints. We have obtained a crystal structure of 4‐phenoxymethyl‐GABA bound as an external aldimine with PLP in the effector binding site of GabR, which suggests that this compound is capable of binding and reacting in the same manner as the native effector ligand. Inhibition assays demonstrate high selectivity of 4‐phenoxymethyl‐GABA for bacterial GabR versus several selected eukaryotic enzymes. Single‐molecule fluorescence resonance energy transfer (smFRET) experiments reveal a ligand‐induced DNA distortion that is very similar to that of the native effector GABA, suggesting that the compound functions as a potential selective agonist of GabR.

show abstract

Crystal structure of the C-terminal domain of Bacillus subtilis GabR reveals a closed conformation by γ-aminobutyric acid binding, inducing transcriptional activation

Cited by 12 publications

References 16 publications

Transcriptional regulation of ectoine catabolism in response to multiple metabolic and environmental cues

Transcriptional regulation of ectoine catabolism in response to multiple metabolic and environmental cues

The MocR‐like transcription factors: pyridoxal 5′‐phosphate‐dependent regulators of bacterial metabolism

(S)‐4‐Amino‐5‐phenoxypentanoate designed as a potential selective agonist of the bacterial transcription factor GabR

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