Discrimination between closely related cellular metabolites by the SAM-I riboswitch.

The SAM-I riboswitch is a cis-acting element of genetic control found in bacterial mRNAs that specifically binds S-adenosylmethionine (SAM). We previously determined the 2.9-A X-ray crystal structure of the effector-binding domain of this RNA element, revealing details of RNA-ligand recognition. To improve this structure, variations were made to the RNA sequence to alter lattice contacts, resulting in a 0.5-A improvement in crystallographic resolution and allowing for a more accurate refinement of the crystallographic model. The basis for SAM specificity was addressed by a structural analysis of the RNA complexed to S-adenosylhomocysteine (SAH) and sinefungin and by measuring the affinity of SAM and SAH for a series of mutants using isothermal titration calorimetry. These data illustrate the importance of two universally conserved base pairs in the RNA that form electrostatic interactions with the positively charged sulfonium group of SAM, thereby providing a basis for discrimination between SAM and SAH.

[1]  J. Tellinghuisen.  Optimizing experimental parameters in isothermal titration calorimetry: variable volume procedures. , 2007, The journal of physical chemistry. B.

[2]  A. Ferré-D’Amaré,et al.  Crystal structures of the thi-box riboswitch bound to thiamine pyrophosphate analogs reveal adaptive RNA-small molecule recognition. , 2006, Structure.

[3]  P Argos,et al.  Accessibility to internal cavities and ligand binding sites monitored by protein crystallographic thermal factors , 1998, Proteins.

[4]  S. Phillips,et al.  Electrostatic activation of Escherichia coli methionine repressor. , 1994, Structure.

[5]  N. Ban,et al.  Structural basis of thiamine pyrophosphate analogues binding to the eukaryotic riboswitch. , 2008, Journal of the American Chemical Society.

[6]  Zheng Yuan,et al.  Flexibility analysis of enzyme active sites by crystallographic temperature factors. , 2003, Protein engineering.

[7]  U. Baumann,et al.  An efficient one-step site-directed and site-saturation mutagenesis protocol. , 2004, Nucleic acids research.

[8]  T. Cech,et al.  Structure of the Tetrahymena ribozyme: base triple sandwich and metal ion at the active site. , 2004, Molecular cell.

[9]  Joseph D. Bauman,et al.  Crystal engineering of HIV-1 reverse transcriptase for structure-based drug design , 2008, Nucleic acids research.

[10]  R. Batey,et al.  Crystal Structure of the Lysine Riboswitch Regulatory mRNA Element* , 2008, Journal of Biological Chemistry.

[11]  R. Breaker,et al.  Riboswitches as antibacterial drug targets , 2006, Nature Biotechnology.

[12]  J. Wedekind,et al.  A posteriori design of crystal contacts to improve the X-ray diffraction properties of a small RNA enzyme , 2007, Acta crystallographica. Section D, Biological crystallography.

[13]  R. Breaker,et al.  Molecular-recognition characteristics of SAM-binding riboswitches. , 2006, Angewandte Chemie.

[14]  R J Read,et al.  Crystallography & NMR system: A new software suite for macromolecular structure determination. , 1998, Acta crystallographica. Section D, Biological crystallography.

[15]  Jeffrey E. Barrick,et al.  Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria , 2005, Genome Biology.

[16]  P. Ueland.  Pharmacological and biochemical aspects of S-adenosylhomocysteine and S-adenosylhomocysteine hydrolase. , 1982, Pharmacological reviews.

[17]  Feng Guo,et al.  Evolution of Tetrahymena ribozyme mutants with increased structural stability , 2002, Nature Structural Biology.

[18]  H. Yamaguchi,et al.  ‘Crystal lattice engineering,’ an approach to engineer protein crystal contacts by creating intermolecular symmetry: Crystallization and structure determination of a mutant human RNase 1 with a hydrophobic interface of leucines , 2007, Protein science : a publication of the Protein Society.

[19]  T. Henkin,et al.  The SMK box is a new SAM-binding RNA for translational regulation of SAM synthetase , 2006, Nature Structural &Molecular Biology.

[20]  T. Henkin,et al.  Crystal structures of the SAM-III/SMK riboswitch reveal the SAM-dependent translation inhibition mechanism , 2008, Nature Structural &Molecular Biology.

[21]  T. Cech,et al.  Structural basis of the enhanced stability of a mutant ribozyme domain and a detailed view of RNA--solvent interactions. , 2001, Structure.

[22]  P. Vekilov,et al.  Entropy and surface engineering in protein crystallization. , 2006, Acta crystallographica. Section D, Biological crystallography.

[23]  R. Batey,et al.  Structure of the SAM-II riboswitch bound to S-adenosylmethionine , 2008, Nature Structural &Molecular Biology.

[24]  Zasha Weinberg,et al.  The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches. , 2008, RNA.

[25]  Martin Phillips,et al.  Toward the structural genomics of complexes: crystal structure of a PE/PPE protein complex from Mycobacterium tuberculosis. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[26]  A. Serganov,et al.  Structural insights into amino acid binding and gene control by a lysine riboswitch , 2008, Nature.

[27]  S. Parthasarathy,et al.  Analysis of temperature factor distribution in high‐resolution protein structures , 1997, Protein science : a publication of the Protein Society.

[28]  R. Shoeman,et al.  Regulation of methionine synthesis in Escherichia coli: Effect of metJ gene product and S-adenosylmethionine on the expression of the metF gene. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[29]  D. Lilley,et al.  The kink-turn motif in RNA is dimorphic, and metal ion-dependent. , 2004, RNA.

[30]  D. Lilley,et al.  The role of specific 2'-hydroxyl groups in the stabilization of the folded conformation of kink-turn RNA. , 2006, RNA.

[31]  Wade C Winkler,et al.  Riboswitches and the role of noncoding RNAs in bacterial metabolic control. , 2005, Current opinion in chemical biology.

[32]  Andrea L Edwards,et al.  Adaptive ligand binding by the purine riboswitch in the recognition of guanine and adenine analogs. , 2009, Structure.

[33]  Z. Otwinowski,et al.  Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.

[34]  R. Montange,et al.  Structure of the S-adenosylmethionine riboswitch regulatory mRNA element , 2006, Nature.

[35]  T. Henkin,et al.  Transcription termination control of the S box system: Direct measurement of S-adenosylmethionine by the leader RNA , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[36]  Randy J Read,et al.  Electronic Reprint Biological Crystallography Phenix: Building New Software for Automated Crystallographic Structure Determination Biological Crystallography Phenix: Building New Software for Automated Crystallographic Structure Determination , 2022 .

[37]  J. Tellinghuisen.  Isothermal titration calorimetry at very low c. , 2008, Analytical biochemistry.

[38]  Jeffrey E. Barrick,et al.  The distributions, mechanisms, and structures of metabolite-binding riboswitches , 2007, Genome Biology.

[39]  J F Brandts,et al.  Rapid measurement of binding constants and heats of binding using a new titration calorimeter. , 1989, Analytical biochemistry.

[40]  R. Gumport,et al.  Structures of Liganded and Unliganded RsrI N6-Adenine DNA Methyltransferase , 2003, Journal of Biological Chemistry.

[41]  J. Pflugrath,et al.  The finer things in X-ray diffraction data collection. , 1999, Acta crystallographica. Section D, Biological crystallography.

[42]  Quentin Vicens,et al.  Local RNA structural changes induced by crystallization are revealed by SHAPE. , 2007, RNA.

[43]  T. Yeates,et al.  Crystal structure of a protein repair methyltransferase from Pyrococcus furiosus with its L-isoaspartyl peptide substrate. , 2001, Journal of molecular biology.

[44]  J. Kieft,et al.  A general method for rapid and nondenaturing purification of RNAs. , 2004, RNA.

[45]  Kevin Cowtan,et al.  research papers Acta Crystallographica Section D Biological , 2005 .

[46]  Douglas L. Theobald,et al.  THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures , 2006, Bioinform..

[47]  Susan Budavari,et al.  The Merck index , 1998 .

[48]  W Bruce Turnbull,et al.  On the value of c: can low affinity systems be studied by isothermal titration calorimetry? , 2003, Journal of the American Chemical Society.

[49]  Ali Nahvi,et al.  An mRNA structure that controls gene expression by binding S-adenosylmethionine , 2003, Nature Structural Biology.

[50]  R. Breaker,et al.  Riboswitches that sense S-adenosylmethionine and S-adenosylhomocysteine. , 2008, Biochemistry and cell biology = Biochimie et biologie cellulaire.

[51]  Vitaly Epshtein,et al.  The riboswitch-mediated control of sulfur metabolism in bacteria , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[52]  R. Montange,et al.  Structural studies of the purine and SAM binding riboswitches. , 2006, Cold Spring Harbor symposia on quantitative biology.