Home LiteratureArticle Details
PMID: 20006621 Published · ppublish English Journal Article Research Support, N.I.H., Extramural

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

Journal of molecular biology ·Vol. 396 ·No. 3 ·2010-02-26 ·Pages 761-72

Montange RK, Mondragón E, van Tyne D, Garst AD, Ceres P, Batey RT

Abstract

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.

MeSH Terms
Adenosine/analogs & derivatives,metabolism Base Pairing Conserved Sequence Crystallography, X-Ray Kinetics Models, Molecular Mutation Nucleic Acid Conformation RNA, Bacterial/chemistry,genetics,metabolism RNA, Messenger/chemistry,genetics,metabolism S-Adenosylhomocysteine/metabolism S-Adenosylmethionine/metabolism
Chemicals
RNA, Bacterial RNA, Messenger S-Adenosylmethionine S-Adenosylhomocysteine Adenosine sinefungin
Authors & Affiliations
6 authors, click to expand affiliations / ORCID
Montange Rebecca K
Department of Chemistry and Biochemistry, University of Colorado, Boulder, Campus Box 215, Boulder, CO 80309-0215, USA.
Mondragón Estefanía
van Tyne Daria
Garst Andrew D
Ceres Pablo
Batey Robert T
References (51)
51 references, click to expand
  1. The riboswitch-mediated control of sulfur metabolism in bacteria.
    Proc Natl Acad Sci U S A. 2003 Apr 29;100(9):5052-6 PMID: 12702767
  2. Structural basis of thiamine pyrophosphate analogues binding to the eukaryotic riboswitch.
    J Am Chem Soc. 2008 Jul 2;130(26):8116-7 PMID: 18533652
  3. Processing of X-ray diffraction data collected in oscillation mode.
    Methods Enzymol. 1997;276:307-26 PMID: 27754618
  4. Optimizing experimental parameters in isothermal titration calorimetry: variable volume procedures.
    J Phys Chem B. 2007 Oct 4;111(39):11531-7 PMID: 17850136
  5. An efficient one-step site-directed and site-saturation mutagenesis protocol.
    Nucleic Acids Res. 2004 Aug 10;32(14):e115 PMID: 15304544
  6. The finer things in X-ray diffraction data collection.
    Acta Crystallogr D Biol Crystallogr. 1999 Oct;55(Pt 10):1718-25 PMID: 10531521
  7. PHENIX: building new software for automated crystallographic structure determination.
    Acta Crystallogr D Biol Crystallogr. 2002 Nov;58(Pt 11):1948-54 PMID: 12393927
  8. A general method for rapid and nondenaturing purification of RNAs.
    RNA. 2004 Jun;10(6):988-95 PMID: 15146082
  9. Evolution of Tetrahymena ribozyme mutants with increased structural stability.
    Nat Struct Biol. 2002 Nov;9(11):855-61 PMID: 12368901
  10. Toward the structural genomics of complexes: crystal structure of a PE/PPE protein complex from Mycobacterium tuberculosis.
    Proc Natl Acad Sci U S A. 2006 May 23;103(21):8060-5 PMID: 16690741
  11. The kink-turn motif in RNA is dimorphic, and metal ion-dependent.
    RNA. 2004 Feb;10(2):254-64 PMID: 14730024
  12. Riboswitches as antibacterial drug targets.
    Nat Biotechnol. 2006 Dec;24(12):1558-64 PMID: 17160062
  13. The role of specific 2'-hydroxyl groups in the stabilization of the folded conformation of kink-turn RNA.
    RNA. 2007 Feb;13(2):200-10 PMID: 17158708
  14. Structure of the SAM-II riboswitch bound to S-adenosylmethionine.
    Nat Struct Mol Biol. 2008 Feb;15(2):177-82 PMID: 18204466
  15. Transcription termination control of the S box system: direct measurement of S-adenosylmethionine by the leader RNA.
    Proc Natl Acad Sci U S A. 2003 Mar 18;100(6):3083-8 PMID: 12626738
  16. Crystal structure of the lysine riboswitch regulatory mRNA element.
    J Biol Chem. 2008 Aug 15;283(33):22347-51 PMID: 18593706
  17. Local RNA structural changes induced by crystallization are revealed by SHAPE.
    RNA. 2007 Apr;13(4):536-48 PMID: 17299128
  18. Isothermal titration calorimetry at very low c.
    Anal Biochem. 2008 Feb 15;373(2):395-7 PMID: 17920027
  19. Pharmacological and biochemical aspects of S-adenosylhomocysteine and S-adenosylhomocysteine hydrolase.
    Pharmacol Rev. 1982 Sep;34(3):223-53 PMID: 6760211
  20. Rapid measurement of binding constants and heats of binding using a new titration calorimeter.
    Anal Biochem. 1989 May 15;179(1):131-7 PMID: 2757186
  21. Structure of the S-adenosylmethionine riboswitch regulatory mRNA element.
    Nature. 2006 Jun 29;441(7097):1172-5 PMID: 16810258
  22. Structures of liganded and unliganded RsrI N6-adenine DNA methyltransferase: a distinct orientation for active cofactor binding.
    J Biol Chem. 2003 Jul 11;278(28):26094-101 PMID: 12732637
  23. Riboswitches that sense S-adenosylmethionine and S-adenosylhomocysteine.
    Biochem Cell Biol. 2008 Apr;86(2):157-68 PMID: 18443629
  24. The distributions, mechanisms, and structures of metabolite-binding riboswitches.
    Genome Biol. 2007;8(11):R239 PMID: 17997835
  25. Structural studies of the purine and SAM binding riboswitches.
    Cold Spring Harb Symp Quant Biol. 2006;71:259-68 PMID: 17381305
  26. Crystallography & NMR system: A new software suite for macromolecular structure determination.
    Acta Crystallogr D Biol Crystallogr. 1998 Sep 1;54(Pt 5):905-21 PMID: 9757107
  27. '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.
    Protein Sci. 2007 Jul;16(7):1389-97 PMID: 17586772
  28. Evidence for a second class of S-adenosylmethionine riboswitches and other regulatory RNA motifs in alpha-proteobacteria.
    Genome Biol. 2005;6(8):R70 PMID: 16086852
  29. Crystal structures of the thi-box riboswitch bound to thiamine pyrophosphate analogs reveal adaptive RNA-small molecule recognition.
    Structure. 2006 Sep;14(9):1459-68 PMID: 16962976
  30. Crystal structure of a protein repair methyltransferase from Pyrococcus furiosus with its L-isoaspartyl peptide substrate.
    J Mol Biol. 2001 Nov 9;313(5):1103-16 PMID: 11700066
  31. Accessibility to internal cavities and ligand binding sites monitored by protein crystallographic thermal factors.
    Proteins. 1998 May 1;31(2):201-13 PMID: 9593193
  32. Structural insights into amino acid binding and gene control by a lysine riboswitch.
    Nature. 2008 Oct 30;455(7217):1263-7 PMID: 18784651
  33. Regulation of methionine synthesis in Escherichia coli: Effect of metJ gene product and S-adenosylmethionine on the expression of the metF gene.
    Proc Natl Acad Sci U S A. 1985 Jun;82(11):3601-5 PMID: 16593564
  34. Electrostatic activation of Escherichia coli methionine repressor.
    Structure. 1994 Apr 15;2(4):309-16 PMID: 8087557
  35. On the value of c: can low affinity systems be studied by isothermal titration calorimetry?
    J Am Chem Soc. 2003 Dec 3;125(48):14859-66 PMID: 14640663
  36. Crystal engineering of HIV-1 reverse transcriptase for structure-based drug design.
    Nucleic Acids Res. 2008 Sep;36(15):5083-92 PMID: 18676450
  37. Entropy and surface engineering in protein crystallization.
    Acta Crystallogr D Biol Crystallogr. 2006 Jan;62(Pt 1):116-24 PMID: 16369101
  38. Structural basis of the enhanced stability of a mutant ribozyme domain and a detailed view of RNA--solvent interactions.
    Structure. 2001 Mar 7;9(3):221-31 PMID: 11286889
  39. Analysis of temperature factor distribution in high-resolution protein structures.
    Protein Sci. 1997 Dec;6(12):2561-7 PMID: 9416605
  40. THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures.
    Bioinformatics. 2006 Sep 1;22(17):2171-2 PMID: 16777907
  41. Coot: model-building tools for molecular graphics.
    Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2126-32 PMID: 15572765
  42. Structure of the Tetrahymena ribozyme: base triple sandwich and metal ion at the active site.
    Mol Cell. 2004 Nov 5;16(3):351-62 PMID: 15525509
  43. A posteriori design of crystal contacts to improve the X-ray diffraction properties of a small RNA enzyme.
    Acta Crystallogr D Biol Crystallogr. 2007 Jul;63(Pt 7):812-25 PMID: 17582172
  44. Crystal structures of the SAM-III/S(MK) riboswitch reveal the SAM-dependent translation inhibition mechanism.
    Nat Struct Mol Biol. 2008 Oct;15(10):1076-83 PMID: 18806797
  45. Adaptive ligand binding by the purine riboswitch in the recognition of guanine and adenine analogs.
    Structure. 2009 Jun 10;17(6):857-68 PMID: 19523903
  46. The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches.
    RNA. 2008 May;14(5):822-8 PMID: 18369181
  47. Molecular-recognition characteristics of SAM-binding riboswitches.
    Angew Chem Int Ed Engl. 2006 Jan 30;45(6):964-8 PMID: 16381055
  48. The S(MK) box is a new SAM-binding RNA for translational regulation of SAM synthetase.
    Nat Struct Mol Biol. 2006 Mar;13(3):226-33 PMID: 16491091
  49. An mRNA structure that controls gene expression by binding S-adenosylmethionine.
    Nat Struct Biol. 2003 Sep;10(9):701-7 PMID: 12910260
  50. Flexibility analysis of enzyme active sites by crystallographic temperature factors.
    Protein Eng. 2003 Feb;16(2):109-14 PMID: 12676979
  51. Riboswitches and the role of noncoding RNAs in bacterial metabolic control.
    Curr Opin Chem Biol. 2005 Dec;9(6):594-602 PMID: 16226486
Article Info
Journal
Journal of molecular biology
Abbr.
J Mol Biol
ISSN
1089-8638
DOI
10.1016/j.jmb.2009.12.007
Published
2010-02-26
Epub
2009-00-16
Pages
761-72
Language
English
Region
England
NLM ID
2985088R
PMCID
PMC2822714
Subset
IM
Grants
NIGMS NIH HHS · R01 GM083953 · United States
NIGMS NIH HHS · R01 GM083953-02 · United States
NIGMS NIH HHS · T32 GM-065103 · United States
NIBIB NIH HHS · P30 EB009998 · United States
NIGMS NIH HHS · GM-083953 · United States
NIGMS NIH HHS · T32 GM065103 · United States
External Links
PubMed source DOI: 10.1016/j.jmb.2009.12.007 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2