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PDBsum entry 3d0x
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RNA PDB id
3d0x

 

 

 

 

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Contents
DNA/RNA
Waters ×60
PDB id:
3d0x
Name: RNA
Title: Crystal structure of the unbound lysine riboswitch
Structure: RNA (161-mer). Chain: a. Fragment: ligand binding domain. Engineered: yes
Source: Synthetic: yes
Resolution:
2.95Å     R-factor:   0.191     R-free:   0.220
Authors: R.T.Batey,A.D.Garst,A.Heroux,R.P.Rambo
Key ref: A.D.Garst et al. (2008). Crystal structure of the lysine riboswitch regulatory mRNA element. J Biol Chem, 283, 22347-22351. PubMed id: 18593706
Date:
02-May-08     Release date:   01-Jul-08    
 Headers
 References

DNA/RNA chain
  G-G-A-C-G-G-A-G-G-C-G-C-G-C-C-C-G-A-G-A-U-G-A-G-U-A-G-G-C-U-G-U-C-C-C-A-U-C-A- 161 bases

 

 
J Biol Chem 283:22347-22351 (2008)
PubMed id: 18593706  
 
 
Crystal structure of the lysine riboswitch regulatory mRNA element.
A.D.Garst, A.Héroux, R.P.Rambo, R.T.Batey.
 
  ABSTRACT  
 
Riboswitches are metabolite-sensitive elements found in mRNAs that control gene expression through a regulatory secondary structural switch. Along with regulation of lysine biosynthetic genes, mutations within the lysine-responsive riboswitch (L-box) play a role in the acquisition of resistance to antimicrobial lysine analogs. To understand the structural basis for lysine binding, we have determined the 2.8 angstroms resolution crystal structure of lysine bound to the Thermotoga maritima asd lysine riboswitch ligand-binding domain. The structure reveals a complex architecture scaffolding a binding pocket completely enveloping lysine. Mutations conferring antimicrobial resistance cluster around this site as well as highly conserved long range interactions, indicating that they disrupt lysine binding or proper folding of the RNA. Comparison of the free and bound forms by x-ray crystallography, small angle x-ray scattering, and chemical probing reveals almost identical structures, indicating that lysine induces only limited and local conformational changes upon binding.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
22868764 K.S.Keating, and A.M.Pyle (2012).
RCrane: semi-automated RNA model building.
  Acta Crystallogr D Biol Crystallogr, 68, 985-995.  
21068070 A.Werner (2011).
Predicting translational diffusion of evolutionary conserved RNA structures by the nucleotide number.
  Nucleic Acids Res, 39, e17.  
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.
  Nat Chem Biol, 7, 384-392.  
21169337 S.Blouin, R.Chinnappan, and D.A.Lafontaine (2011).
Folding of the lysine riboswitch: importance of peripheral elements for transcriptional regulation.
  Nucleic Acids Res, 39, 3373-3387.  
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
20637410 J.E.Wedekind (2010).
The apo riboswitch as a molecular hydra.
  Structure, 18, 757-758.  
19969538 J.M.Kelley, and D.Hamelberg (2010).
Atomistic basis for the on-off signaling mechanism in SAM-II riboswitch.
  Nucleic Acids Res, 38, 1392-1400.  
20581129 J.Ouellet, S.Melcher, A.Iqbal, Y.Ding, and D.M.Lilley (2010).
Structure of the three-way helical junction of the hepatitis C virus IRES element.
  RNA, 16, 1597-1609.  
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.  
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.  
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.  
19515936 A.Villa, J.Wöhnert, and G.Stock (2009).
Molecular dynamics simulation study of the binding of purine bases to the aptamer domain of the guanine sensing riboswitch.
  Nucleic Acids Res, 37, 4774-4786.  
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.  
19651704 M.Naville, and D.Gautheret (2009).
Transcription attenuation in bacteria: theme and variations.
  Brief Funct Genomic Proteomic, 8, 482-492.  
19898478 N.Kulshina, N.J.Baird, and A.R.Ferré-D'Amaré (2009).
Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch.
  Nat Struct Mol Biol, 16, 1212-1217.
PDB code: 3iwn
19523903 S.D.Gilbert, F.E.Reyes, A.L.Edwards, and R.T.Batey (2009).
Adaptive ligand binding by the purine riboswitch in the recognition of guanine and adenine analogs.
  Structure, 17, 857-868.
PDB codes: 3fo4 3fo6 3g4m 3gao 3ger 3ges 3gog 3got
18996893 I.Lebars, P.Legrand, A.Aimé, N.Pinaud, S.Fribourg, and C.Di Primo (2008).
Exploring TAR-RNA aptamer loop-loop interaction by X-ray crystallography, UV spectroscopy and surface plasmon resonance.
  Nucleic Acids Res, 36, 7146-7156.
PDB code: 2jlt
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 codes are shown on the right.

 

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