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PDBsum entry 1m5k

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protein dna_rna metals Protein-protein interface(s) links
Translation/RNA PDB id
1m5k
Jmol
Contents
Protein chain
92 a.a. *
DNA/RNA
Metals
_CA ×33
_CL ×2
Waters ×103
* Residue conservation analysis
PDB id:
1m5k
Name: Translation/RNA
Title: Crystal structure of a hairpin ribozyme in the catalytically conformation
Structure: RNA inhibitor substrate. Chain: a, d. Engineered: yes. RNA hairpin ribozyme. Chain: b, e. Engineered: yes. Protein (u1 small nuclear ribonucleoprotein a). Chain: c, f. Fragment: u1a RNA binding domain.
Source: Synthetic: yes. Other_details: this sequence occurs naturally in satellite ringspot virus. Homo sapiens. Human. Organism_taxid: 9606. Gene: snrpa. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Trimer (from PQS)
Resolution:
2.40Å     R-factor:   0.229     R-free:   0.284
Authors: P.B.Rupert,A.R.Ferre-D'Amare
Key ref:
P.B.Rupert and A.R.Ferré-D'Amaré (2001). Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis. Nature, 410, 780-786. PubMed id: 11298439 DOI: 10.1038/35071009
Date:
09-Jul-02     Release date:   02-Aug-02    
Supersedes: 1hp6
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P09012  (SNRPA_HUMAN) -  U1 small nuclear ribonucleoprotein A
Seq:
Struc:
282 a.a.
92 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     nuclear mRNA splicing, via spliceosome   1 term 
  Biochemical function     nucleotide binding     3 terms  

 

 
DOI no: 10.1038/35071009 Nature 410:780-786 (2001)
PubMed id: 11298439  
 
 
Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis.
P.B.Rupert, A.R.Ferré-D'Amaré.
 
  ABSTRACT  
 
The hairpin ribozyme catalyses sequence-specific cleavage of RNA. The active site of this natural RNA results from the docking of two irregular helices: stems A and B. One strand of stem A harbours the scissile bond. The 2.4 A resolution structure of a hairpin ribozyme-inhibitor complex reveals that the ribozyme aligns the 2'-OH nucleophile and the 5'-oxo leaving group by twisting apart the nucleotides that flank the scissile phosphate. The base of the nucleotide preceding the cleavage site is stacked within stem A; the next nucleotide, a conserved guanine, is extruded from stem A and accommodated by a highly complementary pocket in the minor groove of stem B. Metal ions are absent from the active site. The bases of four conserved purines are positioned potentially to serve as acid-base catalysts. This is the first structure determination of a fully assembled ribozyme active site that catalyses a phosphodiester cleavage without recourse to metal ions.
 
  Selected figure(s)  
 
Figure 2.
Figure 2: Architecture of the hairpin ribozyme. The backbone of the two RNA strands is depicted as ribbons; the nucleotide bases as sticks (colour code as in Fig. 1). Two tightly bound calcium ions are represented as green spheres. a, Stereoview of the docked conformation of the hairpin ribozyme. The scissile bond lies between the two yellow nucleotides, which are splayed apart. The U1A protein is shown as a grey ribbon. b, c, Views orthogonal to that in a, showing the path of the RNA chains in the four-helix junction, the crossing angle between stems A and B, and the approximately 30° bend at the site of the bulged nucleotides in stem B.
Figure 5.
Figure 5: Active site architecture. a, Interface of stems A and B, seen from the side opposite to that of Fig. 2a. b, Detail of the G+1-binding pocket. c, Simulated-annealing |F[o]|-|F[c]| omit density map contoured around A-1 at one s.d. The arrow points to the bulge in the density that corresponds to the methyl group blocking the 2' oxygen. d, Stereoview of the active site, showing the in-line-attack conformation and several purine bases that may participate in catalysis.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2001, 410, 780-786) copyright 2001.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20876687 C.Geary, A.Chworos, and L.Jaeger (2011).
Promoting RNA helical stacking via A-minor junctions.
  Nucleic Acids Res, 39, 1066-1080.  
21428954 D.M.Lilley (2011).
Catalysis by the nucleolytic ribozymes.
  Biochem Soc Trans, 39, 641-646.  
21132831 E.Paredes, and S.R.Das (2011).
Click chemistry for rapid labeling and ligation of RNA.
  Chembiochem, 12, 125-131.  
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.  
21138969 I.V.Novikova, B.H.Hassan, M.G.Mirzoyan, and N.B.Leontis (2011).
Engineering cooperative tecto-RNA complexes having programmable stoichiometries.
  Nucleic Acids Res, 39, 2903-2917.  
21333656 J.Wang, and E.P.Nikonowicz (2011).
Solution structure of the K-turn and Specifier Loop domains from the Bacillus subtilis tyrS T-box leader RNA.
  J Mol Biol, 408, 99.  
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.  
20554048 A.R.Ferré-D'Amaré (2010).
Use of the spliceosomal protein U1A to facilitate crystallization and structure determination of complex RNAs.
  Methods, 52, 159-167.  
20852642 C.L.Ng, K.Lang, N.A.Meenan, A.Sharma, A.C.Kelley, C.Kleanthous, and V.Ramakrishnan (2010).
Structural basis for 16S ribosomal RNA cleavage by the cytotoxic domain of colicin E3.
  Nat Struct Mol Biol, 17, 1241-1246.
PDB codes: 2xfz 2xg0 2xg1 2xg2
20110252 J.Wang, T.M.Henkin, and E.P.Nikonowicz (2010).
NMR structure and dynamics of the Specifier Loop domain from the Bacillus subtilis tyrS T box leader RNA.
  Nucleic Acids Res, 38, 3388-3398.
PDB code: 2khy
19754142 M.A.Ditzler, M.Otyepka, J.Sponer, and N.G.Walter (2010).
Molecular dynamics and quantum mechanics of RNA: conformational and chemical change we can believe in.
  Acc Chem Res, 43, 40-47.  
20204525 M.Giel-Pietraszuk, A.Fedoruk-Wyszomirska, and J.Barciszewski (2010).
Effect of high hydrostatic pressure on hydration and activity of ribozymes.
  Mol Biol Rep, 37, 3713-3719.  
19948769 N.Kulshina, T.E.Edwards, and A.R.Ferré-D'Amaré (2010).
Thermodynamic analysis of ligand binding and ligand binding-induced tertiary structure formation by the thiamine pyrophosphate riboswitch.
  RNA, 16, 186-196.
PDB code: 3k0j
20192764 S.A.Woodson (2010).
Compact intermediates in RNA folding.
  Annu Rev Biophys, 39, 61-77.  
  20948783 S.P.Ryder (2010).
Hidden ribozymes in eukaryotic genome sequence.
  F1000 Biol Rep, 2, 0.  
20547881 T.J.Wilson, N.S.Li, J.Lu, J.K.Frederiksen, J.A.Piccirilli, and D.M.Lilley (2010).
Nucleobase-mediated general acid-base catalysis in the Varkud satellite ribozyme.
  Proc Natl Acad Sci U S A, 107, 11751-11756.  
19409996 B.Gong, J.H.Chen, R.Yajima, Y.Chen, E.Chase, D.M.Chadalavada, B.L.Golden, P.R.Carey, and P.C.Bevilacqua (2009).
Raman crystallography of RNA.
  Methods, 49, 101-111.  
19718544 C.Reymond, J.D.Beaudoin, and J.P.Perreault (2009).
Modulating RNA structure and catalysis: lessons from small cleaving ribozymes.
  Cell Mol Life Sci, 66, 3937-3950.  
19299141 F.Michel, M.Costa, and E.Westhof (2009).
The ribozyme core of group II introns: a structure in want of partners.
  Trends Biochem Sci, 34, 189-199.  
19623596 J.Buck, Y.L.Li, C.Richter, J.Vergne, M.C.Maurel, and H.Schwalbe (2009).
NMR spectroscopic characterization of the adenine-dependent hairpin ribozyme.
  Chembiochem, 10, 2100-2110.  
19186984 J.L.Fiore, B.Kraemer, F.Koberling, R.Edmann, and D.J.Nesbitt (2009).
Enthalpy-driven RNA folding: single-molecule thermodynamics of tetraloop-receptor tertiary interaction.
  Biochemistry, 48, 2550-2558.  
19301873 J.Liu, Z.Cao, and Y.Lu (2009).
Functional nucleic acid sensors.
  Chem Rev, 109, 1948-1998.  
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.  
19476496 M.Ztouti, H.Kaddour, F.Miralles, C.Simian, J.Vergne, G.Hervé, and M.C.Maurel (2009).
Adenine, a hairpin ribozyme cofactor - high-pressure and competition studies.
  FEBS J, 276, 2574-2588.  
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
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.  
19294348 Q.Wu, L.Huang, and Y.Zhang (2009).
The structure and function of catalytic RNAs.
  Sci China C Life Sci, 52, 232-244.  
19559088 R.C.Spitale, and J.E.Wedekind (2009).
Exploring ribozyme conformational changes with X-ray crystallography.
  Methods, 49, 87.  
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
19054068 Y.L.Li, J.Vergne, C.Torchet, and M.C.Maurel (2009).
In vitro selection of adenine-dependent ribozyme against Tpl2/Cot oncogene.
  FEBS J, 276, 303-314.  
19915655 A.Bashan, and A.Yonath (2008).
The linkage between ribosomal crystallography, metal ions, heteropolytungstates and functional flexibility.
  J Mol Struct, 890, 289-294.  
18729108 B.Lippert (2008).
Ligand-pKa shifts through metals: potential relevance to ribozyme chemistry.
  Chem Biodivers, 5, 1455-1474.  
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
18836455 D.B.Ritchie, M.J.Schellenberg, E.M.Gesner, S.A.Raithatha, D.T.Stuart, and A.M.Macmillan (2008).
Structural elucidation of a PRP8 core domain from the heart of the spliceosome.
  Nat Struct Mol Biol, 15, 1199-1205.
PDB code: 3enb
18755052 D.M.Lilley (2008).
Analysis of branched nucleic acid structure using comparative gel electrophoresis.
  Q Rev Biophys, 41, 1.  
18162543 J.D.Ye, V.Tereshko, J.K.Frederiksen, A.Koide, F.A.Fellouse, S.S.Sidhu, S.Koide, A.A.Kossiakoff, and J.A.Piccirilli (2008).
Synthetic antibodies for specific recognition and crystallization of structured RNA.
  Proc Natl Acad Sci U S A, 105, 82-87.
PDB code: 2r8s
19325748 J.Sheng, and Z.Huang (2008).
Selenium Derivatization of Nucleic Acids for Phase and Structure Determination in Nucleic Acid X-ray Crystallography.
  Int J Mol Sci, 9, 258-271.  
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.  
18988629 M.A.Ditzler, D.Rueda, J.Mo, K.Håkansson, and N.G.Walter (2008).
A rugged free energy landscape separates multiple functional RNA folds throughout denaturation.
  Nucleic Acids Res, 36, 7088-7099.  
18566509 M.P.Robertson, and W.G.Scott (2008).
A general method for phasing novel complex RNA crystal structures without heavy-atom derivatives.
  Acta Crystallogr D Biol Crystallogr, 64, 738-744.  
18573075 R.K.Montange, and R.T.Batey (2008).
Riboswitches: emerging themes in RNA structure and function.
  Annu Rev Biophys, 37, 117-133.  
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.  
17846637 A.Serganov, and D.J.Patel (2007).
Ribozymes, riboswitches and beyond: regulation of gene expression without proteins.
  Nat Rev Genet, 8, 776-790.  
17488874 A.T.Torelli, J.Krucinska, and J.E.Wedekind (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.
PDB codes: 2p7d 2p7e 2p7f
17637337 A.Y.Keel, R.P.Rambo, R.T.Batey, and J.S.Kieft (2007).
A general strategy to solve the phase problem in RNA crystallography.
  Structure, 15, 761-772.
PDB codes: 2pxb 2pxd 2pxe 2pxf 2pxk 2pxl 2pxp 2pxq 2pxt 2pxu 2pxv
16996258 B.Hall, J.R.Hesselberth, and A.D.Ellington (2007).
Computational selection of nucleic acid biosensors via a slip structure model.
  Biosens Bioelectron, 22, 1939-1947.  
17806104 C.G.Hoogstraten, and M.Sumita (2007).
Structure-function relationships in RNA and RNP enzymes: recent advances.
  Biopolymers, 87, 317-328.  
17472738 C.Hammann, and E.Westhof (2007).
Searching genomes for ribozymes and riboswitches.
  Genome Biol, 8, 210.  
17582172 C.MacElrevey, R.C.Spitale, J.Krucinska, and J.E.Wedekind (2007).
A posteriori design of crystal contacts to improve the X-ray diffraction properties of a small RNA enzyme.
  Acta Crystallogr D Biol Crystallogr, 63, 812-825.
PDB codes: 2npy 2npz
17688253 G.Todd, and K.Karbstein (2007).
RNA takes center stage.
  Biopolymers, 87, 275-278.  
17196404 J.C.Cochrane, S.V.Lipchock, and S.A.Strobel (2007).
Structural investigation of the GlmS ribozyme bound to Its catalytic cofactor.
  Chem Biol, 14, 97.
PDB code: 2nz4
17351263 J.W.Cottrell, Y.I.Kuzmin, and M.J.Fedor (2007).
Functional analysis of hairpin ribozyme active site architecture.
  J Biol Chem, 282, 13498-13507.  
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.  
17456566 M.Roychowdhury-Saha, and D.H.Burke (2007).
Distinct reaction pathway promoted by non-divalent-metal cations in a tertiary stabilized hammerhead ribozyme.
  RNA, 13, 841-848.  
18158891 N.G.Walter (2007).
Ribozyme catalysis revisited: is water involved?
  Mol Cell, 28, 923-929.  
17931443 N.J.Baird, X.W.Fang, N.Srividya, T.Pan, and T.R.Sosnick (2007).
Folding of a universal ribozyme: the ribonuclease P RNA.
  Q Rev Biophys, 40, 113-161.  
17391549 P.C.Bevilacqua, A.L.Cerrone-Szakal, and N.A.Siegfried (2007).
Insight into the functional versatility of RNA through model-making with applications to data fitting.
  Q Rev Biophys, 40, 55-85.  
17299128 Q.Vicens, A.R.Gooding, A.Laederach, and T.R.Cech (2007).
Local RNA structural changes induced by crystallization are revealed by SHAPE.
  RNA, 13, 536-548.  
17438124 R.A.Owens, and T.Baumstark (2007).
Structural differences within the loop E motif imply alternative mechanisms of viroid processing.
  RNA, 13, 824-834.  
17666711 R.Przybilski, and C.Hammann (2007).
The tolerance to exchanges of the Watson Crick base pair in the hammerhead ribozyme core is determined by surrounding elements.
  RNA, 13, 1625-1630.  
17507661 R.Tyagi, and D.H.Mathews (2007).
Predicting helical coaxial stacking in RNA multibranch loops.
  RNA, 13, 939-951.  
17496145 S.Liu, G.Bokinsky, N.G.Walter, and X.Zhuang (2007).
Dissecting the multistep reaction pathway of an RNA enzyme by single-molecule kinetic "fingerprinting".
  Proc Natl Acad Sci U S A, 104, 12634-12639.  
17940139 S.Valadkhan, A.Mohammadi, C.Wachtel, and J.L.Manley (2007).
Protein-free spliceosomal snRNAs catalyze a reaction that resembles the first step of splicing.
  RNA, 13, 2300-2311.  
17574837 T.E.Edwards, D.J.Klein, and A.R.Ferré-D'Amaré (2007).
Riboswitches: small-molecule recognition by gene regulatory RNAs.
  Curr Opin Struct Biol, 17, 273-279.  
17464286 T.J.Wilson, A.C.McLeod, and D.M.Lilley (2007).
A guanine nucleobase important for catalysis by the VS ribozyme.
  EMBO J, 26, 2489-2500.  
17135184 A.Lescoute, and E.Westhof (2006).
The interaction networks of structured RNAs.
  Nucleic Acids Res, 34, 6587-6604.  
16345112 A.R.Feldman, E.K.Leung, A.J.Bennet, and D.Sen (2006).
The RNA-cleaving bipartite DNAzyme is a distinctive metalloenzyme.
  Chembiochem, 7, 98.  
16484375 A.Roth, A.Nahvi, M.Lee, I.Jona, and R.R.Breaker (2006).
Characteristics of the glmS ribozyme suggest only structural roles for divalent metal ions.
  RNA, 12, 607-619.  
16690998 A.T.Perrotta, T.S.Wadkins, and M.D.Been (2006).
Chemical rescue, multiple ionizable groups, and general acid-base catalysis in the HDV genomic ribozyme.
  RNA, 12, 1282-1291.  
16533049 C.D.Downey, J.L.Fiore, C.D.Stoddard, J.H.Hodak, D.J.Nesbitt, and A.Pardi (2006).
Metal ion dependence, thermodynamics, and kinetics for intramolecular docking of a GAAA tetraloop and receptor connected by a flexible linker.
  Biochemistry, 45, 3664-3673.  
16990543 D.J.Klein, and A.R.Ferré-D'Amaré (2006).
Structural basis of glmS ribozyme activation by glucosamine-6-phosphate.
  Science, 313, 1752-1756.
PDB codes: 2gcs 2gcv 2h0s 2h0w 2h0x 2h0z 2ho6 2ho7
16411759 D.Lambert, J.E.Heckman, and J.M.Burke (2006).
Cation-specific structural accommodation within a catalytic RNA.
  Biochemistry, 45, 829-838.  
16411744 J.Salter, J.Krucinska, S.Alam, V.Grum-Tokars, and J.E.Wedekind (2006).
Water in the active site of an all-RNA hairpin ribozyme and effects of Gua8 base variants on the geometry of phosphoryl transfer.
  Biochemistry, 45, 686-700.
PDB codes: 1zfr 1zft 1zfv 1zfx 2bcy 2bcz 2fgp 2oue
16522648 L.Nasalean, S.Baudrey, N.B.Leontis, and L.Jaeger (2006).
Controlling RNA self-assembly to form filaments.
  Nucleic Acids Res, 34, 1381-1392.  
16938834 M.M.Rhodes, K.Réblová, J.Sponer, and N.G.Walter (2006).
Trapped water molecules are essential to structural dynamics and function of a ribozyme.
  Proc Natl Acad Sci U S A, 103, 13380-13385.  
16859740 M.Martick, and W.G.Scott (2006).
Tertiary contacts distant from the active site prime a ribozyme for catalysis.
  Cell, 126, 309-320.
PDB codes: 2goz 3zd5
16413034 S.Cao, and S.J.Chen (2006).
Free energy landscapes of RNA/RNA complexes: with applications to snRNA complexes in spliceosomes.
  J Mol Biol, 357, 292-312.  
17381305 S.D.Gilbert, R.K.Montange, C.D.Stoddard, and R.T.Batey (2006).
Structural studies of the purine and SAM binding riboswitches.
  Cold Spring Harb Symp Quant Biol, 71, 259-268.  
16675665 S.Thore, M.Leibundgut, and N.Ban (2006).
Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand.
  Science, 312, 1208-1211.
PDB code: 2cky
16396624 A.V.Vlassov, B.H.Johnston, and S.A.Kazakov (2005).
Hairpin ribozyme-catalyzed ligation in water-alcohol solutions.
  Oligonucleotides, 15, 303-309.  
15919196 D.M.Lilley (2005).
Structure, folding and mechanisms of ribozymes.
  Curr Opin Struct Biol, 15, 313-323.  
15722480 E.J.Borda, and S.T.Sigurdsson (2005).
Investigation of Mg2+- and temperature-dependent folding of the hairpin ribozyme by photo-crosslinking: effects of photo-crosslinker tether length and chemistry.
  Nucleic Acids Res, 33, 1058-1068.  
16141058 H.F.Noller (2005).
RNA structure: reading the ribosome.
  Science, 309, 1508-1514.  
15870731 J.A.Doudna, and J.R.Lorsch (2005).
Ribozyme catalysis: not different, just worse.
  Nat Struct Mol Biol, 12, 395-402.  
15744318 J.N.Pitt, and A.R.Ferré-D'Amaré (2005).
How RNA closes a Diel.
  Nat Struct Mol Biol, 12, 206-208.  
15869397 K.F.Blount, and O.C.Uhlenbeck (2005).
The structure-function dilemma of the hammerhead ribozyme.
  Annu Rev Biophys Biomol Struct, 34, 415-440.  
15956979 M.J.Fedor, and J.R.Williamson (2005).
The catalytic diversity of RNAs.
  Nat Rev Mol Cell Biol, 6, 399-412.  
16100381 M.Xiao, T.Li, X.Yuan, Y.Shang, F.Wang, S.Chen, and Y.Zhang (2005).
A peripheral element assembles the compact core structure essential for group I intron self-splicing.
  Nucleic Acids Res, 33, 4602-4611.  
16128815 S.A.Ivanov, S.Vauléon, and S.Müller (2005).
Efficient RNA ligation by reverse-joined hairpin ribozymes and engineering of twin ribozymes consisting of conventional and reverse-joined hairpin ribozyme units.
  FEBS J, 272, 4464-4474.  
16407982 S.A.Strobel (2005).
Ribonucleic general acid.
  Nat Chem Biol, 1, 5-6.  
16199761 S.H.Najafi-Shoushtari, and M.Famulok (2005).
Competitive regulation of modular allosteric aptazymes by a small molecule and oligonucleotide effector.
  RNA, 11, 1514-1520.  
15870387 S.Tobé, T.Heams, J.Vergne, G.Hervé, and M.C.Maurel (2005).
The catalytic mechanism of hairpin ribozyme studied by hydrostatic pressure.
  Nucleic Acids Res, 33, 2557-2564.  
16298301 T.J.McCarthy, M.A.Plog, S.A.Floy, J.A.Jansen, J.K.Soukup, and G.A.Soukup (2005).
Ligand requirements for glmS ribozyme self-cleavage.
  Chem Biol, 12, 1221-1226.  
15731266 Z.Zhang, and J.M.Burke (2005).
Inhibition of viral replication by ribozyme: mutational analysis of the site and mechanism of antiviral activity.
  J Virol, 79, 3728-3736.  
15141216 A.Ke, K.Zhou, F.Ding, J.H.Cate, and J.A.Doudna (2004).
A conformational switch controls hepatitis delta virus ribozyme catalysis.
  Nature, 429, 201-205.
PDB codes: 1sj3 1sj4 1sjf 1vbx 1vby 1vbz 1vc0 1vc5 1vc6 1vc7
15064361 A.P.Massey, and S.T.Sigurdsson (2004).
Chemical syntheses of inhibitory substrates of the RNA-RNA ligation reaction catalyzed by the hairpin ribozyme.
  Nucleic Acids Res, 32, 2017-2022.  
14691941 A.R.Ferré-D'Amaré (2004).
The hairpin ribozyme.
  Biopolymers, 73, 71-78.  
15454471 B.Okumus, T.J.Wilson, D.M.Lilley, and T.Ha (2004).
Vesicle encapsulation studies reveal that single molecule ribozyme heterogeneities are intrinsic.
  Biophys J, 87, 2798-2806.  
15543154 D.G.Sashital, G.Cornilescu, C.J.McManus, D.A.Brow, and S.E.Butcher (2004).
U2-U6 RNA folding reveals a group II intron-like domain and a four-helix junction.
  Nat Struct Mol Biol, 11, 1237-1242.
PDB code: 1xhp
14730013 D.M.Lilley (2004).
The Varkud satellite ribozyme.
  RNA, 10, 151-158.  
15218105 D.Rueda, G.Bokinsky, M.M.Rhodes, M.J.Rust, X.Zhuang, and N.G.Walter (2004).
Single-molecule enzymology of RNA: essential functional groups impact catalysis from a distance.
  Proc Natl Acad Sci U S A, 101, 10066-10071.  
15240479 G.Pljevaljcić, D.P.Millar, and A.A.Deniz (2004).
Freely diffusing single hairpin ribozymes provide insights into the role of secondary structure and partially folded states in RNA folding.
  Biophys J, 87, 457-467.  
15100442 J.C.Penedo, T.J.Wilson, S.D.Jayasena, A.Khvorova, and D.M.Lilley (2004).
Folding of the natural hammerhead ribozyme is enhanced by interaction of auxiliary elements.
  RNA, 10, 880-888.  
15475966 M.K.Nahas, T.J.Wilson, S.Hohng, K.Jarvie, D.M.Lilley, and T.Ha (2004).
Observation of internal cleavage and ligation reactions of a ribozyme.
  Nat Struct Mol Biol, 11, 1107-1113.  
15007109 N.Carrasco, Y.Buzin, E.Tyson, E.Halpert, and Z.Huang (2004).
Selenium derivatization and crystallization of DNA and RNA oligonucleotides for X-ray crystallography using multiple anomalous dispersion.
  Nucleic Acids Res, 32, 1638-1646.  
14691943 P.C.Bevilacqua, T.S.Brown, S.Nakano, and R.Yajima (2004).
Catalytic roles for proton transfer and protonation in ribozymes.
  Biopolymers, 73, 90.  
15175762 P.L.Adams, M.R.Stahley, A.B.Kosek, J.Wang, and S.A.Strobel (2004).
Crystal structure of a self-splicing group I intron with both exons.
  Nature, 430, 45-50.
PDB codes: 1t42 1u6b
15547134 P.L.Adams, M.R.Stahley, M.L.Gill, A.B.Kosek, J.Wang, and S.A.Strobel (2004).
Crystal structure of a group I intron splicing intermediate.
  RNA, 10, 1867-1887.  
14970385 R.Pinard, D.Lambert, G.Pothiawala, F.Major, and J.M.Burke (2004).
Modifications and deletions of helices within the hairpin ribozyme-substrate complex: an active ribozyme lacking helix 1.
  RNA, 10, 395-402.  
15199169 S.H.Najafi-Shoushtari, G.Mayer, and M.Famulok (2004).
Sensing complex regulatory networks by conformationally controlled hairpin ribozymes.
  Nucleic Acids Res, 32, 3212-3219.  
14730024 T.A.Goody, S.E.Melcher, D.G.Norman, and D.M.Lilley (2004).
The kink-turn motif in RNA is dimorphic, and metal ion-dependent.
  RNA, 10, 254-264.  
14993665 T.Sunami, J.Kondo, I.Hirao, K.Watanabe, K.Miura, and A.Takénaka (2004).
Structures of d(GCGAAGC) and d(GCGAAAGC) (tetragonal form): a switching of partners of the sheared G.A pairs to form a functional G.AxA.G crossing.
  Acta Crystallogr D Biol Crystallogr, 60, 422-431.
PDB codes: 1ub8 1ue4
14555657 B.Sargueil, K.J.Hampel, D.Lambert, and J.M.Burke (2003).
In vitro selection of second site revertants analysis of the hairpin ribozyme active site.
  J Biol Chem, 278, 52783-52791.  
12595703 D.B.Hoggan, J.A.Chao, G.S.Prasad, C.D.Stout, and J.R.Williamson (2003).
Combinatorial crystallization of an RNA-protein complex.
  Acta Crystallogr D Biol Crystallogr, 59, 466-473.  
12942136 D.M.Lilley (2003).
Ribozymes--a snip too far?
  Nat Struct Biol, 10, 672-673.  
13678961 D.M.Lilley (2003).
The origins of RNA catalysis in ribozymes.
  Trends Biochem Sci, 28, 495-501.  
12736317 E.Ennifar, P.Walter, and P.Dumas (2003).
A crystallographic study of the binding of 13 metal ions to two related RNA duplexes.
  Nucleic Acids Res, 31, 2671-2682.
PDB codes: 1nlc 1nle 1o3z 1wvd 1y6s 1y6t 1y73 1y90 1y95 2oij
12697343 E.Puerta-Fernández, C.Romero-López, A.Barroso-delJesus, and A.Berzal-Herranz (2003).
Ribozymes: recent advances in the development of RNA tools.
  FEMS Microbiol Rev, 27, 75-97.  
12883002 E.Tan, T.J.Wilson, M.K.Nahas, R.M.Clegg, D.M.Lilley, and T.Ha (2003).
A four-way junction accelerates hairpin ribozyme folding via a discrete intermediate.
  Proc Natl Acad Sci U S A, 100, 9308-9313.  
12869691 G.Bokinsky, D.Rueda, V.K.Misra, M.M.Rhodes, A.Gordus, H.P.Babcock, N.G.Walter, and X.Zhuang (2003).
Single-molecule transition-state analysis of RNA folding.
  Proc Natl Acad Sci U S A, 100, 9302-9307.  
12824338 M.Andronescu, R.Aguirre-Hernández, A.Condon, and H.H.Hoos (2003).
RNAsoft: A suite of RNA secondary structure prediction and design software tools.
  Nucleic Acids Res, 31, 3416-3422.  
12519767 M.Meli, J.Vergne, and M.C.Maurel (2003).
In vitro selection of adenine-dependent hairpin ribozymes.
  J Biol Chem, 278, 9835-9842.  
12907727 N.Lee, R.J.Gorelick, and K.Musier-Forsyth (2003).
Zinc finger-dependent HIV-1 nucleocapsid protein-TAR RNA interactions.
  Nucleic Acids Res, 31, 4847-4855.  
12876372 P.B.Rupert, H.Xiao, and A.R.Ferré-D'Amaré (2003).
U1A RNA-binding domain at 1.8 A resolution.
  Acta Crystallogr D Biol Crystallogr, 59, 1521-1524.
PDB code: 1nu4
12540850 R.Pudi, S.Abhiman, N.Srinivasan, and S.Das (2003).
Hepatitis C virus internal ribosome entry site-mediated translation is stimulated by specific interaction of independent regions of human La autoantigen.
  J Biol Chem, 278, 12231-12240.  
12616637 S.Vauléon, and S.Müller (2003).
External regulation of hairpin ribozyme activity by an oligonucleotide effector.
  Chembiochem, 4, 220-224.  
11788713 B.N.van Buuren, T.Hermann, S.S.Wijmenga, and E.Westhof (2002).
Brownian-dynamics simulations of metal-ion binding to four-way junctions.
  Nucleic Acids Res, 30, 507-514.  
12006498 D.A.Lafontaine, D.G.Norman, and D.M.Lilley (2002).
The global structure of the VS ribozyme.
  EMBO J, 21, 2461-2471.  
12466539 H.Saito, and H.Suga (2002).
Outersphere and innersphere coordinated metal ions in an aminoacyl-tRNA synthetase ribozyme.
  Nucleic Acids Res, 30, 5151-5159.  
12045114 I.H.Shih, and M.D.Been (2002).
Catalytic strategies of the hepatitis delta virus ribozymes.
  Annu Rev Biochem, 71, 887-917.  
11911369 M.J.Dickman, M.J.Conroy, J.A.Grasby, and D.P.Hornby (2002).
RNA footprinting analysis using ion pair reverse phase liquid chromatography.
  RNA, 8, 247-251.  
12429689 M.Yarus (2002).
Primordial genetics: phenotype of the ribocyte.
  Annu Rev Genet, 36, 125-151.  
12198171 S.L.Hiley, V.D.Sood, J.Fan, and R.A.Collins (2002).
4-thio-U cross-linking identifies the active site of the VS ribozyme.
  EMBO J, 21, 4691-4698.  
11884625 S.P.Ryder, and S.A.Strobel (2002).
Comparative analysis of hairpin ribozyme structures and interference data.
  Nucleic Acids Res, 30, 1287-1291.  
12022226 T.J.Wilson, and D.M.Lilley (2002).
Metal ion binding and the folding of the hairpin ribozyme.
  RNA, 8, 587-600.  
11861903 V.D.Sood, S.Yekta, and R.A.Collins (2002).
The contribution of 2'-hydroxyls to the cleavage activity of the Neurospora VS ribozyme.
  Nucleic Acids Res, 30, 1132-1138.  
12323370 V.J.DeRose (2002).
Two decades of RNA catalysis.
  Chem Biol, 9, 961-969.  
11839295 X.Cheng, and R.M.Blumenthal (2002).
Cytosines do it, thymines do it, even pseudouridines do it--base flipping by an enzyme that acts on RNA.
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12084911 X.W.Fang, P.Thiyagarajan, T.R.Sosnick, and T.Pan (2002).
The rate-limiting step in the folding of a large ribozyme without kinetic traps.
  Proc Natl Acad Sci U S A, 99, 8518-8523.  
12119023 Y.Komatsu, K.Nobuoka, N.Karino-Abe, A.Matsuda, and E.Ohtsuka (2002).
In vitro selection of hairpin ribozymes activated with short oligonucleotides.
  Biochemistry, 41, 9090-9098.  
11779468 C.Hoang, and A.R.Ferré-D'Amaré (2001).
Cocrystal structure of a tRNA Psi55 pseudouridine synthase: nucleotide flipping by an RNA-modifying enzyme.
  Cell, 107, 929-939.
PDB code: 1k8w
11702070 E.Ennifar, P.Walter, B.Ehresmann, C.Ehresmann, and P.Dumas (2001).
Crystal structures of coaxially stacked kissing complexes of the HIV-1 RNA dimerization initiation site.
  Nat Struct Biol, 8, 1064-1068.
PDB codes: 1jjm 1jjn 1k9w 2b8r 2b8s
11738588 J.M.Murray, and J.A.Doudna (2001).
Creative catalysis: pieces of the RNA world jigsaw.
  Trends Biochem Sci, 26, 699-701.  
11707414 R.Pinard, K.J.Hampel, J.E.Heckman, D.Lambert, P.A.Chan, F.Major, and J.M.Burke (2001).
Functional involvement of G8 in the hairpin ribozyme cleavage mechanism.
  EMBO J, 20, 6434-6442.  
11406380 S.E.Butcher (2001).
Structure and function of the small ribozymes.
  Curr Opin Struct Biol, 11, 315-320.  
11574478 S.L.Hiley, and R.A.Collins (2001).
Rapid formation of a solvent-inaccessible core in the Neurospora Varkud satellite ribozyme.
  EMBO J, 20, 5461-5469.  
  11680850 S.P.Ryder, A.K.Oyelere, J.L.Padilla, D.Klostermeier, D.P.Millar, and S.A.Strobel (2001).
Investigation of adenosine base ionization in the hairpin ribozyme by nucleotide analog interference mapping.
  RNA, 7, 1454-1463.  
11573091 T.K.Stage-Zimmermann, and O.C.Uhlenbeck (2001).
A covalent crosslink converts the hammerhead ribozyme from a ribonuclease to an RNA ligase.
  Nat Struct Biol, 8, 863-867.  
11685244 X.Yang, T.Gérczei, L.T.Glover, and C.C.Correll (2001).
Crystal structures of restrictocin-inhibitor complexes with implications for RNA recognition and base flipping.
  Nat Struct Biol, 8, 968-973.
PDB codes: 1jbr 1jbs 1jbt
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