spacer
spacer

PDBsum entry 1koc
Go to PDB code: 
dna_rna ligands links
RNA PDB id
1koc

 

 

 

 

Loading ...

 
JSmol PyMol  
Contents
DNA/RNA
Ligands
ARG
PDB id:
1koc
Name: RNA
Title: RNA aptamer complexed with arginine, nmr
Structure: RNA (5'-r(p Ap Gp Ap Ap Gp Gp Ap Gp Cp Gp U)-3'). Chain: a. Engineered: yes. RNA (5'-r(p Ap Cp Ap Gp Gp Up Ap Gp Gp Up Cp Gp Cp U)-3'). Chain: b. Engineered: yes
Source: Synthetic: yes. Synthetic: yes
NMR struc: 1 models
Authors: Y.S.Yang,M.Kochoyan,P.Burgstaller,E.Westhof,M.Famulok
Key ref: Y.Yang et al. (1996). Structural basis of ligand discrimination by two related RNA aptamers resolved by NMR spectroscopy. Science, 272, 1343-1347. PubMed id: 8650546 DOI: 10.1126/science.272.5266.1343
Date:
28-Mar-96     Release date:   17-Aug-96    
 Headers
 References

DNA/RNA chains
  A-G-A-A-G-G-A-G-C-G-U 11 bases
  A-C-A-G-G-U-A-G-G-U-C-G-C-U 14 bases

 

 
DOI no: 10.1126/science.272.5266.1343 Science 272:1343-1347 (1996)
PubMed id: 8650546  
 
 
Structural basis of ligand discrimination by two related RNA aptamers resolved by NMR spectroscopy.
Y.Yang, M.Kochoyan, P.Burgstaller, E.Westhof, M.Famulok.
 
  ABSTRACT  
 
In a previous study, an RNA aptamer for the specific recognition of arginine was evolved from a parent sequence that bound citrulline specifically. The two RNAs differ at only 3 positions out of 44. The solution structures of the two aptamers complexed to their cognate amino acids have now been determined by two-dimensional nuclear magnetic resonance spectroscopy. Both aptamers contain two asymmetrical internal loops that are not well ordered in the free RNA but that fold into a compact structure upon ligand binding. Those nucleotides common to both RNAs include a conserved cluster of purine residues, three of which form an uneven plane containing a G:G pair, and two other residues nearly perpendicular to that surface. Two of the three variant nucleotides are stacked on the cluster of purines and form a triple contact to the amino acid side chain, whereas the edge of the third variant nucleotide is capping the binding pocket.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21194122 J.Zhou, B.Soontornworajit, M.P.Snipes, and Y.Wang (2011).
Structural prediction and binding analysis of hybridized aptamers.
  J Mol Recognit, 24, 119-126.  
20214401 S.W.Lee, L.Zhao, A.Pardi, and T.Xia (2010).
Ultrafast dynamics show that the theophylline and 3-methylxanthine aptamers employ a conformational capture mechanism for binding their ligands.
  Biochemistry, 49, 2943-2951.  
21110883 W.Ma (2010).
The scenario on the origin of translation in the RNA world: in principle of replication parsimony.
  Biol Direct, 5, 65.  
17994225 J.Müller, O.El-Maarri, J.Oldenburg, B.Pötzsch, and G.Mayer (2008).
Monitoring the progression of the in vitro selection of nucleic acid aptamers by denaturing high-performance liquid chromatography.
  Anal Bioanal Chem, 390, 1033-1037.  
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.  
16982640 K.H.Link, L.Guo, and R.R.Breaker (2006).
Examination of the structural and functional versatility of glmS ribozymes by using in vitro selection.
  Nucleic Acids Res, 34, 4968-4975.  
17118149 V.Thodima, M.Pirooznia, and Y.Deng (2006).
RiboaptDB: A Comprehensive Database of Ribozymes and Aptamers.
  BMC Bioinformatics, 7, S6.  
16143977 C.André, A.Xicluna, and Y.C.Guillaume (2005).
Aptamer-oligonucleotide binding studied by capillary electrophoresis: cation effect and separation efficiency.
  Electrophoresis, 26, 3247-3255.  
16228005 E.A.Curtis, and D.P.Bartel (2005).
New catalytic structures from an existing ribozyme.
  Nat Struct Mol Biol, 12, 994.  
15999244 I.Majerfeld, D.Puthenvedu, and M.Yarus (2005).
RNA affinity for molecular L-histidine; genetic code origins.
  J Mol Evol, 61, 226-235.  
16186130 I.Majerfeld, and M.Yarus (2005).
A diminutive and specific RNA binding site for L-tryptophan.
  Nucleic Acids Res, 33, 5482-5493.  
15952885 M.Yarus, J.G.Caporaso, and R.Knight (2005).
Origins of the genetic code: the escaped triplet theory.
  Annu Rev Biochem, 74, 179-198.  
14695514 J.Flinders, S.C.DeFina, D.M.Brackett, C.Baugh, C.Wilson, and T.Dieckmann (2004).
Recognition of planar and nonplanar ligands in the malachite green-RNA aptamer complex.
  Chembiochem, 5, 62-72.
PDB code: 1q8n
15452272 L.Weill, D.Louis, and B.Sargueil (2004).
Selection and evolution of NTP-specific aptamers.
  Nucleic Acids Res, 32, 5045-5058.  
12925993 D.S.Pilch, M.Kaul, C.M.Barbieri, and J.E.Kerrigan (2003).
Thermodynamics of aminoglycoside-rRNA recognition.
  Biopolymers, 70, 58-79.  
12579577 H.Gouda, I.D.Kuntz, D.A.Case, and P.A.Kollman (2003).
Free energy calculations for theophylline binding to an RNA aptamer: Comparison of MM-PBSA and thermodynamic integration methods.
  Biopolymers, 68, 16-34.  
12618190 V.Tereshko, E.Skripkin, and D.J.Patel (2003).
Encapsulating streptomycin within a small 40-mer RNA.
  Chem Biol, 10, 175-187.
PDB codes: 1nta 1ntb
14624002 Z.Huang, and J.W.Szostak (2003).
Evolution of aptamers with a new specificity and new secondary structures from an ATP aptamer.
  RNA, 9, 1456-1463.  
12429689 M.Yarus (2002).
Primordial genetics: phenotype of the ribocyte.
  Annu Rev Genet, 36, 125-151.  
12762023 M.Yarus (2001).
On translation by RNAs alone.
  Cold Spring Harb Symp Quant Biol, 66, 207-215.  
10786840 A.D.Ellington, M.Khrapov, and C.A.Shaw (2000).
The scene of a frozen accident.
  RNA, 6, 485-498.  
10851193 A.D.Frankel (2000).
Fitting peptides into the RNA world.
  Curr Opin Struct Biol, 10, 332-340.  
10836787 G.R.Zimmermann, C.L.Wick, T.P.Shields, R.D.Jenison, and A.Pardi (2000).
Molecular interactions and metal binding in the theophylline-binding core of an RNA aptamer.
  RNA, 6, 659-667.  
10792052 L.W.Hung, E.L.Holbrook, and S.R.Holbrook (2000).
The crystal structure of the Rev binding element of HIV-1 reveals novel base pairing and conformational variability.
  Proc Natl Acad Sci U S A, 97, 5107-5112.
PDB code: 1duq
10995243 M.E.Burkard, and D.H.Turner (2000).
NMR structures of r(GCAGGCGUGC)2 and determinants of stability for single guanosine-guanosine base pairs.
  Biochemistry, 39, 11748-11762.
PDB codes: 1f5g 1f5h
10786839 M.Yarus (2000).
RNA-ligand chemistry: a testable source for the genetic code.
  RNA, 6, 475-484.  
10786841 R.D.Knight, and L.F.Landweber (2000).
Guilt by association: the arginine case revisited.
  RNA, 6, 499-510.  
10653638 S.A.Robertson, K.Harada, A.D.Frankel, and D.E.Wemmer (2000).
Structure determination and binding kinetics of a DNA aptamer-argininamide complex.
  Biochemistry, 39, 946-954.
PDB code: 1db6
10924119 S.J.Schroeder, and D.H.Turner (2000).
Factors affecting the thermodynamic stability of small asymmetric internal loops in RNA.
  Biochemistry, 39, 9257-9274.  
10397790 C.Schneider, and J.Sühnel (1999).
A molecular dynamics simulation of the flavin mononucleotide-RNA aptamer complex.
  Biopolymers, 50, 287-302.  
10872462 D.S.Wilson, J.W.Szostak, and J.W.Szostak (1999).
In vitro selection of functional nucleic acids.
  Annu Rev Biochem, 68, 611-647.  
10573122 G.A.Soukup, and R.R.Breaker (1999).
Relationship between internucleotide linkage geometry and the stability of RNA.
  RNA, 5, 1308-1325.  
10089439 J.C.Nix, A.R.Newhoff, and C.Wilson (1999).
Preliminary crystallographic characterization of an in vitro evolved biotin-binding RNA pseudoknot.
  Acta Crystallogr D Biol Crystallogr, 55, 323-325.  
10361088 M.Famulok (1999).
Oligonucleotide aptamers that recognize small molecules.
  Curr Opin Struct Biol, 9, 324-329.  
10415510 R.D.Knight, and L.F.Landweber (1999).
Is the genetic code really a frozen accident? New evidence from in vitro selection.
  Ann N Y Acad Sci, 870, 408-410.  
11295748 S.J.Schroeder, M.E.Burkard, and D.H.Turner (1999).
The energetics of small internal loops in RNA.
  Biopolymers, 52, 157-167.  
10791023 Y.Chen, D.B.Carlini, J.F.Baines, J.Parsch, J.M.Braverman, S.Tanda, and W.Stephan (1999).
RNA secondary structure and compensatory evolution.
  Genes Genet Syst, 74, 271-286.  
9479477 A.Jenne, and M.Famulok (1998).
A novel ribozyme with ester transferase activity.
  Chem Biol, 5, 23-34.  
9818148 C.H.Lin, W.Wang, R.A.Jones, and D.J.Patel (1998).
Formation of an amino-acid-binding pocket through adaptive zippering-up of a large DNA hairpin loop.
  Chem Biol, 5, 555-572.
PDB code: 2arg
9772167 C.Wilson, J.Nix, and J.Szostak (1998).
Functional requirements for specific ligand recognition by a biotin-binding RNA pseudoknot.
  Biochemistry, 37, 14410-14419.  
9512549 D.Kiga, Y.Futamura, K.Sakamoto, and S.Yokoyama (1998).
An RNA aptamer to the xanthine/guanine base with a distinctive mode of purine recognition.
  Nucleic Acids Res, 26, 1755-1760.  
9503589 J.Kjems, and J.Egebjerg (1998).
Modern methods for probing RNA structure.
  Curr Opin Biotechnol, 9, 59-65.  
9751648 R.D.Knight, and L.F.Landweber (1998).
Rhyme or reason: RNA-arginine interactions and the genetic code.
  Chem Biol, 5, R215-R220.  
9204272 A.Ramos, C.C.Gubser, and G.Varani (1997).
Recent solution structures of RNA and its complexes with drugs, peptides and proteins.
  Curr Opin Struct Biol, 7, 317-323.  
9222502 B.E.Eaton, L.Gold, B.J.Hicke, N.Janjić, F.M.Jucker, D.P.Sebesta, T.M.Tarasow, M.C.Willis, and D.A.Zichi (1997).
Post-SELEX combinatorial optimization of aptamers.
  Bioorg Med Chem, 5, 1087-1096.  
9384529 C.H.Lin, and D.J.Patel (1997).
Structural basis of DNA folding and recognition in an AMP-DNA aptamer complex: distinct architectures but common recognition motifs for DNA and RNA aptamers complexed to AMP.
  Chem Biol, 4, 817-832.
PDB code: 1aw4
9245404 C.Mannironi, A.Di Nardo, P.Fruscoloni, and G.P.Tocchini-Valentini (1997).
In vitro selection of dopamine RNA ligands.
  Biochemistry, 36, 9726-9734.  
9384530 D.H.Burke, D.C.Hoffman, A.Brown, M.Hansen, A.Pardi, and L.Gold (1997).
RNA aptamers to the peptidyl transferase inhibitor chloramphenicol.
  Chem Biol, 4, 833-843.  
  8990394 D.H.Mathews, A.R.Banerjee, D.D.Luan, T.H.Eickbush, and D.H.Turner (1997).
Secondary structure model of the RNA recognized by the reverse transcriptase from the R2 retrotransposable element.
  RNA, 3, 1.  
9242901 G.J.Narlikar, and D.Herschlag (1997).
Mechanistic aspects of enzymatic catalysis: lessons from comparison of RNA and protein enzymes.
  Annu Rev Biochem, 66, 19-59.  
9253403 H.A.Heus (1997).
RNA aptamers.
  Nat Struct Biol, 4, 597-600.  
9131998 J.Tao, L.Chen, and A.D.Frankel (1997).
Dissection of the proposed base triple in human immunodeficiency virus TAR RNA indicates the importance of the Hoogsteen interaction.
  Biochemistry, 36, 3491-3495.  
9261068 K.A.Marshall, M.P.Robertson, and A.D.Ellington (1997).
A biopolymer by any other name would bind as well: a comparison of the ligand-binding pockets of nucleic acids and proteins.
  Structure, 5, 729-734.  
8939686 A.J.Hager, J.D.Pollard, and J.W.Szostak (1996).
Ribozymes: aiming at RNA replication and protein synthesis.
  Chem Biol, 3, 717-725.  
8946859 C.H.Lin, and D.J.Patel (1996).
Encapsulating an amino acid in a DNA fold.
  Nat Struct Biol, 3, 1046-1050.
PDB code: 1old
8807893 J.Feigon, T.Dieckmann, and F.W.Smith (1996).
Aptamer structures from A to zeta.
  Chem Biol, 3, 611-617.  
8946856 X.Ye, A.Gorin, A.D.Ellington, and D.J.Patel (1996).
Deep penetration of an alpha-helix into a widened RNA major groove in the HIV-1 rev peptide-RNA aptamer complex.
  Nat Struct Biol, 3, 1026-1033.
PDB code: 1ull
8811096 Y.Lin, D.Nieuwlandt, A.Magallanez, B.Feistner, and S.D.Jayasena (1996).
High-affinity and specific recognition of human thyroid stimulating hormone (hTSH) by in vitro-selected 2'-amino-modified RNA.
  Nucleic Acids Res, 24, 3407-3414.  
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.

 

spacer
spacer