-
1
-
-
67349123194
-
Comparative enzymology and structural biology of RNA self-cleavage
-
Fedor, M. J. (2009) Comparative enzymology and structural biology of RNA self-cleavage Annu. Rev. Biophys. 38, 271-299
-
(2009)
Annu. Rev. Biophys.
, vol.38
, pp. 271-299
-
-
Fedor, M.J.1
-
2
-
-
79958042255
-
Emerging structural themes in large RNA molecules
-
Reiter, N. J., Chan, C. W., and Mondragon, A. (2011) Emerging structural themes in large RNA molecules Curr. Opin. Struct. Biol. 21, 319-326
-
(2011)
Curr. Opin. Struct. Biol.
, vol.21
, pp. 319-326
-
-
Reiter, N.J.1
Chan, C.W.2
Mondragon, A.3
-
3
-
-
79958042263
-
Base ionization and ligand binding: How small ribozymes and riboswitches gain a foothold in a protein world
-
Liberman, J. A. and Wedekind, J. E. (2011) Base ionization and ligand binding: How small ribozymes and riboswitches gain a foothold in a protein world Curr. Opin. Struct. Biol. 21, 327-334
-
(2011)
Curr. Opin. Struct. Biol.
, vol.21
, pp. 327-334
-
-
Liberman, J.A.1
Wedekind, J.E.2
-
4
-
-
0038170015
-
Metal ion binding to catalytic RNA molecules
-
DeRose, V. J. (2003) Metal ion binding to catalytic RNA molecules Curr. Opin. Struct. Biol. 13, 317-324
-
(2003)
Curr. Opin. Struct. Biol.
, vol.13
, pp. 317-324
-
-
Derose, V.J.1
-
5
-
-
56649102324
-
High tolerance for ionizable residues in the hydrophobic interior of proteins
-
Isom, D. G., Cannon, B. R., Castaneda, C. A., Robinson, A., and Garcia-Moreno, B. (2008) High tolerance for ionizable residues in the hydrophobic interior of proteins Proc. Natl. Acad. Sci. U.S.A. 105, 17784-17788
-
(2008)
Proc. Natl. Acad. Sci. U.S.A.
, vol.105
, pp. 17784-17788
-
-
Isom, D.G.1
Cannon, B.R.2
Castaneda, C.A.3
Robinson, A.4
Garcia-Moreno, B.5
-
9
-
-
0026669321
-
A small metalloribozyme with a two-step mechanism
-
Pan, T. and Uhlenbeck, O. C. (1992) A small metalloribozyme with a two-step mechanism Nature 358, 560-563
-
(1992)
Nature
, vol.358
, pp. 560-563
-
-
Pan, T.1
Uhlenbeck, O.C.2
-
10
-
-
0037172779
-
Metal ion requirements for structure and catalysis of an RNA ligase ribozyme
-
DOI 10.1021/bi012179b
-
Glasner, M. E., Bergman, N. H., and Bartel, D. P. (2002) Metal ion requirements for structure and catalysis of an RNA ligase ribozyme Biochemistry 41, 8103-8112 (Pubitemid 34655179)
-
(2002)
Biochemistry
, vol.41
, Issue.25
, pp. 8103-8112
-
-
Glasner, M.E.1
Bergman, N.H.2
Bartel, D.P.3
-
11
-
-
0035340961
-
Defining the catalytic metal ion interactions in the Tetrahymena ribozyme reaction
-
Shan, S., Kravchuk, A. V., Piccirilli, J. A., and Herschlag, D. (2001) Defining the catalytic metal ion interactions in the Tetrahymena ribozyme reaction Biochemistry 40, 5161-5171 (Pubitemid 32373998)
-
(2001)
Biochemistry
, vol.40
, Issue.17
, pp. 5161-5171
-
-
Shan, S.1
Kravchuk, A.V.2
Piccirilli, J.A.3
Herschlag, D.4
-
12
-
-
0032497521
-
Crystal structure of a hepatitis delta virus ribozyme
-
DOI 10.1038/26912
-
Ferre-DAmare, A. R., Zhou, K. H., and Doudna, J. A. (1998) Crystal structure of a hepatitis delta virus ribozyme Nature 395, 567-574 (Pubitemid 28475703)
-
(1998)
Nature
, vol.395
, Issue.6702
, pp. 567-574
-
-
Ferre-D'Amare, A.R.1
Zhou, K.2
Doudna, J.A.3
-
13
-
-
0034712097
-
General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme
-
DOI 10.1126/science.287.5457.1493
-
Nakano, S., Chadalavada, D. M., and Bevilacqua, P. C. (2000) General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme Science 287, 1493-1497 (Pubitemid 30127144)
-
(2000)
Science
, vol.287
, Issue.5457
, pp. 1493-1497
-
-
Nakano, S.-I.1
Chadalavada, D.M.2
Bevilacqua, P.C.3
-
14
-
-
0035833978
-
Mechanistic characterization of the HDV genomic ribozyme: Assessing the catalytic and structural contributions of divalent metal ions within a multichannel reaction mechanism
-
DOI 10.1021/bi011253n
-
Nakano, S., Proctor, D. J., and Bevilacqua, P. C. (2001) Mechanistic characterization of the HDV genomic ribozyme: Assessing the catalytic and structural contributions of divalent metal ions within a multichannel reaction mechanism Biochemistry 40, 12022-12038 (Pubitemid 32946544)
-
(2001)
Biochemistry
, vol.40
, Issue.40
, pp. 12022-12038
-
-
Nakano, S.1
Proctor, D.J.2
Bevilacqua, P.C.3
-
15
-
-
61749093844
-
A catalytic metal ion interacts with the cleavage site G·U wobble in the HDV ribozyme
-
Chen, J. H., Gong, B., Bevilacqua, P. C., Carey, P. R., and Golden, B. L. (2009) A catalytic metal ion interacts with the cleavage site G·U wobble in the HDV ribozyme Biochemistry 48, 1498-1507
-
(2009)
Biochemistry
, vol.48
, pp. 1498-1507
-
-
Chen, J.H.1
Gong, B.2
Bevilacqua, P.C.3
Carey, P.R.4
Golden, B.L.5
-
16
-
-
0037154091
-
Reaction pathway of the trans-acting hepatitis delta virus ribozyme: A conformational change accompanies catalysis
-
DOI 10.1021/bi011963t
-
Pereira, M. J., Harris, D. A., Rueda, D., and Walter, N. G. (2002) Reaction pathway of the trans-acting hepatitis delta virus ribozyme: A conformational change accompanies catalysis Biochemistry 41, 730-740 (Pubitemid 34061973)
-
(2002)
Biochemistry
, vol.41
, Issue.3
, pp. 730-740
-
-
Pereira, M.J.B.1
Harris, D.A.2
Rueda, D.3
Walter, N.G.4
-
17
-
-
2442641641
-
A conformational switch controls hepatitis delta virus ribozyme catalysis
-
DOI 10.1038/nature02522
-
Ke, A., Zhou, K., Ding, F., Cate, J. H., and Doudna, J. A. (2004) A conformational switch controls hepatitis delta virus ribozyme catalysis Nature 429, 201-205 (Pubitemid 38656198)
-
(2004)
Nature
, vol.429
, Issue.6988
, pp. 201-205
-
-
Ke, A.1
Zhou, K.2
Ding, F.3
Cate, J.H.D.4
Doudna, J.A.5
-
18
-
-
23444456517
-
Structural dynamics of precursor and product of the RNA enzyme from the hepatitis delta virus as revealed by molecular dynamics simulations
-
DOI 10.1016/j.jmb.2005.06.016, PII S0022283605006662
-
Krasovska, M. V., Sefcikova, J., Spackova, N., Sponer, J., and Walter, N. G. (2005) Structural dynamics of precursor and product of the RNA enzyme from the hepatitis delta virus as revealed by molecular dynamics simulations J. Mol. Biol. 351, 731-748 (Pubitemid 41111892)
-
(2005)
Journal of Molecular Biology
, vol.351
, Issue.4
, pp. 731-748
-
-
Krasovska, M.V.1
Sefcikova, J.2
Spackova, N.3
Sponer, J.4
Walter, N.G.5
-
19
-
-
8644229237
-
Structure of the tetrahymena ribozyme: Base triple sandwich and metal ion at the active site
-
DOI 10.1016/j.molcel.2004.10.003, PII S1097276504005921
-
Guo, F., Gooding, A., and Cech, T. R. (2004) Structure of the Tetrahymena ribozyme: Base triple sandwich and metal ion at the active site Mol. Cell 16, 351-362 (Pubitemid 39504790)
-
(2004)
Molecular Cell
, vol.16
, Issue.3
, pp. 351-362
-
-
Guo, F.1
Gooding, A.R.2
Cech, T.R.3
-
20
-
-
3042848954
-
Crystal structure of a self-splicing group I intron with both exons
-
DOI 10.1038/nature02642
-
Adams, P. L., Stahley, M. R., Kosek, A. B., Wang, J., and Strobel, S. A. (2004) Crystal structure of a self-splicing group I intron with both exons Nature 430, 45-50 (Pubitemid 38915218)
-
(2004)
Nature
, vol.430
, Issue.6995
, pp. 45-50
-
-
Adams, P.L.1
Stahley, M.R.2
Kosek, A.B.3
Wang, J.4
Strobel, S.A.5
-
21
-
-
11444263264
-
Crystal structure of a phage Twort group I ribozyme-product complex
-
DOI 10.1038/nsmb868
-
Golden, B. L., Kim, H., and Chase, E. (2005) Crystal structure of a phage Twort group I ribozyme-product complex Nat. Struct. Mol. Biol. 12, 82-89 (Pubitemid 40082921)
-
(2005)
Nature Structural and Molecular Biology
, vol.12
, Issue.1
, pp. 82-89
-
-
Golden, B.L.1
Kim, H.2
Chase, E.3
-
22
-
-
41749109563
-
Crystal structure of a self-spliced group II intron
-
DOI 10.1126/science.1153803
-
Toor, N., Keating, K. S., Taylor, S. D., and Pyle, A. M. (2008) Crystal structure of a self-spliced group II intron Science 320, 77-82 (Pubitemid 351490756)
-
(2008)
Science
, vol.320
, Issue.5872
, pp. 77-82
-
-
Toor, N.1
Keating, K.S.2
Taylor, S.D.3
Pyle, A.M.4
-
23
-
-
78650175123
-
Structure of a bacterial ribonuclease P holoenzyme in complex with tRNA
-
Reiter, N. J., Osterman, A., Torres-Larios, A., Swinger, K. K., Pan, T., and Mondragon, A. (2010) Structure of a bacterial ribonuclease P holoenzyme in complex with tRNA Nature 468, 784-789
-
(2010)
Nature
, vol.468
, pp. 784-789
-
-
Reiter, N.J.1
Osterman, A.2
Torres-Larios, A.3
Swinger, K.K.4
Pan, T.5
Mondragon, A.6
-
24
-
-
78751487465
-
Do the hairpin and VS ribozymes share a common catalytic mechanism based on general acid-base catalysis? A critical assessment of available experimental data
-
Wilson, T. J. and Lilley, D. M. (2011) Do the hairpin and VS ribozymes share a common catalytic mechanism based on general acid-base catalysis? A critical assessment of available experimental data RNA 17, 213-221
-
(2011)
RNA
, vol.17
, pp. 213-221
-
-
Wilson, T.J.1
Lilley, D.M.2
-
25
-
-
0032192761
-
The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone
-
Murray, J. B., Seyhan, A. A., Walter, N. G., Burke, J. M., and Scott, W. G. (1998) The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone Chem. Biol. 5, 587-595 (Pubitemid 29000118)
-
(1998)
Chemistry and Biology
, vol.5
, Issue.10
, pp. 587-595
-
-
Murray, J.B.1
Seyhan, A.A.2
Walter, N.G.3
Burke, J.M.4
Scott, W.G.5
-
26
-
-
0024209351
-
Characterization of self-cleaving RNA sequences on the genome and antigenome of human hepatitis delta virus
-
Kuo, M. Y., Sharmeen, L., Dinter-Gottlieb, G., and Taylor, J. (1988) Characterization of self-cleaving RNA sequences on the genome and antigenome of human hepatitis delta virus J. Virol. 62, 4439-4444 (Pubitemid 19006103)
-
(1988)
Journal of Virology
, vol.62
, Issue.12
, pp. 4439-4444
-
-
Kuo, M.Y.-P.1
Sharmeen, L.2
Dinter-Gottlieb, G.3
Taylor, J.4
-
27
-
-
33746228126
-
Tertiary Contacts Distant from the Active Site Prime a Ribozyme for Catalysis
-
DOI 10.1016/j.cell.2006.06.036, PII S0092867406008567
-
Martick, M. and Scott, W. G. (2006) Tertiary contacts distant from the active site prime a ribozyme for catalysis Cell 126, 309-320 (Pubitemid 44092962)
-
(2006)
Cell
, vol.126
, Issue.2
, pp. 309-320
-
-
Martick, M.1
Scott, W.G.2
-
28
-
-
33749034196
-
A genomewide search for ribozymes reveals an HDV-like sequence in the human CPEB3 gene
-
DOI 10.1126/science.1129308
-
Salehi-Ashtiani, K., Luptak, A., Litovchick, A., and Szostak, J. W. (2006) A genomewide search for ribozymes reveals an HDV-like sequence in the human CPEB3 gene Science 313, 1788-1792 (Pubitemid 44454155)
-
(2006)
Science
, vol.313
, Issue.5794
, pp. 1788-1792
-
-
Salehi-Ashtiani, K.1
Luptak, A.2
Litovchick, A.3
Szostak, J.W.4
-
29
-
-
72449145407
-
Widespread occurrence of self-cleaving ribozymes
-
Webb, C. H., Riccitelli, N. J., Ruminski, D. J., and Luptak, A. (2009) Widespread occurrence of self-cleaving ribozymes Science 326, 953
-
(2009)
Science
, vol.326
, pp. 953
-
-
Webb, C.H.1
Riccitelli, N.J.2
Ruminski, D.J.3
Luptak, A.4
-
30
-
-
77953379568
-
R2 retrotransposons encode a self-cleaving ribozyme for processing from an rRNA cotranscript
-
Eickbush, D. G. and Eickbush, T. H. (2010) R2 retrotransposons encode a self-cleaving ribozyme for processing from an rRNA cotranscript Mol. Cell. Biol. 30, 3142-3150
-
(2010)
Mol. Cell. Biol.
, vol.30
, pp. 3142-3150
-
-
Eickbush, D.G.1
Eickbush, T.H.2
-
31
-
-
0033215448
-
Imidazole rescue of a cytosine mutation in a self-cleaving ribozyme
-
DOI 10.1126/science.286.5437.123
-
Perrotta, A. T., Shih, I., and Been, M. D. (1999) Imidazole rescue of a cytosine mutation in a self-cleaving ribozyme Science 286, 123-126 (Pubitemid 29484491)
-
(1999)
Science
, vol.286
, Issue.5437
, pp. 123-126
-
-
Perrotta, A.T.1
Shih, I.-H.2
Been, M.D.3
-
32
-
-
0036161836
-
Ribozyme activity in the genomic and antigenomic RNA strands of hepatitis delta virus
-
DOI 10.1007/s00018-002-8409-7
-
Wadkins, T. S. and Been, M. D. (2002) Ribozyme activity in the genomic and antigenomic RNA strands of hepatitis delta virus Cell. Mol. Life Sci. 59, 112-125 (Pubitemid 34117360)
-
(2002)
Cellular and Molecular Life Sciences
, vol.59
, Issue.1
, pp. 112-125
-
-
Wadkins, T.S.1
Been, M.D.2
-
33
-
-
77955258795
-
A 1.9 Å crystal structure of the HDV ribozyme precleavage suggests both Lewis acid and general acid mechanisms contribute to phosphodiester cleavage
-
Chen, J. H., Yajima, R., Chadalavada, D. M., Chase, E., Bevilacqua, P. C., and Golden, B. L. (2010) A 1.9 Å crystal structure of the HDV ribozyme precleavage suggests both Lewis acid and general acid mechanisms contribute to phosphodiester cleavage Biochemistry 49, 6508-6518
-
(2010)
Biochemistry
, vol.49
, pp. 6508-6518
-
-
Chen, J.H.1
Yajima, R.2
Chadalavada, D.M.3
Chase, E.4
Bevilacqua, P.C.5
Golden, B.L.6
-
34
-
-
0035848837
-
Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis
-
DOI 10.1038/35071009
-
Rupert, P. B. and Ferre-DAmare, A. R. (2001) Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis Nature 410, 780-786 (Pubitemid 32303769)
-
(2001)
Nature
, vol.410
, Issue.6830
, pp. 780-786
-
-
Rupert, P.B.1
Ferre-D'Amare, A.R.2
-
35
-
-
27644434706
-
Conformational heterogeneity at position U37 of an all-RNA hairpin ribozyme with implications for metal binding and the catalytic structure of the S-turn
-
DOI 10.1021/bi051550i
-
Alam, S., Grum-Tokars, V., Krucinska, J., Kundracik, M. L., and Wedekind, J. E. (2005) Conformational heterogeneity at position U37 of an all-RNA hairpin ribozyme with implications for metal binding and the catalytic structure of the S-turn Biochemistry 44, 14396-14408 (Pubitemid 41567448)
-
(2005)
Biochemistry
, vol.44
, Issue.44
, pp. 14396-14408
-
-
Alam, S.1
Grum-Tokars, V.2
Krucinska, J.3
Kundracik, M.L.4
Wedekind, J.E.5
-
36
-
-
33748325570
-
Structural basis of glmS ribozyme activation by glucosamine-6-phosphate
-
DOI 10.1126/science.1129666
-
Klein, D. J. and Ferre-DAmare, A. R. (2006) Structural basis of glmS ribozyme activation by glucosamine-6-phosphate Science 313, 1752-1756 (Pubitemid 44454144)
-
(2006)
Science
, vol.313
, Issue.5794
, pp. 1752-1756
-
-
Klein, D.J.1
Ferre-D'Amare, A.R.2
-
37
-
-
33846279049
-
Structural Investigation of the GlmS Ribozyme Bound to Its Catalytic Cofactor
-
DOI 10.1016/j.chembiol.2006.12.005, PII S1074552106004601
-
Cochrane, J. C., Lipchock, S. V., and Strobel, S. A. (2007) Structural investigation of the GlmS ribozyme bound to its catalytic cofactor Chem. Biol. 14, 97-105 (Pubitemid 46124067)
-
(2007)
Chemistry and Biology
, vol.14
, Issue.1
, pp. 97-105
-
-
Cochrane, J.C.1
Lipchock, S.V.2
Strobel, S.A.3
-
38
-
-
77956170803
-
Long-distance communication in the HDV ribozyme: Insights from molecular dynamics and experiments
-
Veeraraghavan, N., Bevilacqua, P. C., and Hammes-Schiffer, S. (2010) Long-distance communication in the HDV ribozyme: Insights from molecular dynamics and experiments J. Mol. Biol. 402, 278-291
-
(2010)
J. Mol. Biol.
, vol.402
, pp. 278-291
-
-
Veeraraghavan, N.1
Bevilacqua, P.C.2
Hammes-Schiffer, S.3
-
39
-
-
79953205188
-
Metal binding motif in the active site of the HDV ribozyme binds divalent and monovalent ions
-
Veeraraghavan, N., Ganguly, A., Chen, J. H., Bevilacqua, P. C., Hammes-Schiffer, S., and Golden, B. L. (2011) Metal binding motif in the active site of the HDV ribozyme binds divalent and monovalent ions Biochemistry 50, 2672-2682
-
(2011)
Biochemistry
, vol.50
, pp. 2672-2682
-
-
Veeraraghavan, N.1
Ganguly, A.2
Chen, J.H.3
Bevilacqua, P.C.4
Hammes-Schiffer, S.5
Golden, B.L.6
-
40
-
-
35848964370
-
a near neutrality for the catalytic cytosine in the genomic HDV ribozyme using raman crystallography
-
DOI 10.1021/ja0743893
-
a near neutrality for the catalytic cytosine in the genomic HDV ribozyme using Raman crystallography J. Am. Chem. Soc. 129, 13335-13342 (Pubitemid 350058377)
-
(2007)
Journal of the American Chemical Society
, vol.129
, Issue.43
, pp. 13335-13342
-
-
Gong, B.1
Chen, J.-H.2
Chase, E.3
Chadalavada, D.M.4
Yajima, R.5
Golden, B.L.6
Bevilacqua, P.C.7
Carey, P.R.8
-
41
-
-
33947356675
-
Mechanistic characterization of the HDV genomic ribozyme: A mutant of the C41 motif provides insight into the positioning and thermodynamic linkage of metal ions and protons
-
DOI 10.1021/bi061732s
-
Nakano, S. and Bevilacqua, P. C. (2007) Mechanistic characterization of the HDV genomic ribozyme: A mutant of the C41 motif provides insight into the positioning and thermodynamic linkage of metal ions and protons Biochemistry 46, 3001-3012 (Pubitemid 46449124)
-
(2007)
Biochemistry
, vol.46
, Issue.11
, pp. 3001-3012
-
-
Nakano, S.-I.1
Bevilacqua, P.C.2
-
42
-
-
24644454458
-
General acid catalysis by the hepatitis delta virus ribozyme
-
Das, S. R. and Piccirilli, J. A. (2005) General acid catalysis by the hepatitis delta virus ribozyme Nat. Chem. Biol. 1, 45-52
-
(2005)
Nat. Chem. Biol.
, vol.1
, pp. 45-52
-
-
Das, S.R.1
Piccirilli, J.A.2
-
43
-
-
33846804221
-
as in RNA: On the Structural Origins and Functional Roles of Protonated Nucleotides
-
DOI 10.1016/j.jmb.2006.12.001, PII S0022283606016482
-
as in RNA: On the structural origins and functional roles of protonated nucleotides J. Mol. Biol. 366, 1475-1496 (Pubitemid 46215598)
-
(2007)
Journal of Molecular Biology
, vol.366
, Issue.5
, pp. 1475-1496
-
-
Tang, C.L.1
Alexov, E.2
Pyle, A.M.3
Honig, B.4
-
45
-
-
70349095576
-
a in the active site of a small ribozyme in a precatalytic conformation
-
a in the active site of a small ribozyme in a precatalytic conformation J. Am. Chem. Soc. 131, 12908-12909
-
(2009)
J. Am. Chem. Soc.
, vol.131
, pp. 12908-12909
-
-
Guo, M.1
Spitale, R.C.2
Volpini, R.3
Krucinska, J.4
Cristalli, G.5
Carey, P.R.6
Wedekind, J.E.7
-
46
-
-
79955954695
-
The pH dependence of hairpin ribozyme catalysis reflects ionization of an active site adenine
-
Cottrell, J. W., Scott, L. G., and Fedor, M. J. (2011) The pH dependence of hairpin ribozyme catalysis reflects ionization of an active site adenine J. Biol. Chem. 286, 17658-17664
-
(2011)
J. Biol. Chem.
, vol.286
, pp. 17658-17664
-
-
Cottrell, J.W.1
Scott, L.G.2
Fedor, M.J.3
-
47
-
-
0037111875
-
Transition state stabilization by a catalytic RNA
-
DOI 10.1126/science.1076093
-
Rupert, P. B., Massey, A. P., Sigurdsson, S. T., and Ferre-DAmare, A. R. (2002) Transition state stabilization by a catalytic RNA Science 298, 1421-1424 (Pubitemid 35346142)
-
(2002)
Science
, vol.298
, Issue.5597
, pp. 1421-1424
-
-
Rupert, P.B.1
Massey, A.P.2
Sigurdsson, S.Th.3
Ferre-D'Amare, A.R.4
-
48
-
-
34250888277
-
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
-
DOI 10.1261/rna.510807
-
Torelli, A. T., Krucinska, J., and Wedekind, J. E. (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 (Pubitemid 46984896)
-
(2007)
RNA
, vol.13
, Issue.7
, pp. 1052-1070
-
-
Torelli, A.T.1
Krucinska, J.2
Wedekind, J.E.3
-
49
-
-
80051751284
-
GlmS riboswitch binding to the glucosamine-6-phosphate α-anomer shifts the pKa toward neutrality
-
Davis, J. H., Dunican, B. F., and Strobel, S. A. (2011) glmS riboswitch binding to the glucosamine-6-phosphate α-anomer shifts the pKa toward neutrality Biochemistry 50, 7236-7242
-
(2011)
Biochemistry
, vol.50
, pp. 7236-7242
-
-
Davis, J.H.1
Dunican, B.F.2
Strobel, S.A.3
-
51
-
-
0035085466
-
Structural basis of the enhanced stability of a mutant ribozyme domain and a detailed view of RNA-solvent interactions
-
DOI 10.1016/S0969-2126(01)00579-2, PII S0969212601005792
-
Juneau, K., Podell, E., Harrington, D. J., and Cech, T. R. (2001) Structural basis of the enhanced stability of a mutant ribozyme domain and a detailed view of RNA-solvent interactions Structure 9, 221-231 (Pubitemid 32245873)
-
(2001)
Structure
, vol.9
, Issue.3
, pp. 221-231
-
-
Juneau, K.1
Podell, E.2
Harrington, D.J.3
Cech, T.R.4
-
52
-
-
34447260753
-
A General Strategy to Solve the Phase Problem in RNA Crystallography
-
DOI 10.1016/j.str.2007.06.003, PII S0969212607002080
-
Keel, A. Y., Rambo, R. P., Batey, R. T., and Kieft, J. S. (2007) A general strategy to solve the phase problem in RNA crystallography Structure 15, 761-772 (Pubitemid 47042432)
-
(2007)
Structure
, vol.15
, Issue.7
, pp. 761-772
-
-
Keel, A.Y.1
Rambo, R.P.2
Batey, R.T.3
Kieft, J.S.4
-
53
-
-
33847691104
-
Structural Roles of Monovalent Cations in the HDV Ribozyme
-
DOI 10.1016/j.str.2007.01.017, PII S0969212607000731
-
Ke, A., Ding, F., Batchelor, J. D., and Doudna, J. A. (2007) Structural roles of monovalent cations in the HDV ribozyme Structure 15, 281-287 (Pubitemid 46366724)
-
(2007)
Structure
, vol.15
, Issue.3
, pp. 281-287
-
-
Ke, A.1
Ding, F.2
Batchelor, J.D.3
Doudna, J.A.4
-
54
-
-
0032516471
-
Unusual metal ion catalysis in an acyl-transferase ribozyme
-
DOI 10.1021/bi980432a
-
Suga, H., Cowan, J. A., and Szostak, J. W. (1998) Unusual metal ion catalysis in an acyl-transferase ribozyme Biochemistry 37, 10118-10125 (Pubitemid 28366366)
-
(1998)
Biochemistry
, vol.37
, Issue.28
, pp. 10118-10125
-
-
Suga, H.1
Cowan, J.A.2
Szostak, J.W.3
-
55
-
-
0031194873
-
A unique mechanism for RNA catalysis: The role of metal cofactors in hairpin ribozyme cleavage
-
Hampel, A. and Cowan, J. A. (1997) A unique mechanism for RNA catalysis: The role of metal cofactors in hairpin ribozyme cleavage Chem. Biol. 4, 513-517 (Pubitemid 27335766)
-
(1997)
Chemistry and Biology
, vol.4
, Issue.7
, pp. 513-517
-
-
Hampel, A.1
Cowan, J.A.2
-
56
-
-
0031215134
-
An unusual pH-independent and metal-ion-independent mechanism for hairpin ribozyme catalysis
-
Nesbitt, S., Hegg, L. A., and Fedor, M. J. (1997) An unusual pH-independent and metal-ion-independent mechanism for hairpin ribozyme catalysis Chem. Biol. 4, 619-630 (Pubitemid 27398764)
-
(1997)
Chemistry and Biology
, vol.4
, Issue.8
, pp. 619-630
-
-
Nesbitt, S.1
Hegg, L.A.2
Fedor, M.J.3
-
57
-
-
0030629751
-
Determination of catalytic parameters for hairpin ribozymes
-
DeYoung, M. B., Siwkowski, A., and Hampel, A. (1997) Determination of catalytic parameters for hairpin ribozymes Methods Mol. Biol. 74, 209-220
-
(1997)
Methods Mol. Biol.
, vol.74
, pp. 209-220
-
-
Deyoung, M.B.1
Siwkowski, A.2
Hampel, A.3
-
58
-
-
78650028802
-
Analysis of metal ion dependence in glmS ribozyme self-cleavage and coenzyme binding
-
Klawuhn, K., Jansen, J. A., Souchek, J., Soukup, G. A., and Soukup, J. K. (2010) Analysis of metal ion dependence in glmS ribozyme self-cleavage and coenzyme binding ChemBioChem 11, 2567-2571
-
(2010)
ChemBioChem
, vol.11
, pp. 2567-2571
-
-
Klawuhn, K.1
Jansen, J.A.2
Souchek, J.3
Soukup, G.A.4
Soukup, J.K.5
-
59
-
-
79953227362
-
Rapid steps in the glmS ribozyme catalytic pathway: Cation and ligand requirements
-
Brooks, K. M. and Hampel, K. J. (2011) Rapid steps in the glmS ribozyme catalytic pathway: Cation and ligand requirements Biochemistry 50, 2424-2433
-
(2011)
Biochemistry
, vol.50
, pp. 2424-2433
-
-
Brooks, K.M.1
Hampel, K.J.2
-
60
-
-
0035965132
-
The A730 loop is an important component of the active site of the VS ribozyme
-
DOI 10.1006/jmbi.2001.4996
-
Lafontaine, D. A., Wilson, T. J., Norman, D. G., and Lilley, D. M. (2001) The A730 loop is an important component of the active site of the VS ribozyme J. Mol. Biol. 312, 663-674 (Pubitemid 33116731)
-
(2001)
Journal of Molecular Biology
, vol.312
, Issue.4
, pp. 663-674
-
-
Lafontaine, D.A.1
Wilson, T.J.2
Norman, D.G.3
Lilley, D.M.J.4
-
61
-
-
34249098371
-
A guanine nucleobase important for catalysis by the VS ribozyme
-
DOI 10.1038/sj.emboj.7601698, PII 7601698
-
Wilson, T. J., McLeod, A. C., and Lilley, D. M. (2007) A guanine nucleobase important for catalysis by the VS ribozyme EMBO J. 26, 2489-2500 (Pubitemid 46788324)
-
(2007)
EMBO Journal
, vol.26
, Issue.10
, pp. 2489-2500
-
-
Wilson, T.J.1
McLeod, A.C.2
Lilley, D.M.J.3
-
62
-
-
0037452909
-
Mechanistic characterization of the HDV genomic ribozyme: Classifying the catalytic and structural metal ion sites within a multichannel reaction mechanism
-
DOI 10.1021/bi026815x
-
Nakano, S., Cerrone, A. L., and Bevilacqua, P. C. (2003) Mechanistic characterization of the HDV genomic ribozyme: Classifying the catalytic and structural metal ion sites within a multichannel reaction mechanism Biochemistry 42, 2982-2994 (Pubitemid 36331542)
-
(2003)
Biochemistry
, vol.42
, Issue.10
, pp. 2982-2994
-
-
Nakano, S.-I.1
Cerrone, A.L.2
Bevilacqua, P.C.3
-
63
-
-
34249059298
-
Distinct reaction pathway promoted by non-divalent-metal cations in a tertiary stabilized hammerhead ribozyme
-
DOI 10.1261/rna.339207
-
Roychowdhury-Saha, M. and Burke, D. H. (2007) Distinct reaction pathway promoted by non-divalent-metal cations in a tertiary stabilized hammerhead ribozyme RNA 13, 841-848 (Pubitemid 46799818)
-
(2007)
RNA
, vol.13
, Issue.6
, pp. 841-848
-
-
Roychowdhury-Saha, M.1
Burke, D.H.2
-
64
-
-
50649109849
-
Mechanistic characterization of the HDV genomic ribozyme: The cleavage site base pair plays a structural role in facilitating catalysis
-
Cerrone-Szakal, A. L., Chadalavada, D. M., Golden, B. L., and Bevilacqua, P. C. (2008) Mechanistic characterization of the HDV genomic ribozyme: The cleavage site base pair plays a structural role in facilitating catalysis RNA 14, 1746-1760
-
(2008)
RNA
, vol.14
, pp. 1746-1760
-
-
Cerrone-Szakal, A.L.1
Chadalavada, D.M.2
Golden, B.L.3
Bevilacqua, P.C.4
-
66
-
-
0035001461
-
Comparison of the hammerhead cleavage reactions stimulated by monovalent and divalent cations
-
DOI 10.1017/S1355838201002461
-
ORear, J. L., Wang, S., Feig, A. L., Beigelman, L., Uhlenbeck, O. C., and Herschlag, D. (2001) Comparison of the hammerhead cleavage reactions stimulated by monovalent and divalent cations RNA 7, 537-545 (Pubitemid 32416811)
-
(2001)
RNA
, vol.7
, Issue.4
, pp. 537-545
-
-
O'Rear, J.L.1
Wang, S.2
Feig, A.L.3
Beigelman, L.4
Uhlenbeck, O.C.5
Herschlag, D.6
-
67
-
-
0035020626
-
The hammerhead cleavage reaction in monovalent cations
-
DOI 10.1017/S1355838201002357
-
Curtis, E. A. and Bartel, D. P. (2001) The hammerhead cleavage reaction in monovalent cations RNA 7, 546-552 (Pubitemid 32416812)
-
(2001)
RNA
, vol.7
, Issue.4
, pp. 546-552
-
-
Curtis, E.A.1
Bartel, D.P.2
-
68
-
-
41949138497
-
Solvent Structure and Hammerhead Ribozyme Catalysis
-
DOI 10.1016/j.chembiol.2008.03.010, PII S1074552108001221
-
Martick, M., Lee, T. S., York, D. M., and Scott, W. G. (2008) Solvent structure and hammerhead ribozyme catalysis Chem. Biol. 15, 332-342 (Pubitemid 351508433)
-
(2008)
Chemistry and Biology
, vol.15
, Issue.4
, pp. 332-342
-
-
Martick, M.1
Lee, T.-S.2
York, D.M.3
Scott, W.G.4
-
69
-
-
70449416220
-
The identity of the nucleophile substitution may influence metal interactions with the cleavage site of the minimal hammerhead ribozyme
-
Osborne, E. M., Ward, W. L., Ruehle, M. Z., and DeRose, V. J. (2009) The identity of the nucleophile substitution may influence metal interactions with the cleavage site of the minimal hammerhead ribozyme Biochemistry 48, 10654-10664
-
(2009)
Biochemistry
, vol.48
, pp. 10654-10664
-
-
Osborne, E.M.1
Ward, W.L.2
Ruehle, M.Z.3
Derose, V.J.4
-
70
-
-
41449099097
-
2+ in hammerhead ribozyme catalysis from molecular simulation
-
DOI 10.1021/ja076529e
-
2+ in hammerhead ribozyme catalysis from molecular simulation J. Am. Chem. Soc. 130, 3053-3064 (Pubitemid 351455976)
-
(2008)
Journal of the American Chemical Society
, vol.130
, Issue.10
, pp. 3053-3064
-
-
Lee, T.-S.1
Lopez, C.S.2
Giambasu, G.M.3
Martick, M.4
Scott, W.G.5
York, D.M.6
-
71
-
-
78651371352
-
Active participation of Mg ion in the reaction coordinate of RNA self-cleavage catalyzed by the hammerhead ribozyme
-
Wong, K. Y., Lee, T. S., and York, D. M. (2011) Active participation of Mg ion in the reaction coordinate of RNA self-cleavage catalyzed by the hammerhead ribozyme J. Chem. Theory Comput. 7, 1-3
-
(2011)
J. Chem. Theory Comput.
, vol.7
, pp. 1-3
-
-
Wong, K.Y.1
Lee, T.S.2
York, D.M.3
-
72
-
-
0029964591
-
Core sequences and a cleavage site wobble pair required for HDV antigenomic ribozyme self-cleavage
-
DOI 10.1093/nar/24.7.1314
-
Perrotta, A. T. and Been, M. D. (1996) Core sequences and a cleavage site wobble pair required for HDV antigenomic ribozyme self-cleavage Nucleic Acids Res. 24, 1314-1321 (Pubitemid 26102683)
-
(1996)
Nucleic Acids Research
, vol.24
, Issue.7
, pp. 1314-1321
-
-
Perrotta, A.T.1
Been, M.D.2
-
73
-
-
0028446537
-
A three-dimensional model of hepatitis delta virus ribozyme based on biochemical and mutational analyses
-
Tanner, N. K., Schaff, S., Thill, G., Petit-Koskas, E., Crain-Denoyelle, A. M., and Westhof, E. (1994) A three-dimensional model of hepatitis delta virus ribozyme based on biochemical and mutational analyses Curr. Biol. 4, 488-498
-
(1994)
Curr. Biol.
, vol.4
, pp. 488-498
-
-
Tanner, N.K.1
Schaff, S.2
Thill, G.3
Petit-Koskas, E.4
Crain-Denoyelle, A.M.5
Westhof, E.6
-
74
-
-
0027937331
-
Identification of phosphate oxygens that are important for self-cleavage activity of the HDV ribozyme by phosphorothioate substitution interference analysis
-
Jeoung, Y. H., Kumar, P. K., Suh, Y. A., Taira, K., and Nishikawa, S. (1994) Identification of phosphate oxygens that are important for self-cleavage activity of the HDV ribozyme by phosphorothioate substitution interference analysis Nucleic Acids Res. 22, 3722-3727 (Pubitemid 24299852)
-
(1994)
Nucleic Acids Research
, vol.22
, Issue.18
, pp. 3722-3727
-
-
Jeoung, Y.-H.1
Kumar, P.K.R.2
Suh, Y.-A.3
Taira, K.4
Nishikawa, S.5
-
75
-
-
0036444163
-
Site-specific modification of functional groups in genomic hepatitis delta virus (HDV) ribozyme
-
DOI 10.1046/j.1432-1033.2002.03280.x
-
Nishikawa, F., Shirai, M., and Nishikawa, S. (2002) Site-specific modification of functional groups in genomic hepatitis delta virus (HDV) ribozyme Eur. J. Biochem. 269, 5792-5803 (Pubitemid 35425577)
-
(2002)
European Journal of Biochemistry
, vol.269
, Issue.23
, pp. 5792-5803
-
-
Nishikawa, F.1
Shirai, M.2
Nishikawa, S.3
-
76
-
-
0030798881
-
Analysis of the cleavage reaction of a trans-acting human hepatitis delta virus ribozyme
-
DOI 10.1093/nar/25.15.3124
-
Fauzi, H., Kawakami, J., Nishikawa, F., and Nishikawa, S. (1997) Analysis of the cleavage reaction of a trans-acting human hepatitis delta virus ribozyme Nucleic Acids Res. 25, 3124-3130 (Pubitemid 27331408)
-
(1997)
Nucleic Acids Research
, vol.25
, Issue.15
, pp. 3124-3130
-
-
Fauzi, H.1
Kawakami, J.2
Nishikawa, F.3
Nishikawa, S.4
-
77
-
-
52949104434
-
Metal ion specificities for folding and cleavage activity in the Schistosoma hammerhead ribozyme
-
Boots, J. L., Canny, M. D., Azimi, E., and Pardi, A. (2008) Metal ion specificities for folding and cleavage activity in the Schistosoma hammerhead ribozyme RNA 14, 2212-2222
-
(2008)
RNA
, vol.14
, pp. 2212-2222
-
-
Boots, J.L.1
Canny, M.D.2
Azimi, E.3
Pardi, A.4
-
78
-
-
0027305803
-
Self-cleavage activity of the genomic HDV ribozyme in the presence of various divalent metal ions
-
Suh, Y. A., Kumar, P. K., Taira, K., and Nishikawa, S. (1993) Self-cleavage activity of the genomic HDV ribozyme in the presence of various divalent metal ions Nucleic Acids Res. 21, 3277-3280 (Pubitemid 23230500)
-
(1993)
Nucleic Acids Research
, vol.21
, Issue.14
, pp. 3277-3280
-
-
Suh, Y.-A.1
Kumar, P.K.R.2
Taira, K.3
Nishikawa, S.4
-
79
-
-
0035793217
-
A pH-sensitive RNA tertiary interaction affects self-cleavage activity of the HDV ribozymes in the absence of added divalent metal ion
-
DOI 10.1006/jmbi.2000.4368
-
Wadkins, T. S., Shih, I., Perrotta, A. T., and Been, M. D. (2001) A pH-sensitive RNA tertiary interaction affects self-cleavage activity of the HDV ribozymes in the absence of added divalent metal ion J. Mol. Biol. 305, 1045-1055 (Pubitemid 33027742)
-
(2001)
Journal of Molecular Biology
, vol.305
, Issue.5
, pp. 1045-1055
-
-
Wadkins, T.S.1
Shih, I.-H.2
Perrotta, A.T.3
Been, M.D.4
-
82
-
-
79959537078
-
Mechanistic Strategies in the HDV Ribozyme: Chelated and Diffuse Metal Ion Interactions and Active Site Protonation
-
Veeraraghavan, N., Ganguly, A., Golden, B. L., Bevilacqua, P. C., and Hammes-Schiffer, S. (2011) Mechanistic Strategies in the HDV Ribozyme: Chelated and Diffuse Metal Ion Interactions and Active Site Protonation J. Phys. Chem. B 115, 8346-8357
-
(2011)
J. Phys. Chem. B
, vol.115
, pp. 8346-8357
-
-
Veeraraghavan, N.1
Ganguly, A.2
Golden, B.L.3
Bevilacqua, P.C.4
Hammes-Schiffer, S.5
|