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PDBsum entry 379d

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dna_rna metals links
Ribozyme PDB id
379d
Jmol
Contents
DNA/RNA
Metals
_CO ×8
PDB id:
379d
Name: Ribozyme
Title: The structural basis of hammerhead ribozyme self-cleavage
Structure: RNA (5'- r( Gp Up Gp Gp Up Cp Up Gp Ap Up Gp Ap Gp Gp Cp C)-3'). Chain: a. Engineered: yes. RNA (5'- r( Gp Gp Cp Cp Gp Ap Ap Ap Cp Up Cp Gp Up Ap Ap Gp A p Gp Up Cp Ap Cp Cp Ap C)-3'). Chain: b. Engineered: yes
Source: Synthetic: yes. Synthetic: yes
Biol. unit: Dimer (from PQS)
Resolution:
3.10Å     R-factor:   0.230    
Authors: J.B.Murray,D.P.Terwey,L.Maloney,A.Karpeisky,N.Usman, L.Beigelman,W.G.Scott
Key ref:
J.B.Murray et al. (1998). The structural basis of hammerhead ribozyme self-cleavage. Cell, 92, 665-673. PubMed id: 9506521 DOI: 10.1016/S0092-8674(00)81134-4
Date:
05-Feb-98     Release date:   11-Feb-98    
 Headers
 References

 

 
DOI no: 10.1016/S0092-8674(00)81134-4 Cell 92:665-673 (1998)
PubMed id: 9506521  
 
 
The structural basis of hammerhead ribozyme self-cleavage.
J.B.Murray, D.P.Terwey, L.Maloney, A.Karpeisky, N.Usman, L.Beigelman, W.G.Scott.
 
  ABSTRACT  
 
We have captured an 8.7 A conformational change that takes place in the cleavage site of the hammerhead ribozyme during self-cleavage, using X-ray crystallography combined with physical and chemical trapping techniques. This rearrangement brings the hammerhead ribozyme from the ground state into a conformation that is poised to form the transition state geometry required for hammerhead RNA self-cleavage. Use of a 5'-C-methylated ribose adjacent to the cleavage site permits this ordinarily transient conformational change to be kinetically trapped and observed crystallographically after initiating the hammerhead ribozyme reaction in the crystal. Cleavage of the corresponding unmodified hammerhead ribozyme in the crystal under otherwise identical conditions is faster than in solution, indicating that we have indeed trapped a catalytically relevant intermediate form of this RNA enzyme.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. The Cleavage Site Phosphate Conformational SwitchA schematic diagram illustrating the fact that a helical phosphate conformation is maximally incompatible with (i.e., 90° away from) the conformation required for an in-line attack mechanism. Therefore, any significant movement away from the helical phosphate conformation will bring it closer to the geometry required for in-line attack. Such a change in the scissile phosphate is required by the observed conformational change of C-17 shown in Figure 3a and Figure 3b.
Figure 5.
Figure 5. Stereo Views of the Kinetically Trapped Hammerhead Ribozyme Late-Intermediate Structure(a) Stereo view of the entire kinetically trapped late-conformational-intermediate structure, with the scissile phosphate indicated. The color scheme follows Figure 1b. The position of the scissile phosphate is based upon the difference Fourier peak shown in Figure 3c.(b) Close up stereo view of the catalytic pocket, with residues labeled. Note the position of C-17. The scissile phosphate is shown as having a geometry compatible with the observed requirement for an in-line attack mechanism and further restrained by the position of the phosphorus difference Fourier peak (shown in Figure 3c).
 
  The above figures are reprinted by permission from Cell Press: Cell (1998, 92, 665-673) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20935068 D.H.Burke, and S.S.Rhee (2010).
Assembly and activation of a kinase ribozyme.
  RNA, 16, 2349-2359.  
20047671 L.Martinsen, A.Johnsen, F.Venanzetti, and L.Bachmann (2010).
Phylogenetic footprinting of non-coding RNA: hammerhead ribozyme sequences in a satellite DNA family of Dolichopoda cave crickets (Orthoptera, Rhaphidophoridae).
  BMC Evol Biol, 10, 3.  
19690100 A.Ploner, C.Ploner, M.Lukasser, H.Niederegger, and A.Hüttenhofer (2009).
Methodological obstacles in knocking down small noncoding RNAs.
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19301873 J.Liu, Z.Cao, and Y.Lu (2009).
Functional nucleic acid sensors.
  Chem Rev, 109, 1948-1998.  
19416070 M.J.Fedor (2009).
Comparative enzymology and structural biology of RNA self-cleavage.
  Annu Rev Biophys, 38, 271-299.  
17998291 J.A.Nelson, and O.C.Uhlenbeck (2008).
Minimal and extended hammerheads utilize a similar dynamic reaction mechanism for catalysis.
  RNA, 14, 43-54.  
18725951 M.T.Lee, and J.Kim (2008).
Self containment, a property of modular RNA structures, distinguishes microRNAs.
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18281388 S.Fulle, and H.Gohlke (2008).
Analyzing the flexibility of RNA structures by constraint counting.
  Biophys J, 94, 4202-4219.  
18271579 T.S.Lee, C.Silva López, G.M.Giambasu, M.Martick, W.G.Scott, and D.M.York (2008).
Role of Mg2+ in hammerhead ribozyme catalysis from molecular simulation.
  J Am Chem Soc, 130, 3053-3064.  
18479101 T.S.Lee, and D.M.York (2008).
Origin of mutational effects at the C3 and G8 positions on hammerhead ribozyme catalysis from molecular dynamics simulations.
  J Am Chem Soc, 130, 7168-7169.  
18802606 Y.Tanaka, and A.Ono (2008).
Nitrogen-15 NMR spectroscopy of N-metallated nucleic acids: insights into 15N NMR parameters and N-metal bonds.
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17806104 C.G.Hoogstraten, and M.Sumita (2007).
Structure-function relationships in RNA and RNP enzymes: recent advances.
  Biopolymers, 87, 317-328.  
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.  
17545240 R.Radhakrishnan (2007).
Coupling of fast and slow modes in the reaction pathway of the minimal hammerhead ribozyme cleavage.
  Biophys J, 93, 2391-2399.  
19079784 T.S.Lee, C.S.López, M.Martick, W.G.Scott, and D.M.York (2007).
Insight into the role of Mg in hammerhead ribozyme catalysis from X-ray crystallography and molecular dynamics simulation.
  J Chem Theory Comput, 3, 325-327.  
17570825 W.G.Scott (2007).
Morphing the minimal and full-length hammerhead ribozymes: implications for the cleavage mechanism.
  Biol Chem, 388, 727-735.  
16525552 B.Knobloch, H.Sigel, A.Okruszek, and R.K.Sigel (2006).
Acid-base properties of the nucleic-acid model 2'-deoxyguanylyl(5'-->3')-2'-deoxy-5'-guanylate, d(pGpG)3-, and of related guanine derivatives.
  Org Biomol Chem, 4, 1085-1090.  
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
16991176 R.Przybilski, and C.Hammann (2006).
The hammerhead ribozyme structure brought in line.
  Chembiochem, 7, 1641-1644.  
15919196 D.M.Lilley (2005).
Structure, folding and mechanisms of ribozymes.
  Curr Opin Struct Biol, 15, 313-323.  
15870731 J.A.Doudna, and J.R.Lorsch (2005).
Ribozyme catalysis: not different, just worse.
  Nat Struct Mol Biol, 12, 395-402.  
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.  
17191972 M.Gallo, R.Kretschmer-Kazemi Far, G.Sczakiel, and A.M.Iribarren (2005).
Activity and stability of hammerhead ribozymes containing 2'-C-methyluridine: a new RNA mimic.
  Chem Biodivers, 2, 198-204.  
15956979 M.J.Fedor, and J.R.Williamson (2005).
The catalytic diversity of RNAs.
  Nat Rev Mol Cell Biol, 6, 399-412.  
15846405 Y.Tanaka, and K.Taira (2005).
Detection of RNA nucleobase metalation by NMR spectroscopy.
  Chem Commun (Camb), (), 2069-2079.  
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.  
15328556 E.Mayaan, K.Range, and D.M.York (2004).
Structure and binding of Mg(II) ions and di-metal bridge complexes with biological phosphates and phosphoranes.
  J Biol Inorg Chem, 9, 807-817.  
  15215462 I.W.Davis, L.W.Murray, J.S.Richardson, and D.C.Richardson (2004).
MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes.
  Nucleic Acids Res, 32, W615-W619.  
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
14532128 M.De la Peña, S.Gago, and R.Flores (2003).
Peripheral regions of natural hammerhead ribozymes greatly increase their self-cleavage activity.
  EMBO J, 22, 5561-5570.  
12772587 Y.Tanaka (2003).
[Spectroscopic analyses of the interaction between hammerhead ribozymes and metal ions]
  Yakugaku Zasshi, 123, 305-313.  
12110898 J.A.Doudna, and T.R.Cech (2002).
The chemical repertoire of natural ribozymes.
  Nature, 418, 222-228.  
11170470 C.Hammann, A.Cooper, and D.M.Lilley (2001).
Thermodynamics of ion-induced RNA folding in the hammerhead ribozyme: an isothermal titration calorimetric study.
  Biochemistry, 40, 1423-1429.  
11331743 C.Hammann, D.G.Norman, and D.M.Lilley (2001).
Dissection of the ion-induced folding of the hammerhead ribozyme using 19F NMR.
  Proc Natl Acad Sci U S A, 98, 5503-5508.  
11441810 E.A.Doherty, and J.A.Doudna (2001).
Ribozyme structures and mechanisms.
  Annu Rev Biophys Biomol Struct, 30, 457-475.  
11173496 E.Ennifar, P.Walter, and P.Dumas (2001).
An efficient method for solving RNA structures: MAD phasing by replacing magnesium with zinc.
  Acta Crystallogr D Biol Crystallogr, 57, 330-332.  
11345432 J.L.O'Rear, S.Wang, A.L.Feig, L.Beigelman, O.C.Uhlenbeck, and D.Herschlag (2001).
Comparison of the hammerhead cleavage reactions stimulated by monovalent and divalent cations.
  RNA, 7, 537-545.  
11333021 V.Tereshko, S.T.Wallace, N.Usman, F.E.Wincott, and M.Egli (2001).
X-ray crystallographic observation of "in-line" and "adjacent" conformations in a bulged self-cleaving RNA/DNA hybrid.
  RNA, 7, 405-420.
PDB codes: 1i2x 1i2y
11328865 Y.Takagi, M.Warashina, W.J.Stec, K.Yoshinari, and K.Taira (2001).
Recent advances in the elucidation of the mechanisms of action of ribozymes.
  Nucleic Acids Res, 29, 1815-1834.  
10933815 C.G.Hoogstraten, J.R.Wank, and A.Pardi (2000).
Active site dynamics in the lead-dependent ribozyme.
  Biochemistry, 39, 9951-9958.  
10828955 D.J.Earnshaw, M.L.Hamm, J.A.Piccirilli, A.Karpeisky, L.Beigelman, B.S.Ross, M.Manoharan, and M.J.Gait (2000).
Investigation of the proposed interdomain ribose zipper in hairpin ribozyme cleavage using 2'-modified nucleosides.
  Biochemistry, 39, 6410-6421.  
10966470 E.A.Doherty, and J.A.Doudna (2000).
Ribozyme structures and mechanisms.
  Annu Rev Biochem, 69, 597-615.  
11105752 G.Minasov, J.Matulic-Adamic, C.J.Wilds, P.Haeberli, N.Usman, L.Beigelman, and M.Egli (2000).
Crystal structure of an RNA duplex containing phenyl-ribonucleotides, hydrophobic isosteres of the natural pyrimidines.
  RNA, 6, 1516-1528.
PDB code: 1g2j
10710433 H.H.Chen, D.Castanotto, J.M.LeBon, J.J.Rossi, and A.D.Riggs (2000).
In vivo, high-resolution analysis of yeast and mammalian RNA-protein interactions, RNA structure, RNA splicing and ribozyme cleavage by use of terminal transferase-dependent PCR.
  Nucleic Acids Res, 28, 1656-1664.  
10882069 J.B.Murray, H.Szöke, A.Szöke, and W.G.Scott (2000).
Capture and visualization of a catalytic RNA enzyme-product complex using crystal lattice trapping and X-ray holographic reconstruction.
  Mol Cell, 5, 279-287.
PDB code: 488d
10606646 J.Li, W.Zheng, A.H.Kwon, and Y.Lu (2000).
In vitro selection and characterization of a highly efficient Zn(II)-dependent RNA-cleaving deoxyribozyme.
  Nucleic Acids Res, 28, 481-488.  
10968986 J.Sarzynska, T.Kulinski, and L.Nilsson (2000).
Conformational dynamics of a 5S rRNA hairpin domain containing loop D and a single nucleotide bulge.
  Biophys J, 79, 1213-1227.  
10734192 K.Yoshinari, and K.Taira (2000).
A further investigation and reappraisal of the thio effect in the cleavage reaction catalyzed by a hammerhead ribozyme.
  Nucleic Acids Res, 28, 1730-1742.  
11015188 M.Maderia, L.M.Hunsicker, and V.J.DeRose (2000).
Metal-phosphate interactions in the hammerhead ribozyme observed by 31P NMR and phosphorothioate substitutions.
  Biochemistry, 39, 12113-12120.  
11071929 M.Menger, F.Eckstein, and D.Porschke (2000).
Multiple conformational states of the hammerhead ribozyme, broad time range of relaxation and topology of dynamics.
  Nucleic Acids Res, 28, 4428-4434.  
10975454 M.Warashina, Y.Takagi, W.J.Stec, and K.Taira (2000).
Differences among mechanisms of ribozyme-catalyzed reactions.
  Curr Opin Biotechnol, 11, 354-362.  
10968286 S.Alefelder, and S.T.Sigurdsson (2000).
Interstrand disulfide cross-linking of internal sugar residues in duplex RNA.
  Bioorg Med Chem, 8, 269-273.  
10947846 Y.Nakamatsu, M.Warashina, T.Kuwabara, Y.Tanaka, K.Yoshinari, and K.Taira (2000).
Significant activity of a modified ribozyme with N7-deazaguanine at g10.1: the double-metal-ion mechanism of catalysis in reactions catalysed by hammerhead ribozymes.
  Genes Cells, 5, 603-612.  
10410795 A.R.Ferré-D'Amaré, and J.A.Doudna (1999).
RNA folds: insights from recent crystal structures.
  Annu Rev Biophys Biomol Struct, 28, 57-73.  
10385001 C.Bravo, A.Woisard, J.L.Fourrey, P.Laugâa, and A.Favre (1999).
A Y form of hammerhead ribozyme trapped by photo-cross-links retains full cleavage activity.
  Biochimie, 81, 201-212.  
10361084 D.M.Lilley (1999).
Structure, folding and catalysis of the small nucleolytic ribozymes.
  Curr Opin Struct Biol, 9, 330-338.  
11169382 F.Eckstein, and B.Bramlage (1999).
The hammerhead ribozyme.
  Biopolymers, 52, 147-154.  
10573122 G.A.Soukup, and R.R.Breaker (1999).
Relationship between internucleotide linkage geometry and the stability of RNA.
  RNA, 5, 1308-1325.  
10079078 G.S.Bassi, N.E.Møllegaard, A.I.Murchie, and D.M.Lilley (1999).
RNA folding and misfolding of the hammerhead ribozyme.
  Biochemistry, 38, 3345-3354.  
10542074 H.R.Drew, D.Lewy, J.Conaty, K.N.Rand, P.Hendry, and T.Lockett (1999).
RNA hairpin loops repress protein synthesis more strongly than hammerhead ribozymes.
  Eur J Biochem, 266, 260-273.  
10445883 M.R.Hansen, J.P.Simorre, P.Hanson, V.Mokler, L.Bellon, L.Beigelman, and A.Pardi (1999).
Identification and characterization of a novel high affinity metal-binding site in the hammerhead ribozyme.
  RNA, 5, 1099-1104.  
10371033 N.K.Tanner (1999).
Ribozymes: the characteristics and properties of catalytic RNAs.
  FEMS Microbiol Rev, 23, 257-275.  
10387010 S.Bevers, S.B.Ha, and L.W.McLaughlin (1999).
Critical nature of a specific uridine O2-carbonyl for cleavage by the hammerhead ribozyme.
  Biochemistry, 38, 7710-7718.  
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.  
10600729 W.G.Scott (1999).
RNA structure, metal ions, and catalysis.
  Curr Opin Chem Biol, 3, 705-709.  
9814755 A.Peracchi, J.Matulic-Adamic, S.Wang, L.Beigelman, and D.Herschlag (1998).
Structure-function relationships in the hammerhead ribozyme probed by base rescue.
  RNA, 4, 1332-1346.  
9818266 B.L.Stoddard (1998).
New results using Laue diffraction and time-resolved crystallography.
  Curr Opin Struct Biol, 8, 612-618.  
11180044 D.M.Lilley (1998).
Folding of branched RNA species.
  Biopolymers, 48, 101-112.  
9663384 J.A.Doudna (1998).
Ribozymes: the hammerhead swings into action.
  Curr Biol, 8, R495-R497.  
9818150 J.B.Murray, A.A.Seyhan, N.G.Walter, J.M.Burke, and W.G.Scott (1998).
The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone.
  Chem Biol, 5, 587-595.  
9736692 R.A.Torres, and T.C.Bruice (1998).
Molecular dynamics study displays near in-line attack conformations in the hammerhead ribozyme self-cleavage reaction.
  Proc Natl Acad Sci U S A, 95, 11077-11082.  
9846125 S.A.Strobel (1998).
Ribozyme chemogenetics.
  Biopolymers, 48, 65-81.  
9628915 S.G.Chaulk, and A.M.MacMillan (1998).
Caged RNA: photo-control of a ribozyme reaction.
  Nucleic Acids Res, 26, 3173-3178.  
9922178 T.E.Horton, D.R.Clardy, and V.J.DeRose (1998).
Electron paramagnetic resonance spectroscopic measurement of Mn2+ binding affinities to the hammerhead ribozyme and correlation with cleavage activity.
  Biochemistry, 37, 18094-18101.  
9782053 T.Hermann, and E.Westhof (1998).
Exploration of metal ion binding sites in RNA folds by Brownian-dynamics simulations.
  Structure, 6, 1303-1314.  
9914252 W.G.Scott (1998).
RNA catalysis.
  Curr Opin Struct Biol, 8, 720-726.  
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.