Literature DB >> 21439473

Structural basis of cooperative ligand binding by the glycine riboswitch.

Ethan B Butler1, Yong Xiong, Jimin Wang, Scott A Strobel.   

Abstract

The glycine riboswitch regulates gene expression through the cooperative recognition of its amino acid ligand by a tandem pair of aptamers. A 3.6 Å crystal structure of the tandem riboswitch from the glycine permease operon of Fusobacterium nucleatum reveals the glycine binding sites and an extensive network of interactions, largely mediated by asymmetric A-minor contacts, that serve to communicate ligand binding status between the aptamers. These interactions provide a structural basis for how the glycine riboswitch cooperatively regulates gene expression.
Copyright © 2011 Elsevier Ltd. All rights reserved.

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Year:  2011        PMID: 21439473      PMCID: PMC3076126          DOI: 10.1016/j.chembiol.2011.01.013

Source DB:  PubMed          Journal:  Chem Biol        ISSN: 1074-5521


  23 in total

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Journal:  Proc Natl Acad Sci U S A       Date:  2001-04-10       Impact factor: 11.205

2.  Geometric nomenclature and classification of RNA base pairs.

Authors:  N B Leontis; E Westhof
Journal:  RNA       Date:  2001-04       Impact factor: 4.942

Review 3.  Cooperative hemoglobins: conserved fold, diverse quaternary assemblies and allosteric mechanisms.

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Journal:  Trends Biochem Sci       Date:  2001-05       Impact factor: 13.807

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Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2002-10-21

Review 5.  The riboswitch control of bacterial metabolism.

Authors:  Evgeny Nudler; Alexander S Mironov
Journal:  Trends Biochem Sci       Date:  2004-01       Impact factor: 13.807

6.  Refinement of macromolecular structures by the maximum-likelihood method.

Authors:  G N Murshudov; A A Vagin; E J Dodson
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  1997-05-01

7.  Phase combination and cross validation in iterated density-modification calculations.

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Journal:  Acta Crystallogr D Biol Crystallogr       Date:  1996-01-01

8.  New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control.

Authors:  Jeffrey E Barrick; Keith A Corbino; Wade C Winkler; Ali Nahvi; Maumita Mandal; Jennifer Collins; Mark Lee; Adam Roth; Narasimhan Sudarsan; Inbal Jona; J Kenneth Wickiser; Ronald R Breaker
Journal:  Proc Natl Acad Sci U S A       Date:  2004-04-19       Impact factor: 11.205

9.  Automated MAD and MIR structure solution.

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Review 10.  Mutagenic dissection of hemoglobin cooperativity: effects of amino acid alteration on subunit assembly of oxy and deoxy tetramers.

Authors:  G J Turner; F Galacteros; M L Doyle; B Hedlund; D W Pettigrew; B W Turner; F R Smith; W Moo-Penn; D L Rucknagel; G K Ackers
Journal:  Proteins       Date:  1992-11
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  61 in total

1.  An energetically beneficial leader-linker interaction abolishes ligand-binding cooperativity in glycine riboswitches.

Authors:  Eileen M Sherman; Jackie Esquiaqui; Galal Elsayed; Jing-Dong Ye
Journal:  RNA       Date:  2012-01-25       Impact factor: 4.942

2.  Bioinformatic analysis of riboswitch structures uncovers variant classes with altered ligand specificity.

Authors:  Zasha Weinberg; James W Nelson; Christina E Lünse; Madeline E Sherlock; Ronald R Breaker
Journal:  Proc Natl Acad Sci U S A       Date:  2017-03-06       Impact factor: 11.205

3.  Principles for Predicting RNA Secondary Structure Design Difficulty.

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Journal:  J Mol Biol       Date:  2016-02-17       Impact factor: 5.469

4.  Riboswitch structure and dynamics by smFRET microscopy.

Authors:  Krishna C Suddala; Nils G Walter
Journal:  Methods Enzymol       Date:  2014       Impact factor: 1.600

Review 5.  Themes and variations in riboswitch structure and function.

Authors:  Alla Peselis; Alexander Serganov
Journal:  Biochim Biophys Acta       Date:  2014-02-28

6.  Amino Acid Stabilization of Nucleic Acid Secondary Structure: Kinetic Insights from Single-Molecule Studies.

Authors:  David A Nicholson; Abhigyan Sengupta; Hsuan-Lei Sung; David J Nesbitt
Journal:  J Phys Chem B       Date:  2018-10-22       Impact factor: 2.991

7.  Modulation of quaternary structure and enhancement of ligand binding by the K-turn of tandem glycine riboswitches.

Authors:  Nathan J Baird; Adrian R Ferré-D'Amaré
Journal:  RNA       Date:  2012-12-17       Impact factor: 4.942

8.  DNA-rescuable allosteric inhibition of aptamer II ligand affinity by aptamer I element in the shortened Vibrio cholerae glycine riboswitch.

Authors:  Eileen M Sherman; Galal Elsayed; Jackie M Esquiaqui; Mohammed Elsayed; Bryan Brinda; Jing-Dong Ye
Journal:  J Biochem       Date:  2014-08-04       Impact factor: 3.387

9.  Refinement of the Listeria monocytogenes σB regulon through quantitative proteomic analysis.

Authors:  S Mujahid; R H Orsi; P Vangay; K J Boor; M Wiedmann
Journal:  Microbiology       Date:  2013-04-25       Impact factor: 2.777

10.  Structural and Dynamic Basis for Low-Affinity, High-Selectivity Binding of L-Glutamine by the Glutamine Riboswitch.

Authors:  Aiming Ren; Yi Xue; Alla Peselis; Alexander Serganov; Hashim M Al-Hashimi; Dinshaw J Patel
Journal:  Cell Rep       Date:  2015-11-19       Impact factor: 9.423

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