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PDBsum entry 1ikd
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RNA PDB id
1ikd

 

 

 

 

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Contents
DNA/RNA
PDB id:
1ikd
Name: RNA
Title: Acceptor stem, nmr, 30 structures
Structure: tRNA ala acceptor stem. Chain: a. Synonym: acceptor stem. Engineered: yes. Mutation: yes. Other_details: substrate for aminoacylation
Source: Synthetic: yes
NMR struc: 30 models
Authors: A.Ramos,G.Varani
Key ref: A.Ramos and G.Varani (1997). Structure of the acceptor stem of Escherichia coli tRNA Ala: role of the G3.U70 base pair in synthetase recognition. Nucleic Acids Res, 25, 2083-2090. PubMed id: 9153306
Date:
15-Nov-96     Release date:   01-Apr-97    
 Headers
 References

DNA/RNA chain
  G-G-G-G-C-U-C-U-U-C-G-G-A-G-C-U-C-C-A-C-C-A 22 bases

 

 
Nucleic Acids Res 25:2083-2090 (1997)
PubMed id: 9153306  
 
 
Structure of the acceptor stem of Escherichia coli tRNA Ala: role of the G3.U70 base pair in synthetase recognition.
A.Ramos, G.Varani.
 
  ABSTRACT  
 
The fidelity of translation of the genetic code depends on accurate tRNA aminoacylation by cognate aminoacyl-tRNA synthetases. Thus, each tRNA has specificity not only for codon recognition, but also for amino acid identity; this aminoacylation specificity is referred to as tRNA identity. The primary determinant of the acceptor identity of Escherichia coli tRNAAlais a wobble G3.U70 pair within the acceptor stem. Despite extensive biochemical and genetic data, the mechanism by which the G3.U70 pair marks the acceptor end of tRNAAla for aminoacylation with alanine has not been clarified at the molecular level. The solution structure of a microhelix derived from the tRNAAla acceptor end has been determined at high precision using a very extensive set of experimental constraints (approximately 32 per nt) obtained by heteronuclear multidimensional NMR methods. The tRNAAla acceptor end is overall similar to A-form RNA, but important differences are observed. The G3.U70 wobble pair distorts the conformation of the phosphodiester backbone and presents the functional groups of U70 in an unusual spatial location. The discriminator base A73 has extensive stacking overlap with G1 within the G1.C72 base pair at the end of the double helical stem and the -CCA end is significantly less ordered than the rest of the molecule.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19906714 S.Nozinovic, B.Fürtig, H.R.Jonker, C.Richter, and H.Schwalbe (2010).
High-resolution NMR structure of an RNA model system: the 14-mer cUUCGg tetraloop hairpin RNA.
  Nucleic Acids Res, 38, 683-694.
PDB code: 2koc
  19193994 A.Eichert, A.Schreiber, J.P.Fürste, M.Perbandt, C.Betzel, V.A.Erdmann, and C.Förster (2009).
Escherichia coli tRNA(Arg) acceptor-stem isoacceptors: comparative crystallization and preliminary X-ray diffraction analysis.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 98.  
19656186 M.Konno, T.Sumida, E.Uchikawa, Y.Mori, T.Yanagisawa, S.Sekine, and S.Yokoyama (2009).
Modeling of tRNA-assisted mechanism of Arg activation based on a structure of Arg-tRNA synthetase, tRNA, and an ATP analog (ANP).
  FEBS J, 276, 4763-4779.
PDB codes: 2zue 2zuf
18848900 A.Korostelev, D.N.Ermolenko, and H.F.Noller (2008).
Structural dynamics of the ribosome.
  Curr Opin Chem Biol, 12, 674-683.  
18813377 P.Papsai, A.S.Snygg, J.Aldag, and S.K.Elmroth (2008).
Platination of full length tRNA(Ala) and truncated versions of the acceptor stem and anticodon loop.
  Dalton Trans, (), 5225-5234.  
17764954 A.Korostelev, and H.F.Noller (2007).
The ribosome in focus: new structures bring new insights.
  Trends Biochem Sci, 32, 434-441.  
  17909289 C.Förster, K.Szkaradkiewicz, M.Perbandt, A.B.Brauer, T.Borowski, J.P.Fürste, C.Betzel, and V.A.Erdmann (2007).
Human tRNA(Gly) acceptor-stem microhelix: crystallization and preliminary X-ray diffraction analysis at 1.2 A resolution.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 858-861.  
  17183173 C.Förster, M.Perbandt, A.B.Brauer, S.Brode, J.P.Fürste, C.Betzel, and V.A.Erdmann (2007).
Crystallization and preliminary X-ray diffraction analysis of an Escherichia coli tRNA(Gly) acceptor-stem microhelix.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 46-48.  
17526525 D.Xu, T.Landon, N.L.Greenbaum, and M.O.Fenley (2007).
The electrostatic characteristics of G.U wobble base pairs.
  Nucleic Acids Res, 35, 3836-3847.  
16962654 A.Korostelev, S.Trakhanov, M.Laurberg, and H.F.Noller (2006).
Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangements.
  Cell, 126, 1065-1077.
PDB codes: 1vsa 2ow8
16522645 A.Mokdad, M.V.Krasovska, J.Sponer, and N.B.Leontis (2006).
Structural and evolutionary classification of G/U wobble basepairs in the ribosome.
  Nucleic Acids Res, 34, 1326-1341.  
16353093 A.N.Lazar, A.W.Coleman, S.Terenzi, and P.Strazewski (2006).
Observation of the formation of supported bilayers by amphiphilic peptidyl-RNA.
  Chem Commun (Camb), (), 63-65.  
17041234 F.Joli, N.Bouchemal, A.Laigle, B.Hartmann, and E.Hantz (2006).
Solution structure of a purine rich hexaloop hairpin belonging to PGY/MDR1 mRNA and targeted by antisense oligonucleotides.
  Nucleic Acids Res, 34, 5740-5751.
PDB code: 2gvo
16537400 W.H.McClain (2006).
Surprising contribution to aminoacylation and translation of non-Watson-Crick pairs in tRNA.
  Proc Natl Acad Sci U S A, 103, 4570-4575.  
15026534 A.Ramos, A.N.Lane, D.Hollingworth, and T.W.Fan (2004).
Secondary structure and stability of the selenocysteine insertion sequences (SECIS) for human thioredoxin reductase and glutathione peroxidase.
  Nucleic Acids Res, 32, 1746-1755.  
15489417 M.B.Łobocka, D.J.Rose, G.Plunkett, M.Rusin, A.Samojedny, H.Lehnherr, M.B.Yarmolinsky, and F.R.Blattner (2004).
Genome of bacteriophage P1.
  J Bacteriol, 186, 7032-7068.  
15103128 S.B.Jang, K.Baeyens, M.S.Jeong, J.SantaLucia, D.Turner, and S.R.Holbrook (2004).
Structures of two RNA octamers containing tandem G.A base pairs.
  Acta Crystallogr D Biol Crystallogr, 60, 829-835.
PDB codes: 1sa9 1saq
14517358 K.Chandrasekhar, and R.Malathhi (2003).
Non-Watson Crick base pairs might stabilize RNA structural motifs in ribozymes -- a comparative study of group-I intron structures.
  J Biosci, 28, 547-555.  
14654706 M.Seetharaman, C.Williams, C.J.Cramer, and K.Musier-Forsyth (2003).
Effect of G-1 on histidine tRNA microhelix conformation.
  Nucleic Acids Res, 31, 7311-7321.  
11842119 M.S.Gerdeman, T.M.Henkin, and J.V.Hines (2002).
In vitro structure-function studies of the Bacillus subtilis tyrS mRNA antiterminator: evidence for factor-independent tRNA acceptor stem binding specificity.
  Nucleic Acids Res, 30, 1065-1072.  
12022232 P.J.Beuning, M.C.Nagan, C.J.Cramer, K.Musier-Forsyth, J.L.Gelpí, and D.Bashford (2002).
Efficient aminoacylation of the tRNA(Ala) acceptor stem: dependence on the 2:71 base pair.
  RNA, 8, 659-670.  
11532948 M.A.Lovato, J.W.Chihade, and P.Schimmel (2001).
Translocation within the acceptor helix of a major tRNA identity determinant.
  EMBO J, 20, 4846-4853.  
10841758 E.Madore, R.S.Lipman, Y.M.Hou, and J.Lapointe (2000).
Evidence for unfolding of the single-stranded GCCA 3'-End of a tRNA on its aminoacyl-tRNA synthetase from a stacked helical to a foldback conformation.
  Biochemistry, 39, 6791-6798.  
11256617 G.Varani, and W.H.McClain (2000).
The G x U wobble base pair. A fundamental building block of RNA structure crucial to RNA function in diverse biological systems.
  EMBO Rep, 1, 18-23.  
10889033 J.A.Pleiss, A.D.Wolfson, and O.C.Uhlenbeck (2000).
Mapping contacts between Escherichia coli alanyl tRNA synthetase and 2' hydroxyls using a complete tRNA molecule.
  Biochemistry, 39, 8250-8258.  
10871402 M.C.Nagan, P.Beuning, K.Musier-Forsyth, and C.J.Cramer (2000).
Importance of discriminator base stacking interactions: molecular dynamics analysis of A73 microhelix(Ala) variants.
  Nucleic Acids Res, 28, 2527-2534.  
10851190 M.Zacharias (2000).
Simulation of the structure and dynamics of nonhelical RNA motifs.
  Curr Opin Struct Biol, 10, 311-317.  
10518524 K.Y.Chang, G.Varani, S.Bhattacharya, H.Choi, and W.H.McClain (1999).
Correlation of deformability at a tRNA recognition site and aminoacylation specificity.
  Proc Natl Acad Sci U S A, 96, 11764-11769.  
10737860 P.J.Beuning, and K.Musier-Forsyth (1999).
Transfer RNA recognition by aminoacyl-tRNA synthetases.
  Biopolymers, 52, 1.  
10580477 P.Strazewski, E.Biala, K.Gabriel, and W.H.McClain (1999).
The relationship of thermodynamic stability at a G x U recognition site to tRNA aminoacylation specificity.
  RNA, 5, 1490-1494.  
10562565 S.Eiler, A.Dock-Bregeon, L.Moulinier, J.C.Thierry, and D.Moras (1999).
Synthesis of aspartyl-tRNA(Asp) in Escherichia coli--a snapshot of the second step.
  EMBO J, 18, 6532-6541.
PDB code: 1c0a
10334337 U.Mueller, H.Schübel, M.Sprinzl, and U.Heinemann (1999).
Crystal structure of acceptor stem of tRNA(Ala) from Escherichia coli shows unique G.U wobble base pair at 1.16 A resolution.
  RNA, 5, 670-677.
PDB codes: 434d 435d
10417408 U.Mueller, Y.A.Muller, R.Herbst-Irmer, M.Sprinzl, and U.Heinemann (1999).
Disorder and twin refinement of RNA heptamer double helices.
  Acta Crystallogr D Biol Crystallogr, 55, 1405-1413.
PDB codes: 464d 466d
9606200 B.Felden, K.Hanawa, J.F.Atkins, H.Himeno, A.Muto, R.F.Gesteland, J.A.McCloskey, and P.F.Crain (1998).
Presence and location of modified nucleotides in Escherichia coli tmRNA: structural mimicry with tRNA acceptor branches.
  EMBO J, 17, 3188-3196.  
9482926 L.Bénard, N.Mathy, M.Grunberg-Manago, B.Ehresmann, C.Ehresmann, and C.Portier (1998).
Identification in a pseudoknot of a U.G motif essential for the regulation of the expression of ribosomal protein S15.
  Proc Natl Acad Sci U S A, 95, 2564-2567.  
9718295 S.B.Jang, L.W.Hung, Y.I.Chi, E.L.Holbrook, R.J.Carter, and S.R.Holbrook (1998).
Structure of an RNA internal loop consisting of tandem C-A+ base pairs.
  Biochemistry, 37, 11726-11731.
PDB code: 402d
9435214 W.H.McClain, J.Schneider, S.Bhattacharya, and K.Gabriel (1998).
The importance of tRNA backbone-mediated interactions with synthetase for aminoacylation.
  Proc Natl Acad Sci U S A, 95, 460-465.  
9358165 A.U.Metzger, M.Heckl, D.Willbold, K.Breitschopf, U.L.RajBhandary, P.Rösch, and H.J.Gross (1997).
Structural studies on tRNA acceptor stem microhelices: exchange of the discriminator base A73 for G in human tRNALeu switches the acceptor specificity from leucine to serine possibly by decreasing the stability of the terminal G1-C72 base pair.
  Nucleic Acids Res, 25, 4551-4556.  
9396792 M.Liu, W.C.Chu, J.C.Liu, and J.Horowitz (1997).
Role of acceptor stem conformation in tRNAVal recognition by its cognate synthetase.
  Nucleic Acids Res, 25, 4883-4890.  
9294178 P.J.Beuning, F.Yang, P.Schimmel, and K.Musier-Forsyth (1997).
Specific atomic groups and RNA helix geometry in acceptor stem recognition by a tRNA synthetase.
  Proc Natl Acad Sci U S A, 94, 10150-10154.  
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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