Crystal structure details of Vibrio fischeri DarR and mutant DarR-M202I from LTTR family reveals their activation mechanism

Wang, Weiwei; Wu, Heng; Xiao, Qi; Zhou, Huan; Li, Minjun; Xu, Qin; Wang, Qisheng; Yu, Feng; He, Jianhua

doi:10.1016/j.ijbiomac.2021.05.186

Cited by 7 publications

(5 citation statements)

References 39 publications

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“…(B) Multiple amino acid sequence alignment of the DBDs of the ORF-L16 and LysR family transcriptional regulators with complete crystal structures. CbnR is from Burkholderiales [ 30 ], BenM is from Acinetobacter [ 37 ], YfbA is from Yersinia pestis , and DarR is from Aliivibrio fischeri [ 38 ]. …”

Section: Resultsmentioning

confidence: 99%

The LysR family transcriptional regulator ORF-L16 regulates spinosad biosynthesis in Saccharopolyspora spinosa

Mu,

Lei,

Yan

et al. 2024

Synthetic and Systems Biotechnology

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Section: Resultsmentioning

confidence: 99%

The LysR family transcriptional regulator ORF-L16 regulates spinosad biosynthesis in Saccharopolyspora spinosa

Mu,

Lei,

Yan

et al. 2024

Synthetic and Systems Biotechnology

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“…This set of interactions builds tetramers classified for the purpose of this study as type 1 ( Table 1, Figure 1 ). Additional interactions between C-terminal domains may close the ring (type 2), as in AtzR or CbnR, or build more compact particles as in type 3 seen in HinK (PDB ID 3FZV, Wang et al ., 2021). Concomitantly, the distance and relative orientation between both pairs of DNA-binding dimers is different in all types of tetramers.…”

Section: Resultsmentioning

confidence: 99%

“…AtzR (PDB ID 7Z7J), TsaR (PDB ID 3FXQ, Monferrer et al ., 2010), ArgP (PDB ID 3ISP, Zhou et al ., 2010), PA0477 (PDB ID 2ESN), LysG (PDB ID 6XTU, Della Corte et al ., 2020), OxyR (PDB ID 4×6G, Jo et al ., 2015), CbnR (PDB ID 1IXC, Muraoka et al ., 2003), DntR (PDB ID 5AE5, Lerche et al ., 2016), CcmR (PDB ID 5Y2V, Jiang et al ., 2017), OxyR (PDB ID 6G1B, Pedre et al ., 2018), HinK (PDB ID 3FZV, Wang et al ., 2021), OxyR (PDB ID 6G4R, Pedre et al ., 2018), DarR (PDB ID 7DWN, Wang et al ., 2021), HypT (PDB ID 5YDW, Jo et al ., 2019), OxyR (6G1D, Pedre et al ., 2018), AphB (3SZP, Taylor et al ., 2012), 1132 (5Y9S, Jang et al ., 2018) and CrgA (3HHG, Sainsbury et al ., 2009)…”

Section: Methodsmentioning

confidence: 99%

Exploring generality of experimental conformational changes with AlphaFold predictions

Castellví

Medina

Petrillo

et al. 2022

Preprint

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Structural predictions have matched the accuracy of experimental structures in the case of close homologues, outperformed docking methods for multimeric complexes and helped sampling the conformational landscape of transporters and receptors. Such successes prompt the question whether predictions can be used to relate experimental structures in the context of available knowledge. LysR-type transcriptional regulators (LTTR) constitute the most common family of bacterial regulators. Intriguingly, their experimental structures are remarkably diverse. The active species, composed of flexible monomers dimerizing through their N- and C-terminal domains in a circular arrangement, differ across LTTR, due to intrinsic sequence differences or because crystals stabilize diverse snapshots of a common dynamic mechanism. We have used AlphaFold2 (AF) to interrogate the experimental AtzR structure in the context of predictions guided towards the different hetero-multimeric conformations known for other LTTR. Our approach drives AF prediction with the structure-based selection of the information input through sequence alignment and template conformation, linked to examination of the energy with PISA and interactions with ALEPH.

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“…This interface may play a role in conformational changes associated with DNA binding and transcriptional activation in response to effector binding (65). However, since it is missing in many CbnR-like proteins, such as OxyR (59) and DarR (130), a role in quaternary structural assembly is more likely specific to individual LTTRs rather than a general feature.…”

Section: Assembly Of Oligomersmentioning

confidence: 99%

“…Caution should be used in assessing such binding. During experimental procedures, small molecules, such as benzoate (33) and 2-morpholinoethanesulfonic acid monohydrate (130), may bind tightly and cause artifacts. Exhaustive dialysis is recommended to remove tightly bound ligands.…”

Section: Molecular Features Of Effector Bindingmentioning

confidence: 99%

Versatility and Complexity: Common and Uncommon Facets of LysR-Type Transcriptional Regulators

Baugh

Momany

Neidle

2023

Annu. Rev. Microbiol.

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LysR-type transcriptional regulators (LTTRs) form one of the largest families of bacterial regulators. They are widely distributed and contribute to all aspects of metabolism and physiology. Most are homotetramers, with each subunit composed of an N-terminal DNA-binding domain followed by a long helix connecting to an effector-binding domain. LTTRs typically bind DNA in the presence or absence of a small-molecule ligand (effector). In response to cellular signals, conformational changes alter DNA interactions, contact with RNA polymerase, and sometimes contact with other proteins. Many are dual-function repressor–activators, although different modes of regulation may occur at multiple promoters. This review presents an update on the molecular basis of regulation, the complexity of regulatory schemes, and applications in biotechnology and medicine. The abundance of LTTRs reflects their versatility and importance. While a single regulatory model cannot describe all family members, a comparison of similarities and differences provides a framework for future study. Expected final online publication date for the Annual Review of Microbiology, Volume 77 is September 2023. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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Crystal structure details of Vibrio fischeri DarR and mutant DarR-M202I from LTTR family reveals their activation mechanism

Cited by 7 publications

References 39 publications

The LysR family transcriptional regulator ORF-L16 regulates spinosad biosynthesis in Saccharopolyspora spinosa

The LysR family transcriptional regulator ORF-L16 regulates spinosad biosynthesis in Saccharopolyspora spinosa

Exploring generality of experimental conformational changes with AlphaFold predictions

Versatility and Complexity: Common and Uncommon Facets of LysR-Type Transcriptional Regulators

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