Recognition of 5′-YpG-3′ Sequences by Coupled Stacking/Hydrogen Bonding Interactions with Amino Acid Residues

Lamoureux, Jason S.; Maynes, Jason T.; Glover, J. N. Mark

doi:10.1016/j.jmb.2003.10.071

Cited by 54 publications

(46 citation statements)

References 48 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…This dual DNA-binding contact by TnrA/GlnR Arg28/Arg26 is somewhat reminiscent of the so-called 59-pyrimidineguanine-39 (59-YpG-39) interaction identified in multiple protein-DNA structures by Glover and coworkers (Lamoureux et al 2004). However, in a 59-YpG-39 interaction, the arginine makes specific hydrogen bonds to a guanine while simultaneously contacting the preceding pyrimidine, which becomes unstacked (Lamoureux et al 2004). In TnrA/GlnR, the Arg28/Arg26 interacts with a thymine that is 39 to the guanine that it contacts, and the bases are not significantly unstacked.…”

Section: Structures Of the Global Nitrogen Transcription Regulator Tnmentioning

confidence: 81%

Structures of regulatory machinery reveal novel molecular mechanisms controlling B. subtilis nitrogen homeostasis

et al. 2015

View full text Add to dashboard Cite

All cells must sense and adapt to changing nutrient availability. However, detailed molecular mechanisms coordinating such regulatory pathways remain poorly understood. In Bacillus subtilis, nitrogen homeostasis is controlled by a unique circuitry composed of the regulator TnrA, which is deactivated by feedback-inhibited glutamine synthetase (GS) during nitrogen excess and stabilized by GlnK upon nitrogen depletion, and the repressor GlnR. Here we describe a complete molecular dissection of this network. TnrA and GlnR, the global nitrogen homeostatic transcription regulators, are revealed as founders of a new structural family of dimeric DNA-binding proteins with C-terminal, flexible, effector-binding sensors that modulate their dimerization. Remarkably, the TnrA sensor domains insert into GS intersubunit catalytic pores, destabilizing the TnrA dimer and causing an unprecedented GS dodecamer-to-tetradecamer conversion, which concomitantly deactivates GS. In contrast, each subunit of the GlnK trimer “templates” active TnrA dimers. Unlike TnrA, GlnR sensors mediate an autoinhibitory dimer-destabilizing interaction alleviated by GS, which acts as a GlnR chaperone. Thus, these studies unveil heretofore unseen mechanisms by which inducible sensor domains drive metabolic reprograming in the model Gram-positive bacterium B. subtilis.

show abstract

Section: Structures Of the Global Nitrogen Transcription Regulator Tnmentioning

confidence: 81%

Structures of regulatory machinery reveal novel molecular mechanisms controlling B. subtilis nitrogen homeostasis

et al. 2015

View full text Add to dashboard Cite

show abstract

“…Ndt80 is a meiosisspecific transcription factor that binds to MSEs (26,53). The structure of the Ndt80 DNA-binding domain bound to a nearoptimal MSE binding site (consensus, 5=-YGNCACAAAA-3= [where N is any base, and Y is C or T]) has been solved (87,88,116,117). Ndt80 recognizes the MSE through an Ig fold, a conserved DNA-binding motif found in the human p53, NF-B, and STAT transcription factors (141).…”

Section: Middle Genesmentioning

confidence: 99%

The Sum1/Ndt80 Transcriptional Switch and Commitment to Meiosis in Saccharomyces cerevisiae

Winter

2012

Microbiol Mol Biol Rev

105

View full text Add to dashboard Cite

SUMMARY Cells encounter numerous signals during the development of an organism that induce division, differentiation, and apoptosis. These signals need to be present for defined intervals in order to induce stable changes in the cellular phenotype. The point after which an inducing signal is no longer needed for completion of a differentiation program can be termed the “commitment point.” Meiotic development in the yeast Saccharomyces cerevisiae (sporulation) provides a model system to study commitment. Similar to differentiation programs in multicellular organisms, the sporulation program in yeast is regulated by a transcriptional cascade that produces early, middle, and late sets of sporulation-specific transcripts. Although critical meiosis-specific events occur as early genes are expressed, commitment does not take place until middle genes are induced. Middle promoters are activated by the Ndt80 transcription factor, which is produced and activated shortly before most middle genes are expressed. In this article, I discuss the connection between Ndt80 and meiotic commitment. A transcriptional regulatory pathway makes NDT80 transcription contingent on the prior expression of early genes. Once Ndt80 is produced, the recombination (pachytene) checkpoint prevents activation of the Ndt80 protein. Upon activation, Ndt80 triggers a positive autoregulatory loop that leads to the induction of genes that promote exit from prophase, the meiotic divisions, and spore formation. The pathway is controlled by multiple feed-forward loops that give switch-like properties to the commitment transition. The conservation of regulatory components of the meiotic commitment pathway and the recently reported ability of Ndt80 to increase replicative life span are discussed.

show abstract

“…[26,27] Zahlreiche Arbeiten behandeln Kation-pWechselwirkungen in Proteinstrukturen [26][27][28][29][30][31][32][33] und in ProteinLigand- [12,34] und Protein-DNA-Komplexen. [35][36][37] Diese Analysen haben aufgedeckt, dass Ammoniumgruppen bevorzugt in der Nähe von aromatischen Ringen positioniert werden. [28,32] Berechnungen zufolge wirkt diese Wechselwirkung sogar stärker stabilisierend als eine analoge Salzbrü-cke, [38] und sie wird in Wasser weniger stark abgeschirmt.…”

Section: Schlussbemerkungen 9753unclassified

Anion‐π‐Wechselwirkungen ins rechte Licht gerückt

et al. 2011

View full text Add to dashboard Cite

Die supramolekulare Chemie ist ein Gebiet, das die Beziehung zwischen molekularer Struktur und molekularer Funktion erforscht. Es ist die Chemie der nichtkovalenten Bindung, die die Grundlage der spezifischen Erkennung und der Transport‐ und Regulationsvorgänge bildet, die biologische Vorgänge antreiben. Die klassischen Konstruktionsprinzipien der supramolekularen Chemie umfassen starke, gerichtete Wechselwirkungen wie Wasserstoffbrücken, Halogenbrücken und Kation‐π‐Komplexbildung, aber auch weniger gerichtete Kräfte wie Ionenpaarung, π‐π‐, solvophobe und Van‐der‐Waals‐Wechselwirkungen. In den letzten Jahren wurde auch die Anion‐π‐Wechselwirkung (eine anziehende Kraft zwischen einem elektronenarmen aromatischen System und einem Anion) als bis dahin unerforschte nichtkovalente Bindung erkannt, und ihre Natur wurde experimentell und theoretisch untersucht. Die Konstruktion selektiver Anionenrezeptoren und ‐kanäle auf der Grundlage dieser Wechselwirkung war ein wichtiger Fortschritt auf dem Gebiet der supramolekularen Chemie. Ziele dieses Aufsatzes sind: 1) aktuelle Vorstellungen über die Natur dieser Wechselwirkung zu diskutieren, 2) eine Übersicht über die wichtigsten experimentellen Arbeiten zu geben, in denen Anion‐π‐Bindung nachgewiesen wurden, und 3) Einblicke in die Richtungsabhängigkeit von Anion‐π‐Kontakten in Kristallstrukturen zu geben.

show abstract

Recognition of 5′-YpG-3′ Sequences by Coupled Stacking/Hydrogen Bonding Interactions with Amino Acid Residues

Cited by 54 publications

References 48 publications

Structures of regulatory machinery reveal novel molecular mechanisms controlling B. subtilis nitrogen homeostasis

Structures of regulatory machinery reveal novel molecular mechanisms controlling B. subtilis nitrogen homeostasis

The Sum1/Ndt80 Transcriptional Switch and Commitment to Meiosis in Saccharomyces cerevisiae

Anion‐π‐Wechselwirkungen ins rechte Licht gerückt

Contact Info

Product

Resources

About