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Volumn 12, Issue 3, 2005, Pages 218-224

Structural basis for Diels-Alder ribozyme-catalyzed carbon-carbon bond formation

Author keywords

[No Author keywords available]

Indexed keywords

RIBOZYME; CARBON;

EID: 20244375551     PISSN: 15459993     EISSN: 15459985     Source Type: Journal    
DOI: 10.1038/nsmb906     Document Type: Article
Times cited : (185)

References (51)
  • 1
    • 0020417286 scopus 로고
    • Self-splicing RNA: Autoexcision and autocyclization of the ribosomal RNA intervening sequence in Tetrahymena
    • Kruger, K. et al. Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence in Tetrahymena. Cell 31, 145-157 (1982).
    • (1982) Cell , vol.31 , pp. 145-157
    • Kruger, K.1
  • 2
    • 0021013526 scopus 로고
    • The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme
    • Guerrier-Takada, C., Gardiner, K., Marsh, T., Pace, N. & Altman, S. The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell 35, 849-857 (1983).
    • (1983) Cell , vol.35 , pp. 849-857
    • Guerrier-Takada, C.1    Gardiner, K.2    Marsh, T.3    Pace, N.4    Altman, S.5
  • 3
    • 36849148382 scopus 로고
    • The RNA world
    • Gilbert, W. The RNA world. Nature 319, 618-620 (1986).
    • (1986) Nature , vol.319 , pp. 618-620
    • Gilbert, W.1
  • 4
    • 0036863325 scopus 로고    scopus 로고
    • Ribozymes, the first 20 years
    • Cech, T.R. Ribozymes, the first 20 years. Biochem. Soc. Trans. 30, 1162-1166 (2002).
    • (2002) Biochem. Soc. Trans. , vol.30 , pp. 1162-1166
    • Cech, T.R.1
  • 5
    • 0037062949 scopus 로고    scopus 로고
    • The chemical repertoire of natural ribozymes
    • Doudna, J.A. & Cech, T.R. The chemical repertoire of natural ribozymes. Nature 418, 222-228 (2002).
    • (2002) Nature , vol.418 , pp. 222-228
    • Doudna, J.A.1    Cech, T.R.2
  • 6
    • 0042658199 scopus 로고    scopus 로고
    • RNA, the first macromolecular catalyst: The ribosome is a ribozyme
    • Steitz, T.A. & Moore, P.B. RNA, the first macromolecular catalyst: the ribosome is a ribozyme. Trends Biochem. Sci. 28, 411-418 (2003).
    • (2003) Trends Biochem. Sci. , vol.28 , pp. 411-418
    • Steitz, T.A.1    Moore, P.B.2
  • 7
    • 0032853242 scopus 로고    scopus 로고
    • In vitro selection of functional nucleic acids
    • Wilson, D.S. & Szostak, J.W. In vitro selection of functional nucleic acids. Annu. Rev. Biochem. 68, 611-647 (1999).
    • (1999) Annu. Rev. Biochem. , vol.68 , pp. 611-647
    • Wilson, D.S.1    Szostak, J.W.2
  • 9
    • 0346687595 scopus 로고    scopus 로고
    • The riboswitch control of bacterial metabolism
    • Nudler, E, & Mironov, A.S. The riboswitch control of bacterial metabolism. Trends Biochem. Sci. 29, 11-17 (2004).
    • (2004) Trends Biochem. Sci. , vol.29 , pp. 11-17
    • Nudler, E.1    Mironov, A.S.2
  • 10
    • 0035663818 scopus 로고    scopus 로고
    • Creative catalysis: Pieces of the RNA world jigsaw
    • Murray, J.M. & Doudna, J.A. Creative catalysis: pieces of the RNA world jigsaw. Trends Biochem. Sci. 26, 699-701 (2001).
    • (2001) Trends Biochem. Sci. , vol.26 , pp. 699-701
    • Murray, J.M.1    Doudna, J.A.2
  • 11
    • 2942715028 scopus 로고    scopus 로고
    • Analysis of global conformational transitions in ribozymes
    • Lilley, D.M. Analysis of global conformational transitions in ribozymes. Methods Mol. Biol. 252, 77-108 (2004).
    • (2004) Methods Mol. Biol. , vol.252 , pp. 77-108
    • Lilley, D.M.1
  • 13
    • 0033797244 scopus 로고    scopus 로고
    • Nucleic acid aptamers-from selection in vitro to applications in vivo
    • Famulok, M., Mayer, G. & Blind, M. Nucleic acid aptamers-from selection in vitro to applications in vivo. Acc. Chem. Res. 33, 591-599 (2000).
    • (2000) Acc. Chem. Res. , vol.33 , pp. 591-599
    • Famulok, M.1    Mayer, G.2    Blind, M.3
  • 14
    • 0035368080 scopus 로고    scopus 로고
    • Artificial ribozymes and deoxyribozymes
    • Jäschke, A. Artificial ribozymes and deoxyribozymes. Curr. Opin. Struct. Biol. 11, 321-326(2001).
    • (2001) Curr. Opin. Struct. Biol. , vol.11 , pp. 321-326
    • Jäschke, A.1
  • 15
    • 0002622819 scopus 로고    scopus 로고
    • Prospects for understanding the origin of the RNA world
    • (eds. Gesteland, R.F., Cech, T.R. & Atkins, J.F.) (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York)
    • Joyce, G.F. & Orgel, L.E. Prospects for understanding the origin of the RNA world. In The RNA World 2nd edn. (eds. Gesteland, R.F., Cech, T.R. & Atkins, J.F.) 49-77 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 1998).
    • (1998) The RNA World 2nd Edn. , pp. 49-77
    • Joyce, G.F.1    Orgel, L.E.2
  • 16
    • 0033102314 scopus 로고    scopus 로고
    • A small catalytic RNA motif with Diels-Alderase activity
    • Seelig, B. & Jäschke, A. A small catalytic RNA motif with Diels-Alderase activity. Chem. Biol. 6, 167-176 (1999).
    • (1999) Chem. Biol. , vol.6 , pp. 167-176
    • Seelig, B.1    Jäschke, A.2
  • 17
    • 0030963855 scopus 로고    scopus 로고
    • RNA-catalyzed carbon-carbon bond formation
    • Tarasow, T.M., Tarasow, S.L. & Eaton, B.E. RNA-catalyzed carbon-carbon bond formation. Nature 389, 54-57 (1997).
    • (1997) Nature , vol.389 , pp. 54-57
    • Tarasow, T.M.1    Tarasow, S.L.2    Eaton, B.E.3
  • 19
    • 0034671737 scopus 로고    scopus 로고
    • Enantioselective ribozyme catalysis of a bimolecular cycloaddition reaction
    • Seelig, B., Keiper, S., Stuhlmann, F. & Jäschke, A. Enantioselective ribozyme catalysis of a bimolecular cycloaddition reaction. Angew. Chem. Int. Ed. 39, 4576-4579 (2000).
    • (2000) Angew. Chem. Int. Ed. , vol.39 , pp. 4576-4579
    • Seelig, B.1    Keiper, S.2    Stuhlmann, F.3    Jäschke, A.4
  • 20
    • 4644305780 scopus 로고    scopus 로고
    • An architecture of a Diels-Alderase ribozyme with a preformed catalytic pocket
    • Keiper, S., Bebenroth, D., Seelig, B., Westhof, E. & Jäschke, A. An architecture of a Diels-Alderase ribozyme with a preformed catalytic pocket. Chem. Biol. 11, 1217-1227 (2004).
    • (2004) Chem. Biol. , vol.11 , pp. 1217-1227
    • Keiper, S.1    Bebenroth, D.2    Seelig, B.3    Westhof, E.4    Jäschke, A.5
  • 21
    • 0037012440 scopus 로고    scopus 로고
    • Characterization of an RNA active site: Interactions between a Diels-Alderase ribozyme and its substrates and products
    • Stuhlmann, F. & Jäschke, A. Characterization of an RNA active site: interactions between a Diels-Alderase ribozyme and its substrates and products. J. Am. Chem. Soc. 124, 328-344 (2002).
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 328-344
    • Stuhlmann, F.1    Jäschke, A.2
  • 22
    • 0034603154 scopus 로고    scopus 로고
    • Adaptive recognition by nucleic acid aptamers
    • Hermann, T. & Patel, D.J. Adaptive recognition by nucleic acid aptamers. Science 287, 820-825 (2000).
    • (2000) Science , vol.287 , pp. 820-825
    • Hermann, T.1    Patel, D.J.2
  • 23
    • 85069079001 scopus 로고    scopus 로고
    • Internal derivatization of oligonucleotides with selenium for X-ray crystallography with MAD
    • Du, Q, et al. Internal derivatization of oligonucleotides with selenium for X-ray crystallography with MAD. J. Am. Chem. Soc. 124, 2425 (2002).
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 2425
    • Du, Q.1
  • 24
    • 19244379910 scopus 로고    scopus 로고
    • Chemical synthesis of selenium-modified oligoribonucleotides and their enzymatic ligation leading to an U6 snRNA stem-loop segment
    • Höbartner, C. & Micura, R. Chemical synthesis of selenium-modified oligoribonucleotides and their enzymatic ligation leading to an U6 snRNA stem-loop segment. J. Am. Chem. Soc. 126, 1141-1149 (2004).
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 1141-1149
    • Höbartner, C.1    Micura, R.2
  • 25
    • 0036761115 scopus 로고    scopus 로고
    • Covalent incorporation of selenium into oligonucleotides for X-ray crystal structure determination via MAD: Proof of principle
    • Teplova, M. et al. Covalent incorporation of selenium into oligonucleotides for X-ray crystal structure determination via MAD: proof of principle. Biochimie 84, 849-858 (2002).
    • (2002) Biochimie , vol.84 , pp. 849-858
    • Teplova, M.1
  • 26
    • 3042848954 scopus 로고    scopus 로고
    • Crystal structure of a self-splicing group I intron with both exons
    • Adams, P.L., Stahley, M.R., Kosek, A.B., Wang, J. & Strobel, S.A. Crystal structure of a self-splicing group I intron with both exons. Nature 430, 45-50 (2004).
    • (2004) Nature , vol.430 , pp. 45-50
    • Adams, P.L.1    Stahley, M.R.2    Kosek, A.B.3    Wang, J.4    Strobel, S.A.5
  • 27
    • 0028063567 scopus 로고
    • Three-dimensional structure of a hammerhead ribozyme
    • Pley, H., Flaherty, K.M. & McKay, D.B. Three-dimensional structure of a hammerhead ribozyme. Nature 372, 68-74 (1994).
    • (1994) Nature , vol.372 , pp. 68-74
    • Pley, H.1    Flaherty, K.M.2    McKay, D.B.3
  • 28
    • 1642580826 scopus 로고    scopus 로고
    • The Varkud satellite ribozyme
    • Lilley, D.M. The Varkud satellite ribozyme. RNA 10, 151-158 (2004).
    • (2004) RNA , vol.10 , pp. 151-158
    • Lilley, D.M.1
  • 29
    • 0032497521 scopus 로고    scopus 로고
    • Crystal structure of a hepatitis delta virus ribozyme
    • Ferre-D'Amare, A.R., Zhou, K. & Doudna, J.A. Crystal structure of a hepatitis delta virus ribozyme. Nature 395, 567-574 (1998).
    • (1998) Nature , vol.395 , pp. 567-574
    • Ferre-D'Amare, A.R.1    Zhou, K.2    Doudna, J.A.3
  • 30
    • 0035914362 scopus 로고    scopus 로고
    • Translational repression of the Escherichia coli α operon mRNA: Importance of an mRNA conformational switch and a ternary entrapment complex
    • Schlax, P.J., Xavier, K.A., Gluick, T.C. & Draper, D.E. Translational repression of the Escherichia coli α operon mRNA: importance of an mRNA conformational switch and a ternary entrapment complex. J. Biol. Chem. 276, 38494-38501 (2001).
    • (2001) J. Biol. Chem. , vol.276 , pp. 38494-38501
    • Schlax, P.J.1    Xavier, K.A.2    Gluick, T.C.3    Draper, D.E.4
  • 31
    • 0028426892 scopus 로고
    • An RNA pocket for an aliphatic hydrophobe
    • Majerfeld, I. & Yarus, M. An RNA pocket for an aliphatic hydrophobe. Nat. Struct. Biol. 1, 287-292 (1994).
    • (1994) Nat. Struct. Biol. , vol.1 , pp. 287-292
    • Majerfeld, I.1    Yarus, M.2
  • 32
    • 0033784534 scopus 로고    scopus 로고
    • Induced fit in RNA-protein recognition
    • Williamson, J.R. Induced fit in RNA-protein recognition. Nat. Struct. Biol. 7, 834-837 (2000).
    • (2000) Nat. Struct. Biol. , vol.7 , pp. 834-837
    • Williamson, J.R.1
  • 33
    • 0035838382 scopus 로고    scopus 로고
    • Current topics in RNA-protein recognition: Control of specificity and biological function through induced fit and conformational capture
    • Leulliot, N. & Varani, G. Current topics in RNA-protein recognition: control of specificity and biological function through induced fit and conformational capture. Biochemistry 40, 7947-7956 (2001).
    • (2001) Biochemistry , vol.40 , pp. 7947-7956
    • Leulliot, N.1    Varani, G.2
  • 34
    • 0034256638 scopus 로고    scopus 로고
    • A computational study of aromaticity-controlled Diels-Alder reactions
    • Manoharan, M., De Proft, F. & Geerlings, P. A computational study of aromaticity-controlled Diels-Alder reactions. J. Chem. Soc. Perkin Trans. 2, 1767-1773 (2000).
    • (2000) J. Chem. Soc. Perkin Trans. , vol.2 , pp. 1767-1773
    • Manoharan, M.1    De Proft, F.2    Geerlings, P.3
  • 35
    • 0000786273 scopus 로고    scopus 로고
    • Donor-acceptor-assisted Diels-Alder reaction of anthracene and tetracyanoethylene
    • Wise, K.E. & Wheeler, R.A. Donor-acceptor-assisted Diels-Alder reaction of anthracene and tetracyanoethylene. J. Phys. Chem. 103, 8279-8287 (1999).
    • (1999) J. Phys. Chem. , vol.103 , pp. 8279-8287
    • Wise, K.E.1    Wheeler, R.A.2
  • 36
    • 0033579299 scopus 로고    scopus 로고
    • Evolution of shape complementarity and catalytic efficiency from a primordial antibody template
    • Xu, J. et al. Evolution of shape complementarity and catalytic efficiency from a primordial antibody template. Science 286, 23455-2348 (1999).
    • (1999) Science , vol.286 , pp. 23455-32348
    • Xu, J.1
  • 37
    • 0034681063 scopus 로고    scopus 로고
    • Shape complementarity, binding-site dynamics, and transition state stabilization: A theoretical study of Diels-Alder catalysis by antibody 1E9
    • Chen, J., Deng, Q., Wang, R., Houk, K. & Hilvert, D. Shape complementarity, binding-site dynamics, and transition state stabilization: a theoretical study of Diels-Alder catalysis by antibody 1E9. Chembiochem 1, 255-261 (2000).
    • (2000) Chembiochem , vol.1 , pp. 255-261
    • Chen, J.1    Deng, Q.2    Wang, R.3    Houk, K.4    Hilvert, D.5
  • 39
    • 0032549734 scopus 로고    scopus 로고
    • An antibody exo Diels-Alderase inhibitor complex at 1.95 Å resolution
    • Heine, A. et al. An antibody exo Diels-Alderase inhibitor complex at 1.95 Å resolution. Science 279, 1934-1940 (1998).
    • (1998) Science , vol.279 , pp. 1934-1940
    • Heine, A.1
  • 40
    • 0032549776 scopus 로고    scopus 로고
    • Immunological origins of binding and catalysis in a Diels-Alderase antibody
    • Romesberg, F.E., Spiller, B., Schultz, P.G. & Stevens, R.C. Immunological origins of binding and catalysis in a Diels-Alderase antibody. Science 279, 1929-1933 (1998).
    • (1998) Science , vol.279 , pp. 1929-1933
    • Romesberg, F.E.1    Spiller, B.2    Schultz, P.G.3    Stevens, R.C.4
  • 41
    • 0037162554 scopus 로고    scopus 로고
    • A structural basis for the activity of retro-Diels-Alder catalytic antibodies: Evidence for a catalytic aromatic residue
    • Hugot, M. et al. A structural basis for the activity of retro-Diels-Alder catalytic antibodies: Evidence for a catalytic aromatic residue. Proc. Natl. Acad. Sci. USA 99, 9674-9678 (2002).
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 9674-9678
    • Hugot, M.1
  • 42
    • 0037434992 scopus 로고    scopus 로고
    • Insights into a natural Diels-Alder reaction from the structure of macrophomate synthase
    • Ose, T. et al. Insights into a natural Diels-Alder reaction from the structure of macrophomate synthase. Nature 422, 185-189 (2003).
    • (2003) Nature , vol.422 , pp. 185-189
    • Ose, T.1
  • 43
    • 14944342354 scopus 로고    scopus 로고
    • Structure of macrophomate synthase
    • Ose, T. et al. Structure of macrophomate synthase. Acta Crystallogr. D 60, 1187-1197 (2004).
    • (2004) Acta Crystallogr. D , vol.60 , pp. 1187-1197
    • Ose, T.1
  • 44
    • 4644272645 scopus 로고    scopus 로고
    • The effect of mutation on RNA Diels-Alderases
    • Tarasow, T.M. et al. The effect of mutation on RNA Diels-Alderases. J. Am. Chem. Soc. 126, 11843-11851 (2004).
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 11843-11851
    • Tarasow, T.M.1
  • 45
    • 0031059866 scopus 로고    scopus 로고
    • Processing of X-ray diffraction data collected in oscillation mode
    • Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326 (1997).
    • (1997) Methods Enzymol. , vol.276 , pp. 307-326
    • Otwinowski, Z.1    Minor, W.2
  • 47
    • 0031058188 scopus 로고    scopus 로고
    • Maximum-likelihood heavy-atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods
    • De La Fortelle, E. & Bricogne, G. Maximum-likelihood heavy-atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods. Methods Enzymol. 276, 472-494 (1997).
    • (1997) Methods Enzymol. , vol.276 , pp. 472-494
    • De La Fortelle, E.1    Bricogne, G.2
  • 48
    • 0030038464 scopus 로고    scopus 로고
    • Methods used in the structure determination of bovine mitochondrial F1 ATPase
    • Abrahams, J.P. & Leslie, A.G. Methods used in the structure determination of bovine mitochondrial F1 ATPase. Acta Crystallogr. D 52, 30-42 (1996).
    • (1996) Acta Crystallogr. D , vol.52 , pp. 30-42
    • Abrahams, J.P.1    Leslie, A.G.2
  • 49
    • 0028103275 scopus 로고
    • The CCP4 suite: Programs for protein crystallography
    • Collaborative Computational Project, Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D 50, 760-763 (1994).
    • (1994) Acta Crystallogr. D , vol.50 , pp. 760-763
  • 50
    • 0030924992 scopus 로고    scopus 로고
    • Refinement of macromolecular structures by the maximum-likelihood method
    • Murshudov, G.N., Vagin, A.A. & Dodson, E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D 53, 240-245 (1997).
    • (1997) Acta Crystallogr. D , vol.53 , pp. 240-245
    • Murshudov, G.N.1    Vagin, A.A.2    Dodson, E.J.3
  • 51
    • 3543012707 scopus 로고    scopus 로고
    • Crystallography and NMR system: A new software suite for macromolecular structure determination
    • Brunger, A.T. et al. Crystallography and NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905-921 (1998).
    • (1998) Acta Crystallogr. D , vol.54 , pp. 905-921
    • Brunger, A.T.1


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