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PDBsum entry 1cx0

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protein dna_rna metals links
RNA binding protein/RNA PDB id
1cx0
Jmol
Contents
Protein chain
95 a.a. *
DNA/RNA
Metals
_MG ×12
Waters ×64
* Residue conservation analysis
PDB id:
1cx0
Name: RNA binding protein/RNA
Title: Hepatitis delta virus ribozyme
Structure: Hdv ribozyme self-cleaved. Chain: b. Engineered: yes. U1a protein. Chain: a. Fragment: RNA binding domain. Engineered: yes. Mutation: yes
Source: Hepatitis delta virus. Organism_taxid: 12475. Organism_taxid: 12475
Biol. unit: Tetramer (from PQS)
Resolution:
2.30Å     R-factor:   0.246     R-free:   0.279
Authors: A.R.Ferre-D'Amare,K.Zhou,J.A.Doudna
Key ref:
A.R.Ferré-D'Amaré et al. (1998). Crystal structure of a hepatitis delta virus ribozyme. Nature, 395, 567-574. PubMed id: 9783582 DOI: 10.1038/26912
Date:
27-Aug-99     Release date:   08-Sep-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P09012  (SNRPA_HUMAN) -  U1 small nuclear ribonucleoprotein A
Seq:
Struc:
282 a.a.
95 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 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: 10.1038/26912 Nature 395:567-574 (1998)
PubMed id: 9783582  
 
 
Crystal structure of a hepatitis delta virus ribozyme.
A.R.Ferré-D'Amaré, K.Zhou, J.A.Doudna.
 
  ABSTRACT  
 
The self-cleaving ribozyme of the hepatitis delta virus (HDV) is the only catalytic RNA known to be required for the viability of a human pathogen. We obtained crystals of a 72-nucleotide, self-cleaved form of the genomic HDV ribozyme that diffract X-rays to 2.3 A resolution by engineering the RNA to bind a small, basic protein without affecting ribozyme activity. The co-crystal structure shows that the compact catalytic core comprises five helical segments connected as an intricate nested double pseudoknot. The 5'-hydroxyl leaving group resulting from the self-scission reaction is buried deep within an active-site cleft produced by juxtaposition of the helices and five strand-crossovers, and is surrounded by biochemically important backbone and base functional groups in a manner reminiscent of protein enzymes.
 
  Selected figure(s)  
 
Figure 4.
Figure 4 Structural components of the active site. a, Solvent-accessible surface of the ribozyme-U1A-RBD complex, orientated as in Fig. 3a, colour-coded by its curvature (green, convex; grey, concave^49). The atoms of the ribose ring of G1 are shown as red spheres; the 5'-hydroxyl group points away from the reader into the ribozyme. The trajectory proposed to be followed by nucleotides located 5' of the cleavage site in the precursor is indicated by the row of small red dots. b, The substrate-bearing nucleotide G1 forms a wobble pair with U37 which stacks on P1.1. The 5'-hydroxyl group (shown as a larger sphere) is within hydrogen-bonding distance of the Watson-Crick face of C75. Nucleotides are coloured as in Figs 2 and 3. Phosphorus atoms are coloured green. Oxygen and nitrogen atoms that participate in noteworthy hydrogen bonding (denoted by two-headed arrows) are coloured red and blue, respectively. c, Triple-strand junction between P3 and P1, orientated as in Fig. 3a. A hydrogen bond between the N1 group of A78 and the O2' group of G29 is obscured in this view.
Figure 5.
Figure 5 Structural features of the active site. a, The P3-L3 niche cradles the active site. The stereoview shows how the phosphate ribose backbone crosses over from the P3-L3 stack to P1.1 and back, passing through the unstacked nucleotide U23. The ribose of G1 and the bases of the stacked nucleotides from J4/2 are shown. b, The P1.1 helix and the pedestal. c, A A-weighted 2|F[o]| - |F[c]| map44,45, with data from 20 to 2.3 ┼, contoured at 1 s.d., showing the nucleotides of J4/2 as seen from the major groove of P1. d, The trefoil turn (orientated roughly as in Fig. 3b) is the sharp twist in the RNA chain between G74 and A77. This is stabilized by a complex network of interactions between O2' groups and phosphate oxygens, a two-tiered ribose zipper, and base-backbone hydrogen bonds. Figures 3, 4b, c and 5a, b, d were prepared with RIBBONS50.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (1998, 395, 567-574) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22337051 E.A.Dethoff, J.Chugh, A.M.Mustoe, and H.M.Al-Hashimi (2012).
Functional complexity and regulation through RNA dynamics.
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21335320 C.M.Reidys, F.W.Huang, J.E.Andersen, R.C.Penner, P.F.Stadler, and M.E.Nebel (2011).
Topology and prediction of RNA pseudoknots.
  Bioinformatics, 27, 1076-1085.  
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.  
21082721 G.J.Forse, N.Ram, D.R.Banatao, D.Cascio, M.R.Sawaya, H.E.Klock, S.A.Lesley, and T.O.Yeates (2011).
Synthetic symmetrization in the crystallization and structure determination of CelA from Thermotoga maritima.
  Protein Sci, 20, 168-178.
PDB code: 3o7o
21348498 N.Veeraraghavan, A.Ganguly, J.H.Chen, P.C.Bevilacqua, S.Hammes-Schiffer, and B.L.Golden (2011).
Metal binding motif in the active site of the HDV ribozyme binds divalent and monovalent ions.
  Biochemistry, 50, 2672-2682.  
20880077 S.Pascarella, and F.Negro (2011).
Hepatitis D virus: an update.
  Liver Int, 31, 7.  
21210732 T.K.Wong, T.W.Lam, W.K.Sung, B.W.Cheung, and S.M.Yiu (2011).
Structural alignment of RNA with complex pseudoknot structure.
  J Comput Biol, 18, 97.  
20854710 W.Yang (2011).
Nucleases: diversity of structure, function and mechanism.
  Q Rev Biophys, 44, 1.  
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.  
  20495679 B.Liu, D.H.Mathews, and D.H.Turner (2010).
RNA pseudoknots: folding and finding.
  F1000 Biol Rep, 2, 0.  
21134640 C.Reymond, D.Lévesque, M.Bisaillon, and J.P.Perreault (2010).
Developing three-dimensional models of putative-folding intermediates of the HDV ribozyme.
  Structure, 18, 1608-1616.  
20421411 D.G.Eickbush, and T.H.Eickbush (2010).
R2 retrotransposons encode a self-cleaving ribozyme for processing from an rRNA cotranscript.
  Mol Cell Biol, 30, 3142-3150.  
20397215 J.Sheng, and Z.Huang (2010).
Selenium derivatization of nucleic acids for X-ray crystal-structure and function studies.
  Chem Biodivers, 7, 753-785.  
20123730 J.Sperschneider, and A.Datta (2010).
DotKnot: pseudoknot prediction using the probability dot plot under a refined energy model.
  Nucleic Acids Res, 38, e103.  
20223766 L.Lu, C.Yi, X.Jian, G.Zheng, and C.He (2010).
Structure determination of DNA methylation lesions N1-meA and N3-meC in duplex DNA using a cross-linked protein-DNA system.
  Nucleic Acids Res, 38, 4415-4425.
PDB codes: 3h8o 3h8r 3h8x
20517991 M.Egli (2010).
Diffraction techniques in structural biology.
  Curr Protoc Nucleic Acid Chem, (), Unit 7.13.  
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.  
20886091 M.J.Pereira, V.Behera, and N.G.Walter (2010).
Nondenaturing purification of co-transcriptionally folded RNA avoids common folding heterogeneity.
  PLoS One, 5, e12953.  
19952115 N.Toor, K.S.Keating, O.Fedorova, K.Rajashankar, J.Wang, and A.M.Pyle (2010).
Tertiary architecture of the Oceanobacillus iheyensis group II intron.
  RNA, 16, 57-69.
PDB code: 3igi
20651028 S.C.Flores, and R.B.Altman (2010).
Turning limited experimental information into 3D models of RNA.
  RNA, 16, 1769-1778.  
20100813 S.Cao, D.P.Giedroc, and S.J.Chen (2010).
Predicting loop-helix tertiary structural contacts in RNA pseudoknots.
  RNA, 16, 538-552.  
  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.  
18810653 A.Fedoruk-Wyszomirska, M.Giel-Pietraszuk, E.Wyszko, M.Szymański, J.Ciesiołka, M.Z.Barciszewska, and J.Barciszewski (2009).
The mechanism of acidic hydrolysis of esters explains the HDV ribozyme activity.
  Mol Biol Rep, 36, 1647-1650.  
19888753 B.Gong, J.H.Chen, P.C.Bevilacqua, B.L.Golden, and P.R.Carey (2009).
Competition between Co(NH(3)(6)3+ and inner sphere Mg2+ ions in the HDV ribozyme.
  Biochemistry, 48, 11961-11970.  
19965505 C.H.Webb, N.J.Riccitelli, D.J.Ruminski, and A.Lupták (2009).
Widespread occurrence of self-cleaving ribozymes.
  Science, 326, 953.  
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.  
19134473 C.Reymond, M.Bisaillon, and J.P.Perreault (2009).
Monitoring of an RNA multistep folding pathway by isothermal titration calorimetry.
  Biophys J, 96, 132-140.  
18621088 D.P.Giedroc, and P.V.Cornish (2009).
Frameshifting RNA pseudoknots: structure and mechanism.
  Virus Res, 139, 193-208.
PDB codes: 2rp0 2rp1
19178151 J.H.Chen, B.Gong, P.C.Bevilacqua, P.R.Carey, and B.L.Golden (2009).
A catalytic metal ion interacts with the cleavage Site G.U wobble in the HDV ribozyme.
  Biochemistry, 48, 1498-1507.  
18672012 J.S.Kieft (2009).
Comparing the three-dimensional structures of Dicistroviridae IGR IRES RNAs with other viral RNA structures.
  Virus Res, 139, 148-156.  
19710184 L.Zhang, P.Bao, M.J.Leibowitz, and Y.Zhang (2009).
Slow formation of a pseudoknot structure is rate limiting in the productive co-transcriptional folding of the self-splicing Candida intron.
  RNA, 15, 1986-1992.  
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.  
19710925 Q.Vicens, A.R.Gooding, L.F.Duarte, and R.T.Batey (2009).
Preparation of group I introns for biochemical studies and crystallization assays by native affinity purification.
  PLoS One, 4, e6740.  
19294348 Q.Wu, L.Huang, and Y.Zhang (2009).
The structure and function of catalytic RNAs.
  Sci China C Life Sci, 52, 232-244.  
18996016 R.T.Radulescu, and B.Brenig (2009).
Infectious nucleic acids in prion disease: halfway there.
  Trends Biochem Sci, 34, 4.  
19101979 S.Blouin, J.Mulhbacher, J.C.Penedo, and D.A.Lafontaine (2009).
Riboswitches: ancient and promising genetic regulators.
  Chembiochem, 10, 400-416.  
19237463 S.Cao, and S.J.Chen (2009).
Predicting structures and stabilities for H-type pseudoknots with interhelix loops.
  RNA, 15, 696-706.  
18658121 A.L.Cerrone-Szakal, D.M.Chadalavada, B.L.Golden, and P.C.Bevilacqua (2008).
Mechanistic characterization of the HDV genomic ribozyme: the cleavage site base pair plays a structural role in facilitating catalysis.
  RNA, 14, 1746-1760.  
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
18940672 H.Xiao, T.E.Edwards, and A.R.Ferré-D'Amaré (2008).
Structural basis for specific, high-affinity tetracycline binding by an in vitro evolved aptamer and artificial riboswitch.
  Chem Biol, 15, 1125-1137.
PDB code: 3egz
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
18192612 J.S.Richardson, B.Schneider, L.W.Murray, G.J.Kapral, R.M.Immormino, J.J.Headd, D.C.Richardson, D.Ham, E.Hershkovits, L.D.Williams, K.S.Keating, A.M.Pyle, D.Micallef, J.Westbrook, and H.M.Berman (2008).
RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution).
  RNA, 14, 465-481.  
18986998 J.Salon, J.Jiang, J.Sheng, O.O.Gerlits, and Z.Huang (2008).
Derivatization of DNAs with selenium at 6-position of guanine for function and crystal structure studies.
  Nucleic Acids Res, 36, 7009-7018.  
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.  
18464974 J.Sponer, K.E.Riley, and P.Hobza (2008).
Nature and magnitude of aromatic stacking of nucleic acid bases.
  Phys Chem Chem Phys, 10, 2595-2610.  
19325801 K.T.Dayie (2008).
Key labeling technologies to tackle sizeable problems in RNA structural biology.
  Int J Mol Sci, 9, 1214-1240.  
18710542 L.Savochkina, V.Alekseenkova, T.Belyanko, N.Dobrynina, and R.Beabealashvilli (2008).
RNase footprinting demonstrates antigenomic hepatitis delta virus ribozyme structural rearrangement as a result of self-cleavage reaction.
  BMC Res Notes, 1, 15.  
18686993 P.Banás, L.Rulísek, V.Hánosová, D.Svozil, N.G.Walter, J.Sponer, and M.Otyepka (2008).
General base catalysis for cleavage by the active-site cytosine of the hepatitis delta virus ribozyme: QM/MM calculations establish chemical feasibility.
  J Phys Chem B, 112, 11177-11187.  
18573075 R.K.Montange, and R.T.Batey (2008).
Riboswitches: emerging themes in RNA structure and function.
  Annu Rev Biophys, 37, 117-133.  
17981525 R.Russell (2008).
RNA misfolding and the action of chaperones.
  Front Biosci, 13, 1.  
18230758 S.Smit, K.Rother, J.Heringa, and R.Knight (2008).
From knotted to nested RNA structures: a variety of computational methods for pseudoknot removal.
  RNA, 14, 410-416.  
18408159 S.V.Lipchock, and S.A.Strobel (2008).
A relaxed active site after exon ligation by the group I intron.
  Proc Natl Acad Sci U S A, 105, 5699-5704.
PDB codes: 3bo2 3bo3 3bo4
17401565 X.Wang, G.Kapral, L.Murray, D.Richardson, J.Richardson, and J.Snoeyink (2008).
RNABC: forward kinematics to reduce all-atom steric clashes in RNA backbone.
  J Math Biol, 56, 253-278.  
17355864 A.Ke, F.Ding, J.D.Batchelor, and J.A.Doudna (2007).
Structural roles of monovalent cations in the HDV ribozyme.
  Structure, 15, 281-287.
PDB codes: 2oih 2oj3
17933779 A.Nehdi, J.Perreault, J.D.Beaudoin, and J.P.Perreault (2007).
A novel structural rearrangement of hepatitis delta virus antigenomic ribozyme.
  Nucleic Acids Res, 35, 6820-6831.  
17846637 A.Serganov, and D.J.Patel (2007).
Ribozymes, riboswitches and beyond: regulation of gene expression without proteins.
  Nat Rev Genet, 8, 776-790.  
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
17381343 B.Rastegari, and A.Condon (2007).
Parsing nucleic acid pseudoknotted secondary structure: algorithm and applications.
  J Comput Biol, 14, 16-32.  
17472738 C.Hammann, and E.Westhof (2007).
Searching genomes for ribozymes and riboswitches.
  Genome Biol, 8, 210.  
17105991 C.Reymond, J.Ouellet, M.Bisaillon, and J.P.Perreault (2007).
Examination of the folding pathway of the antigenomic hepatitis delta virus ribozyme reveals key interactions of the L3 loop.
  RNA, 13, 44-54.  
17914224 D.Bhattacharyya, S.C.Koripella, A.Mitra, V.B.Rajendran, and B.Sinha (2007).
Theoretical analysis of noncanonical base pairing interactions in RNA molecules.
  J Biosci, 32, 809-825.  
17804015 D.J.Klein, S.R.Wilkinson, M.D.Been, and A.R.Ferré-D'Amaré (2007).
Requirement of helix P2.2 and nucleotide G1 for positioning the cleavage site and cofactor of the glmS ribozyme.
  J Mol Biol, 373, 178-189.
PDB codes: 2z74 2z75
17956974 D.M.Chadalavada, A.L.Cerrone-Szakal, and P.C.Bevilacqua (2007).
Wild-type is the optimal sequence of the HDV ribozyme under cotranscriptional conditions.
  RNA, 13, 2189-2201.  
17570822 D.M.Lilley (2007).
A chemo-genetic approach for the study of nucleobase participation in nucleolytic ribozymes.
  Biol Chem, 388, 699-704.  
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.  
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.  
17688253 G.Todd, and K.Karbstein (2007).
RNA takes center stage.
  Biopolymers, 87, 275-278.  
17632571 I.Brierley, S.Pennell, and R.J.Gilbert (2007).
Viral RNA pseudoknots: versatile motifs in gene expression and replication.
  Nat Rev Microbiol, 5, 598-610.  
17894371 J.E.Stone, J.C.Phillips, P.L.Freddolino, D.J.Hardy, L.G.Trabuco, and K.Schulten (2007).
Accelerating molecular modeling applications with graphics processors.
  J Comput Chem, 28, 2618-2640.  
17169989 J.Jiang, J.Sheng, N.Carrasco, and Z.Huang (2007).
Selenium derivatization of nucleic acids for crystallography.
  Nucleic Acids Res, 35, 477-485.
PDB codes: 1z7i 2dlj 2gpx 2h05
17478505 J.Reeder, P.Steffen, and R.Giegerich (2007).
pknotsRG: RNA pseudoknot folding including near-optimal structures and sliding windows.
  Nucleic Acids Res, 35, W320-W324.  
17337436 J.Sefcikova, M.V.Krasovska, J.Sponer, and N.G.Walter (2007).
The genomic HDV ribozyme utilizes a previously unnoticed U-turn motif to accomplish fast site-specific catalysis.
  Nucleic Acids Res, 35, 1933-1946.  
17253610 J.Sefcikova, M.V.Krasovska, N.Spacková, J.Sponer, and N.G.Walter (2007).
Impact of an extruded nucleotide on cleavage activity and dynamic catalytic core conformation of the hepatitis delta virus ribozyme.
  Biopolymers, 85, 392-406.  
17263541 J.Sheng, J.Jiang, J.Salon, and Z.Huang (2007).
Synthesis of a 2'-Se-thymidine phosphoramidite and its incorporation into oligonucleotides for crystal structure study.
  Org Lett, 9, 749-752.  
17173143 M.Egli, P.Lubini, and P.S.Pallan (2007).
The long and winding road to the structure of homo-DNA.
  Chem Soc Rev, 36, 31-45.  
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.  
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.  
17981494 S.A.Strobel, and J.C.Cochrane (2007).
RNA catalysis: ribozymes, ribosomes, and riboswitches.
  Curr Opin Chem Biol, 11, 636-643.  
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.  
16432262 A.Nehdi, and J.P.Perreault (2006).
Unbiased in vitro selection reveals the unique character of the self-cleaving antigenomic HDV RNA sequence.
  Nucleic Acids Res, 34, 584-592.  
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.  
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
16846240 G.Brandt, N.Carrasco, and Z.Huang (2006).
Efficient substrate cleavage catalyzed by hammerhead ribozymes derivatized with selenium for X-ray crystallography.
  Biochemistry, 45, 8972-8977.  
16391129 K.Fiola, J.P.Perreault, and B.Cousineau (2006).
Gene targeting in the Gram-Positive bacterium Lactococcus lactis, using various delta ribozymes.
  Appl Environ Microbiol, 72, 869-879.  
16990549 K.Salehi-Ashtiani, A.Lupták, A.Litovchick, and J.W.Szostak (2006).
A genomewide search for ribozymes reveals an HDV-like sequence in the human CPEB3 gene.
  Science, 313, 1788-1792.  
16401611 M.K.Smalley, and S.K.Silverman (2006).
Fluorescence of covalently attached pyrene as a general RNA folding probe.
  Nucleic Acids Res, 34, 152-166.  
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
16491487 M.S.Taylor, and E.N.Jacobsen (2006).
Asymmetric catalysis by chiral hydrogen-bond donors.
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15723077 A.Serganov, S.Keiper, L.Malinina, V.Tereshko, E.Skripkin, C.Höbartner, A.Polonskaia, A.T.Phan, R.Wombacher, R.Micura, Z.Dauter, A.Jäschke, and D.J.Patel (2005).
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16199760 J.Ren, B.Rastegari, A.Condon, and H.H.Hoos (2005).
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15064361 A.P.Massey, and S.T.Sigurdsson (2004).
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A detailed view of a ribosomal active site: the structure of the L11-RNA complex.
  Cell, 97, 491-502.
PDB code: 1mms
10454623 D.A.Lafontaine, S.Ananvoranich, and J.P.Perreault (1999).
Presence of a coordinated metal ion in a trans-acting antigenomic delta ribozyme.
  Nucleic Acids Res, 27, 3236-3243.  
10361084 D.M.Lilley (1999).
Structure, folding and catalysis of the small nucleolytic ribozymes.
  Curr Opin Struct Biol, 9, 330-338.  
10573122 G.A.Soukup, and R.R.Breaker (1999).
Relationship between internucleotide linkage geometry and the stability of RNA.
  RNA, 5, 1308-1325.  
10496215 I.H.Shih, and M.D.Been (1999).
Ribozyme cleavage of a 2,5-phosphodiester linkage: mechanism and a restricted divalent metal-ion requirement.
  RNA, 5, 1140-1148.  
  10515997 J.D.Banks, B.O.Kealoha, and M.L.Linial (1999).
An Mpsi-containing heterologous RNA, but not env mRNA, is efficiently packaged into avian retroviral particles.
  J Virol, 73, 8926-8933.  
10371033 N.K.Tanner (1999).
Ribozymes: the characteristics and properties of catalytic RNAs.
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10580471 P.Babin, M.Dolan, P.Wollenzien, and R.R.Gutell (1999).
Identity and geometry of a base triple in 16S rRNA determined by comparative sequence analysis and molecular modeling.
  RNA, 5, 1430-1439.  
10737860 P.J.Beuning, and K.Musier-Forsyth (1999).
Transfer RNA recognition by aminoacyl-tRNA synthetases.
  Biopolymers, 52, 1.  
10423552 P.L.Nixon, C.A.Theimer, and D.P.Giedroc (1999).
Thermodynamics of stabilization of RNA pseudoknots by cobalt(III) hexaammine.
  Biopolymers, 50, 443-458.  
10449375 R.W.Roberts, and W.W.Ja (1999).
In vitro selection of nucleic acids and proteins: What are we learning?
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10588670 S.L.Alam, J.F.Atkins, and R.F.Gesteland (1999).
Programmed ribosomal frameshifting: much ado about knotting!
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10572011 S.Wang, K.Karbstein, A.Peracchi, L.Beigelman, and D.Herschlag (1999).
Identification of the hammerhead ribozyme metal ion binding site responsible for rescue of the deleterious effect of a cleavage site phosphorothioate.
  Biochemistry, 38, 14363-14378.  
10376872 T.S.Wadkins, A.T.Perrotta, A.R.Ferré-D'Amaré, J.A.Doudna, and M.D.Been (1999).
A nested double pseudoknot is required for self-cleavage activity of both the genomic and antigenomic hepatitis delta virus ribozymes.
  RNA, 5, 720-727.  
10600729 W.G.Scott (1999).
RNA structure, metal ions, and catalysis.
  Curr Opin Chem Biol, 3, 705-709.  
10333742 C.W.Hilbers, P.J.Michiels, and H.A.Heus (1998).
New developments in structure determination of pseudoknots.
  Biopolymers, 48, 137-153.  
10333740 D.J.Patel (1998).
Molecular insights into the RNA world.
  Biopolymers, 48, 97.  
10333745 R.N.De Guzman, R.B.Turner, and M.F.Summers (1998).
Protein-RNA recognition.
  Biopolymers, 48, 181-195.  
10333743 T.Hermann, and E.Westhof (1998).
Saccharide-RNA recognition.
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9914252 W.G.Scott (1998).
RNA catalysis.
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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.