PDBsum entry 2p7f

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dna_rna ligands links
NCO ×2
Waters ×15
PDB id:
Name: RNA
Title: The novel use of a 2',5'-phosphodiester linkage as a reaction intermediate at the active site of a small ribozyme
Structure: Substrate strand. Chain: a. Engineered: yes. Other_details: 2',5' phosphodiester substitution at the site of cleavage. Loop a ribozyme strand. Chain: b. Engineered: yes. Loop b ribozyme strand.
Source: Synthetic: yes. Other_details: sequence occurs naturally in tobacco ringspot virus satellite RNA. Ringspot virus satellite RNA
2.35Å     R-factor:   0.227     R-free:   0.252
Authors: A.T.Torelli,J.Krucinska,J.E.Wedekind
Key ref: A.T.Torelli et al. (2007). A comparison of vanadate to a 2'-5' linkage at the active site of a small ribozyme suggests a role for water in transition-state stabilization. RNA, 13, 1052-1070. PubMed id: 17488874
20-Mar-07     Release date:   22-May-07    


RNA 13:1052-1070 (2007)
PubMed id: 17488874  
A comparison of vanadate to a 2'-5' linkage at the active site of a small ribozyme suggests a role for water in transition-state stabilization.
A.T.Torelli, J.Krucinska, J.E.Wedekind.
The potential for water to participate in RNA catalyzed reactions has been the topic of several recent studies. Here, we report crystals of a minimal, hinged hairpin ribozyme in complex with the transition-state analog vanadate at 2.05 A resolution. Waters are present in the active site and are discussed in light of existing views of catalytic strategies employed by the hairpin ribozyme. A second structure harboring a 2',5'-phosphodiester linkage at the site of cleavage was also solved at 2.35 A resolution and corroborates the assignment of active site waters in the structure containing vanadate. A comparison of the two structures reveals that the 2',5' structure adopts a conformation that resembles the reaction intermediate in terms of (1) the positioning of its nonbridging oxygens and (2) the covalent attachment of the 2'-O nucleophile with the scissile G+1 phosphorus. The 2',5'-linked structure was then overlaid with scissile bonds of other small ribozymes including the glmS metabolite-sensing riboswitch and the hammerhead ribozyme, and suggests the potential of the 2',5' linkage to elicit a reaction-intermediate conformation without the need to form metalloenzyme complexes. The hairpin ribozyme structures presented here also suggest how water molecules bound at each of the nonbridging oxygens of G+1 may electrostatically stabilize the transition state in a manner that supplements nucleobase functional groups. Such coordination has not been reported for small ribozymes, but is consistent with the structures of protein enzymes. Overall, this work establishes significant parallels between the RNA and protein enzyme worlds.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21199369 I.Drude, A.Strahl, D.Galla, O.Müller, and S.Müller (2011).
Design of hairpin ribozyme variants with improved activity for poorly processed substrates.
  FEBS J, 278, 622-633.  
20822574 A.R.Ferré-D'Amaré (2010).
The glmS ribozyme: use of a small molecule coenzyme by a gene-regulatory RNA.
  Q Rev Biophys, 43, 423-447.  
20420375 V.Mlýnský, P.Banás, D.Hollas, K.Réblová, N.G.Walter, J.Sponer, and M.Otyepka (2010).
Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H+ forms are most consistent with crystal structures of hairpin ribozyme.
  J Phys Chem B, 114, 6642-6652.  
19528080 C.L.Zirbel, J.E.Sponer, J.Sponer, J.Stombaugh, and N.B.Leontis (2009).
Classification and energetics of the base-phosphate interactions in RNA.
  Nucleic Acids Res, 37, 4898-4918.  
19330013 L.Liu, J.W.Cottrell, L.G.Scott, and M.J.Fedor (2009).
Direct measurement of the ionization state of an essential guanine in the hairpin ribozyme.
  Nat Chem Biol, 5, 351-357.  
19223444 M.A.Ditzler, J.Sponer, and N.G.Walter (2009).
Molecular dynamics suggest multifunctionality of an adenine imino group in acid-base catalysis of the hairpin ribozyme.
  RNA, 15, 560-575.  
19702306 M.Guo, R.C.Spitale, R.Volpini, J.Krucinska, G.Cristalli, P.R.Carey, and J.E.Wedekind (2009).
Direct Raman measurement of an elevated base pKa in the active site of a small ribozyme in a precatalytic conformation.
  J Am Chem Soc, 131, 12908-12909.  
19416070 M.J.Fedor (2009).
Comparative enzymology and structural biology of RNA self-cleavage.
  Annu Rev Biophys, 38, 271-299.  
19398008 P.Banás, P.Jurecka, N.G.Walter, J.Sponer, and M.Otyepka (2009).
Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM.
  Methods, 49, 202-216.  
19559088 R.C.Spitale, and J.E.Wedekind (2009).
Exploring ribozyme conformational changes with X-ray crystallography.
  Methods, 49, 87.  
19354216 R.C.Spitale, R.Volpini, M.G.Heller, J.Krucinska, G.Cristalli, and J.E.Wedekind (2009).
Identification of an imino group indispensable for cleavage by a small ribozyme.
  J Am Chem Soc, 131, 6093-6095.
PDB codes: 3gs1 3gs5 3gs8
19634899 R.C.Spitale, R.Volpini, M.V.Mungillo, J.Krucinska, G.Cristalli, and J.E.Wedekind (2009).
Single-atom imino substitutions at A9 and A10 reveal distinct effects on the fold and function of the hairpin ribozyme catalytic core.
  Biochemistry, 48, 7777-7779.
PDB codes: 3i2q 3i2r 3i2s 3i2u
18423397 A.T.Torelli, R.C.Spitale, J.Krucinska, and J.E.Wedekind (2008).
Shared traits on the reaction coordinates of ribonuclease and an RNA enzyme.
  Biochem Biophys Res Commun, 371, 154-158.
PDB code: 3cqs
18596253 C.MacElrevey, J.D.Salter, J.Krucinska, and J.E.Wedekind (2008).
Structural effects of nucleobase variations at key active site residue Ade38 in the hairpin ribozyme.
  RNA, 14, 1600-1616.
PDB codes: 3b58 3b5a 3b5f 3b5s 3b91 3bbi 3bbk 3bbm 3cr1
18566190 K.Nam, J.Gao, and D.M.York (2008).
Electrostatic interactions in the hairpin ribozyme account for the majority of the rate acceleration without chemical participation by nucleobases.
  RNA, 14, 1501-1507.  
18345664 K.Nam, J.Gao, and D.M.York (2008).
Quantum mechanical/molecular mechanical simulation study of the mechanism of hairpin ribozyme catalysis.
  J Am Chem Soc, 130, 4680-4691.  
17998292 S.Gaur, J.E.Heckman, and J.M.Burke (2008).
Mutational inhibition of ligation in the hairpin ribozyme: substitutions of conserved nucleobases A9 and A10 destabilize tertiary structure and selectively promote cleavage.
  RNA, 14, 55-65.  
17685395 M.A.Ditzler, E.A.Alemán, D.Rueda, and N.G.Walter (2007).
Focus on function: single molecule RNA enzymology.
  Biopolymers, 87, 302-316.  
18158891 N.G.Walter (2007).
Ribozyme catalysis revisited: is water involved?
  Mol Cell, 28, 923-929.  
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.