PDBsum entry 1i2x

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DNA-RNA hybrid PDB id
Waters ×79
PDB id:
Name: DNA-RNA hybrid
Title: 2.4 a structure of a-duplex with bulged adenosine, spermidine form
Structure: DNA/RNA (5'-r( Gp Cp G)-d(p Ap Tp Ap T)- r(p Ap Cp Gp U)-3'). Chain: a, b, d, c. Engineered: yes
Source: Synthetic: yes
Biol. unit: Tetramer (from PQS)
2.40Å     R-factor:   0.249     R-free:   0.278
Authors: V.Tereshko,S.Wallace,N.Usman,F.Wincott,M.Egli
Key ref: V.Tereshko et al. (2001). X-ray crystallographic observation of "in-line" and "adjacent" conformations in a bulged self-cleaving RNA/DNA hybrid. RNA, 7, 405-420. PubMed id: 11333021
12-Feb-01     Release date:   21-Apr-01    


RNA 7:405-420 (2001)
PubMed id: 11333021  
X-ray crystallographic observation of "in-line" and "adjacent" conformations in a bulged self-cleaving RNA/DNA hybrid.
V.Tereshko, S.T.Wallace, N.Usman, F.E.Wincott, M.Egli.
The RNA strand in an RNA/DNA duplex with unpaired ribonucleotides can undergo self-cleavage at bulge sites in the presence of a variety of divalent metal ions (Hüsken et al., Biochemistry, 1996, 35:16591-16600). Transesterification proceeds via an in-line mechanism, with the 2'-OH of the bulged nucleotide attacking the 3'-adjacent phosphate group. The site-specificity of the reaction is most likely a consequence of the greater local conformational freedom of the RNA backbone in the bulge region. A standard A-form backbone geometry prohibits formation of an in-line arrangement between 2'-oxygen and phosphate. However, the backbone in the region of an unpaired nucleotide appears to be conducive to an in-line approach. Therefore, the bulge-mediated phosphoryl transfer reaction represents one of the simplest RNA self-cleavage systems. Here we focus on the conformational features of the RNA that underlie site-specific cleavage. The structures of an RNA/DNA duplex with single ribo-adenosyl bulges were analyzed in two crystal forms, permitting observation of 10 individual conformations of the RNA bulge moiety. The bulge geometries cover a range of relative arrangements between the 2'-oxygen of the bulged nucleotide and the P-O5' bond (including adjacent and near in-line) and give a detailed picture of the conformational changes necessary to line up the 2'-OH nucleophile and scissile bond. Although metal ions are of crucial importance in the catalysis of analogous cleavage reactions by ribozymes, it is clear that local strain or conformational flexibility in the RNA also affect cleavage selectivity and rate (Soukup & Breaker, RNA, 1999, 5:1308-1325). The geometries of the RNA bulges frozen out in the crystals provide snapshots along the reaction pathway prior to the transition state of the phosphoryl transfer reaction.

Literature references that cite this PDB file's key reference

  PubMed id Reference
17186477 E.Mayaan, A.Moser, A.D.MacKerell, and D.M.York (2007).
CHARMM force field parameters for simulation of reactive intermediates in native and thio-substituted ribozymes.
  J Comput Chem, 28, 495-507.  
16399833 A.Barthel, and M.Zacharias (2006).
Conformational transitions in RNA single uridine and adenosine bulge structures: a molecular dynamics free energy simulation study.
  Biophys J, 90, 2450-2462.  
16492787 B.Pan, K.Shi, and M.Sundaralingam (2006).
Base-tetrad swapping results in dimerization of RNA quadruplexes: implications for formation of the i-motif RNA octaplex.
  Proc Natl Acad Sci U S A, 103, 3130-3134.
PDB code: 2awe
16639765 C.Dupouy, N.Iché-Tarrat, M.P.Durrieu, F.Rodriguez, J.M.Escudier, and A.Vigroux (2006).
Watson-Crick base-pairing properties of nucleic acid analogues with stereocontrolled alpha and beta torsion angles (alpha,beta-D-CNAs).
  Angew Chem Int Ed Engl, 45, 3623-3627.  
15048778 N.Korolev, A.P.Lyubartsev, A.Laaksonen, and L.Nordenskiöld (2004).
Molecular dynamics simulation study of oriented polyamine- and Na-DNA: sequence specific interactions and effects on DNA structure.
  Biopolymers, 73, 542-555.  
14530445 N.Korolev, A.P.Lyubartsev, A.Laaksonen, and L.Nordenskiöld (2003).
A molecular dynamics simulation study of oriented DNA with polyamine and sodium counterions: diffusion and averaged binding of water and cations.
  Nucleic Acids Res, 31, 5971-5981.  
14523920 W.C.Winkler, and R.R.Breaker (2003).
Genetic control by metabolite-binding riboswitches.
  Chembiochem, 4, 1024-1032.  
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