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PDBsum entry 2gis
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dna_rna ligands metals links
RNA PDB id
2gis

 

 

 

 

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Contents
DNA/RNA
Ligands
IRI ×4
SAM
Metals
_MG ×2
Waters ×88
PDB id:
2gis
Name: RNA
Title: Structure of the s-adenosylmethionine riboswitch mRNA regulatory element
Structure: Sam-i riboswitch. Chain: a. Engineered: yes
Source: Synthetic: yes. Other_details: this sequence was engineered based on the sam-i riboswitch from the metf-meth operon in thermoanaerobacter tengcongensis
Resolution:
2.90Å     R-factor:   0.266     R-free:   0.289
Authors: R.K.Montange,R.T.Batey
Key ref:
R.K.Montange and R.T.Batey (2006). Structure of the S-adenosylmethionine riboswitch regulatory mRNA element. Nature, 441, 1172-1175. PubMed id: 16810258 DOI: 10.1038/nature04819
Date:
29-Mar-06     Release date:   04-Jul-06    
 Headers
 References

DNA/RNA chain
  G-G-C-U-U-A-U-C-A-A-G-A-G-A-G-G-U-G-G-A-G-G-G-A-C-U-G-G-C-C-C-G-A-U-G-A-A-A-C- 94 bases

 

 
DOI no: 10.1038/nature04819 Nature 441:1172-1175 (2006)
PubMed id: 16810258  
 
 
Structure of the S-adenosylmethionine riboswitch regulatory mRNA element.
R.K.Montange, R.T.Batey.
 
  ABSTRACT  
 
Riboswitches are cis-acting genetic regulatory elements found in the 5'-untranslated regions of messenger RNAs that control gene expression through their ability to bind small molecule metabolites directly. Regulation occurs through the interplay of two domains of the RNA: an aptamer domain that responds to intracellular metabolite concentrations and an expression platform that uses two mutually exclusive secondary structures to direct a decision-making process. In Gram-positive bacteria such as Bacillus species, riboswitches control the expression of more than 2% of all genes through their ability to respond to a diverse set of metabolites including amino acids, nucleobases and protein cofactors. Here we report the 2.9-angstroms resolution crystal structure of an S-adenosylmethionine (SAM)-responsive riboswitch from Thermoanaerobacter tengcongensis complexed with S-adenosylmethionine, an RNA element that controls the expression of several genes involved in sulphur and methionine metabolism. This RNA folds into a complex three-dimensional architecture that recognizes almost every functional group of the ligand through a combination of direct and indirect readout mechanisms. Ligand binding induces the formation of a series of tertiary interactions with one of the helices, serving as a communication link between the aptamer and expression platform domains.
 
  Selected figure(s)  
 
Figure 1.
Figure 1: Secondary and tertiary structure of the SAM-I riboswitch.
Figure 1 : Secondary and tertiary structure of the SAM-I riboswitch. Unfortunately we are unable to provide accessible alternative text for this. If you require assistance to access this image, or to obtain a text description, please contact npg@nature.com-
a, Secondary structure of the SAM-I riboswitch aptamer domain reflecting the tertiary organization; nucleotides more than 95% conserved across phylogeny are highlighted in red. Solid arrows represent the direction of the RNA backbone, and elements of structure are labelled as follows: P, paired; J, joining; KT, kink-turn; PK, pseudoknot. Colours used to denote elements of structure are consistent with subsequent figures. b, Ribbon representation of the three-dimensional structure. The two views represent a front view (left) and a 90° clockwise rotation (right). SAM is in red with its surface represented as dots. 		Figure 4.
Figure 4: Detailed view of SAM recognition by the riboswitch. a, Stereo view of the SAM-binding pocket comprising the P1 and P3 helices and J1/2. b, Hydrogen-bonding interactions between the adenine base of SAM, A45 and U57. The experimental electron density map is shown as an orange cage, contoured at 1.25 . c, Interactions between the main chain atoms of methionine and the G58–C44 pair in P3 and G11 of J1/2. Distances in b and c are given in ångströms. d, SAM binding to the P1 helix; selectivity for SAM is probably mediated through electrostatic interactions with the carbonyl O2 of U7 and U88 (double-headed arrows). e, Ligand-induced interactions between the P3 helix and the 3' side of the P1 helix (black dashed lines).
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2006, 441, 1172-1175) copyright 2006.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21532599 B.Heppell, S.Blouin, A.M.Dussault, J.Mulhbacher, E.Ennifar, J.C.Penedo, and D.A.Lafontaine (2011).
Molecular insights into the ligand-controlled organization of the SAM-I riboswitch.
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21333656 J.Wang, and E.P.Nikonowicz (2011).
Solution structure of the K-turn and Specifier Loop domains from the Bacillus subtilis tyrS T-box leader RNA.
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21348498 N.Veeraraghavan, A.Ganguly, J.H.Chen, P.C.Bevilacqua, S.Hammes-Schiffer, and B.L.Golden (2011).
Metal binding motif in the active site of the HDV ribozyme binds divalent and monovalent ions.
  Biochemistry, 50, 2672-2682.  
21317896 P.Y.Watson, and M.J.Fedor (2011).
The glmS riboswitch integrates signals from activating and inhibitory metabolites in vivo.
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21169337 S.Blouin, R.Chinnappan, and D.A.Lafontaine (2011).
Folding of the lysine riboswitch: importance of peripheral elements for transcriptional regulation.
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20830434 S.Gallo, S.Mundwiler, R.Alberto, and R.K.Sigel (2011).
The change of corrin-amides to carboxylates leads to altered structures of the B12-responding btuB riboswitch.
  Chem Commun (Camb), 47, 403-405.  
21097777 S.P.Hennelly, and K.Y.Sanbonmatsu (2011).
Tertiary contacts control switching of the SAM-I riboswitch.
  Nucleic Acids Res, 39, 2416-2431.  
21850044 Y.Wan, M.Kertesz, R.C.Spitale, E.Segal, and H.Y.Chang (2011).
Understanding the transcriptome through RNA structure.
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20145044 A.H.Antonioli, J.C.Cochrane, S.V.Lipchock, and S.A.Strobel (2010).
Plasticity of the RNA kink turn structural motif.
  RNA, 16, 762-768.
PDB code: 3iin
21143313 A.M.Smith, R.T.Fuchs, F.J.Grundy, and T.M.Henkin (2010).
The SAM-responsive S(MK) box is a reversible riboswitch.
  Mol Microbiol, 78, 1393-1402.  
20637415 C.D.Stoddard, R.K.Montange, S.P.Hennelly, R.P.Rambo, K.Y.Sanbonmatsu, and R.T.Batey (2010).
Free state conformational sampling of the SAM-I riboswitch aptamer domain.
  Structure, 18, 787-797.
PDB codes: 3iqn 3iqp 3iqr
20498460 C.E.Hajdin, F.Ding, N.V.Dokholyan, and K.M.Weeks (2010).
On the significance of an RNA tertiary structure prediction.
  RNA, 16, 1340-1349.  
20637410 J.E.Wedekind (2010).
The apo riboswitch as a molecular hydra.
  Structure, 18, 757-758.  
20562215 K.T.Schroeder, S.A.McPhee, J.Ouellet, and D.M.Lilley (2010).
A structural database for k-turn motifs in RNA.
  RNA, 16, 1463-1468.  
21145485 L.Huang, A.Serganov, and D.J.Patel (2010).
Structural insights into ligand recognition by a sensing domain of the cooperative glycine riboswitch.
  Mol Cell, 40, 774-786.
PDB codes: 3owi 3oww 3owz 3ox0 3oxb 3oxd 3oxe 3oxj 3oxm
19925806 M.Ali, J.Lipfert, S.Seifert, D.Herschlag, and S.Doniach (2010).
The ligand-free state of the TPP riboswitch: a partially folded RNA structure.
  J Mol Biol, 396, 153-165.  
20466811 M.Falb, I.Amata, F.Gabel, B.Simon, and T.Carlomagno (2010).
Structure of the K-turn U4 RNA: a combined NMR and SANS study.
  Nucleic Acids Res, 38, 6274-6285.
PDB code: 2xeb
20106958 N.J.Baird, and A.R.Ferré-D'Amaré (2010).
Idiosyncratically tuned switching behavior of riboswitch aptamer domains revealed by comparative small-angle X-ray scattering analysis.
  RNA, 16, 598-609.  
20006621 R.K.Montange, E.Mondragón, D.van Tyne, A.D.Garst, P.Ceres, and R.T.Batey (2010).
Discrimination between closely related cellular metabolites by the SAM-I riboswitch.
  J Mol Biol, 396, 761-772.
PDB codes: 3gx2 3gx3 3gx5 3gx6 3gx7
20106957 R.P.Rambo, and J.A.Tainer (2010).
Improving small-angle X-ray scattering data for structural analyses of the RNA world.
  RNA, 16, 638-646.  
20097063 R.P.Rambo, and J.A.Tainer (2010).
Bridging the solution divide: comprehensive structural analyses of dynamic RNA, DNA, and protein assemblies by small-angle X-ray scattering.
  Curr Opin Struct Biol, 20, 128-137.  
20230605 Z.Weinberg, J.X.Wang, J.Bogue, J.Yang, K.Corbino, R.H.Moy, and R.R.Breaker (2010).
Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes.
  Genome Biol, 11, R31.  
19595806 A.D.Garst, and R.T.Batey (2009).
A switch in time: detailing the life of a riboswitch.
  Biochim Biophys Acta, 1789, 584-591.  
19298181 A.Roth, and R.R.Breaker (2009).
The structural and functional diversity of metabolite-binding riboswitches.
  Annu Rev Biochem, 78, 305-334.  
19169240 A.Serganov, L.Huang, and D.J.Patel (2009).
Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch.
  Nature, 458, 233-237.
PDB codes: 3f2q 3f2t 3f2w 3f2x 3f2y 3f30 3f4e 3f4g 3f4h
19303767 A.Serganov (2009).
The long and the short of riboswitches.
  Curr Opin Struct Biol, 19, 251-259.  
19776155 E.Poiata, M.M.Meyer, T.D.Ames, and R.R.Breaker (2009).
A variant riboswitch aptamer class for S-adenosylmethionine common in marine bacteria.
  RNA, 15, 2046-2056.  
19152843 H.Fauzi, A.Agyeman, and J.V.Hines (2009).
T box transcription antitermination riboswitch: influence of nucleotide sequence and orientation on tRNA binding by the antiterminator element.
  Biochim Biophys Acta, 1789, 185-191.  
19783814 K.T.Schroeder, and D.M.Lilley (2009).
Ion-induced folding of a kink turn that departs from the conventional sequence.
  Nucleic Acids Res, 37, 7281-7289.  
19625387 M.Sharma, G.Bulusu, and A.Mitra (2009).
MD simulations of ligand-bound and ligand-free aptamer: molecular level insights into the binding and switching mechanism of the add A-riboswitch.
  RNA, 15, 1673-1692.  
19167285 P.C.Whitford, A.Schug, J.Saunders, S.P.Hennelly, J.N.Onuchic, and K.Y.Sanbonmatsu (2009).
Nonlocal helix formation is key to understanding S-adenosylmethionine-1 riboswitch function.
  Biophys J, 96, L7-L9.  
19101979 S.Blouin, J.Mulhbacher, J.C.Penedo, and D.A.Lafontaine (2009).
Riboswitches: ancient and promising genetic regulators.
  Chembiochem, 10, 400-416.  
19720737 W.Huang, J.Kim, S.Jha, and F.Aboul-ela (2009).
A mechanism for S-adenosyl methionine assisted formation of a riboswitch conformation: a small molecule with a strong arm.
  Nucleic Acids Res, 37, 6528-6539.  
18593706 A.D.Garst, A.Héroux, R.P.Rambo, and R.T.Batey (2008).
Crystal structure of the lysine riboswitch regulatory mRNA element.
  J Biol Chem, 283, 22347-22351.
PDB codes: 3d0u 3d0x
18163882 A.Rentmeister, G.Mayer, N.Kuhn, and M.Famulok (2008).
Secondary structures and functional requirements for thiM riboswitches from Desulfovibrio vulgaris, Erwinia carotovora and Rhodobacter spheroides.
  Biol Chem, 389, 127-134.  
18255277 A.Serganov, and D.J.Patel (2008).
Towards deciphering the principles underlying an mRNA recognition code.
  Curr Opin Struct Biol, 18, 120-129.  
18784651 A.Serganov, L.Huang, and D.J.Patel (2008).
Structural insights into amino acid binding and gene control by a lysine riboswitch.
  Nature, 455, 1263-1267.
PDB codes: 3dig 3dil 3dim 3dio 3diq 3dir 3dis 3dix 3diy 3diz 3dj0 3dj2
18268025 C.D.Stoddard, S.D.Gilbert, and R.T.Batey (2008).
Ligand-dependent folding of the three-way junction in the purine riboswitch.
  RNA, 14, 675-684.  
18806797 C.Lu, A.M.Smith, R.T.Fuchs, F.Ding, K.Rajashankar, T.M.Henkin, and A.Ke (2008).
Crystal structures of the SAM-III/S(MK) riboswitch reveal the SAM-dependent translation inhibition mechanism.
  Nat Struct Mol Biol, 15, 1076-1083.
PDB codes: 3e5c 3e5e 3e5f
18084741 D.Xu, H.J.Kwon, and J.W.Suh (2008).
S-Adenosylmethionine induces BldH and activates secondary metabolism by involving the TTA-codon control of bldH expression in Streptomyces lividans.
  Arch Microbiol, 189, 419-426.  
18430893 J.C.Cochrane, and S.A.Strobel (2008).
Riboswitch effectors as protein enzyme cofactors.
  RNA, 14, 993.  
18039762 J.Tomsic, B.A.McDaniel, F.J.Grundy, and T.M.Henkin (2008).
Natural variability in S-adenosylmethionine (SAM)-dependent riboswitches: S-box elements in bacillus subtilis exhibit differential sensitivity to SAM In vivo and in vitro.
  J Bacteriol, 190, 823-833.  
18443629 J.X.Wang, and R.R.Breaker (2008).
Riboswitches that sense S-adenosylmethionine and S-adenosylhomocysteine.
  Biochem Cell Biol, 86, 157-168.  
18573075 R.K.Montange, and R.T.Batey (2008).
Riboswitches: emerging themes in RNA structure and function.
  Annu Rev Biophys, 37, 117-133.  
18369140 R.R.Breaker (2008).
Complex riboswitches.
  Science, 319, 1795-1797.  
18204466 S.D.Gilbert, R.P.Rambo, D.Van Tyne, and R.T.Batey (2008).
Structure of the SAM-II riboswitch bound to S-adenosylmethionine.
  Nat Struct Mol Biol, 15, 177-182.
PDB code: 2qwy
18506875 S.Gallo, M.Oberhuber, R.K.Sigel, and B.Kräutler (2008).
The corrin moiety of coenzyme B12 is the determinant for switching the btuB riboswitch of E. coli.
  Chembiochem, 9, 1408-1414.  
18369181 Z.Weinberg, E.E.Regulski, M.C.Hammond, J.E.Barrick, Z.Yao, W.L.Ruzzo, and R.R.Breaker (2008).
The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches.
  RNA, 14, 822-828.  
17941713 A.M.Wentzell, H.C.Rowe, B.G.Hansen, C.Ticconi, B.A.Halkier, and D.J.Kliebenstein (2007).
Linking metabolic QTLs with network and cis-eQTLs controlling biosynthetic pathways.
  PLoS Genet, 3, 1687-1701.  
17517779 A.Rentmeister, G.Mayer, N.Kuhn, and M.Famulok (2007).
Conformational changes in the expression domain of the Escherichia coli thiM riboswitch.
  Nucleic Acids Res, 35, 3713-3722.  
17846637 A.Serganov, and D.J.Patel (2007).
Ribozymes, riboswitches and beyond: regulation of gene expression without proteins.
  Nat Rev Genet, 8, 776-790.  
17637337 A.Y.Keel, R.P.Rambo, R.T.Batey, and J.S.Kieft (2007).
A general strategy to solve the phase problem in RNA crystallography.
  Structure, 15, 761-772.
PDB codes: 2pxb 2pxd 2pxe 2pxf 2pxk 2pxl 2pxp 2pxq 2pxt 2pxu 2pxv
17881365 B.J.Boese, and R.R.Breaker (2007).
In vitro selection and characterization of cellulose-binding DNA aptamers.
  Nucleic Acids Res, 35, 6378-6388.  
17764952 C.A.Wakeman, W.C.Winkler, and C.E.Dann (2007).
Structural features of metabolite-sensing riboswitches.
  Trends Biochem Sci, 32, 415-424.  
18078545 C.D.Putnam, M.Hammel, G.L.Hura, and J.A.Tainer (2007).
X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution.
  Q Rev Biophys, 40, 191-285.  
17449677 C.Musselman, H.M.Al-Hashimi, and I.Andricioaei (2007).
iRED analysis of TAR RNA reveals motional coupling, long-range correlations, and a dynamical hinge.
  Biophys J, 93, 411-422.  
17573364 E.Freyhult, V.Moulton, and P.Clote (2007).
Boltzmann probability of RNA structural neighbors and riboswitch detection.
  Bioinformatics, 23, 2054-2062.  
17146816 G.Mayer, M.S.Raddatz, J.D.Grunwald, and M.Famulok (2007).
RNA ligands that distinguish metabolite-induced conformations in the TPP riboswitch.
  Angew Chem Int Ed Engl, 46, 557-560.  
17997835 J.E.Barrick, and R.R.Breaker (2007).
The distributions, mechanisms, and structures of metabolite-binding riboswitches.
  Genome Biol, 8, R239.  
17200422 J.F.Lemay, and D.A.Lafontaine (2007).
Core requirements of the adenine riboswitch aptamer for ligand binding.
  RNA, 13, 339-350.  
17118400 J.Lipfert, R.Das, V.B.Chu, M.Kudaravalli, N.Boyd, D.Herschlag, and S.Doniach (2007).
Structural transitions and thermodynamics of a glycine-dependent riboswitch from Vibrio cholerae.
  J Mol Biol, 365, 1393-1406.  
17158708 J.Liu, and D.M.Lilley (2007).
The role of specific 2'-hydroxyl groups in the stabilization of the folded conformation of kink-turn RNA.
  RNA, 13, 200-210.  
17355861 J.Miranda-Ríos (2007).
The THI-box riboswitch, or how RNA binds thiamin pyrophosphate.
  Structure, 15, 259-265.  
17911257 J.N.Kim, A.Roth, and R.R.Breaker (2007).
Guanine riboswitch variants from Mesoplasma florum selectively recognize 2'-deoxyguanosine.
  Proc Natl Acad Sci U S A, 104, 16092-16097.  
17175531 J.Noeske, J.Buck, B.Fürtig, H.R.Nasiri, H.Schwalbe, and J.Wöhnert (2007).
Interplay of 'induced fit' and preorganization in the ligand induced folding of the aptamer domain of the guanine binding riboswitch.
  Nucleic Acids Res, 35, 572-583.  
17967431 J.P.Gallivan (2007).
Toward reprogramming bacteria with small molecules and RNA.
  Curr Opin Chem Biol, 11, 612-619.  
17391549 P.C.Bevilacqua, A.L.Cerrone-Szakal, and N.A.Siegfried (2007).
Insight into the functional versatility of RNA through model-making with applications to data fitting.
  Q Rev Biophys, 40, 55-85.  
17383225 R.L.Coppins, K.B.Hall, and E.A.Groisman (2007).
The intricate world of riboswitches.
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17548432 R.T.Batey, and J.S.Kieft (2007).
Improved native affinity purification of RNA.
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17360376 R.T.Fuchs, F.J.Grundy, and T.M.Henkin (2007).
S-adenosylmethionine directly inhibits binding of 30S ribosomal subunits to the SMK box translational riboswitch RNA.
  Proc Natl Acad Sci U S A, 104, 4876-4880.  
17585050 S.Blouin, and D.A.Lafontaine (2007).
A loop loop interaction and a K-turn motif located in the lysine aptamer domain are important for the riboswitch gene regulation control.
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17960911 S.D.Gilbert, C.E.Love, A.L.Edwards, and R.T.Batey (2007).
Mutational analysis of the purine riboswitch aptamer domain.
  Biochemistry, 46, 13297-13309.
PDB codes: 2ees 2eet 2eeu 2eev 2eew
17574837 T.E.Edwards, D.J.Klein, and A.R.Ferré-D'Amaré (2007).
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17255002 W.Martin, and M.J.Russell (2007).
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  Science, 313, 1752-1756.
PDB codes: 2gcs 2gcv 2h0s 2h0w 2h0x 2h0z 2ho6 2ho7
17381304 E.A.Groisman, M.J.Cromie, Y.Shi, and T.Latifi (2006).
A Mg2+-responding RNA that controls the expression of a Mg2+ transporter.
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17381339 G.J.Hannon, F.V.Rivas, E.P.Murchison, and J.A.Steitz (2006).
The expanding universe of noncoding RNAs.
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17053084 J.Bove, C.L.Hord, and M.A.Mullen (2006).
The blossoming of RNA biology: Novel insights from plant systems.
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Riboswitches as antibacterial drug targets.
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16810234 S.Reichow, and G.Varani (2006).
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The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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