-
1
-
-
33846887629
-
Alternative roles for metal ions in enzyme catalysis and the implication for ribozyme chemistry
-
A review that transfers the knowledge on metalloproteins to ribozymes showing that metal ions can exert their influence on catalysis also from distance.
-
Sigel R.K.O., and Pyle A.M. Alternative roles for metal ions in enzyme catalysis and the implication for ribozyme chemistry. Chem Rev 107 (2007) 97-113. A review that transfers the knowledge on metalloproteins to ribozymes showing that metal ions can exert their influence on catalysis also from distance.
-
(2007)
Chem Rev
, vol.107
, pp. 97-113
-
-
Sigel, R.K.O.1
Pyle, A.M.2
-
2
-
-
12844260994
-
Probing counterion modulated repulsion and attraction between nucleic acid duplexes in solution
-
Bai Y., Das R., Millett I.S., Herschlag D., and Doniach S. Probing counterion modulated repulsion and attraction between nucleic acid duplexes in solution. Proc Natl Acad Sci U S A 102 (2005) 1035-1040
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, pp. 1035-1040
-
-
Bai, Y.1
Das, R.2
Millett, I.S.3
Herschlag, D.4
Doniach, S.5
-
3
-
-
57649130782
-
A repulsive field: advances in the electrostatics of the ion atmosphere
-
Chu V.B., Bai Y., Lipfert J., Herschlag D., and Doniach S. A repulsive field: advances in the electrostatics of the ion atmosphere. Curr Opin Chem Biol 12 (2008) 619-625
-
(2008)
Curr Opin Chem Biol
, vol.12
, pp. 619-625
-
-
Chu, V.B.1
Bai, Y.2
Lipfert, J.3
Herschlag, D.4
Doniach, S.5
-
4
-
-
58749105663
-
RNA folding: thermodynamic and molecular descriptions of the roles of ions
-
Draper D.E. RNA folding: thermodynamic and molecular descriptions of the roles of ions. Biophys J 95 (2008) 5489-5495
-
(2008)
Biophys J
, vol.95
, pp. 5489-5495
-
-
Draper, D.E.1
-
5
-
-
34250613522
-
From nucleotides to ribozymes - a comparison of their metal ion binding properties
-
Freisinger E., and Sigel R.K.O. From nucleotides to ribozymes - a comparison of their metal ion binding properties. Coord Chem Rev 251 (2007) 1834-1851
-
(2007)
Coord Chem Rev
, vol.251
, pp. 1834-1851
-
-
Freisinger, E.1
Sigel, R.K.O.2
-
6
-
-
0038054299
-
Crystallographic characterization of an exocyclic DNA adduct: 3,N4-etheno-2′-deoxycytidine in the dodecamer 5′-CGCGAATTεCGCG-3′
-
Freisinger E., Fernandes A., Grollman A.P., and Kisker C. Crystallographic characterization of an exocyclic DNA adduct: 3,N4-etheno-2′-deoxycytidine in the dodecamer 5′-CGCGAATTεCGCG-3′. J Mol Biol 329 (2003) 685-697
-
(2003)
J Mol Biol
, vol.329
, pp. 685-697
-
-
Freisinger, E.1
Fernandes, A.2
Grollman, A.P.3
Kisker, C.4
-
7
-
-
34250349882
-
A second divalent metal ion in the group II intron reaction center
-
Identification of a second metal ion required for nucleophile activation in the step of exon ligation. Comparison with similar experiments using group I introns suggests a two-metal ion mechanism as a paradigm for large ribozymes.
-
Gordon P.M., Fong R., and Piccirilli J.A. A second divalent metal ion in the group II intron reaction center. Chem Biol 14 (2007) 607-612. Identification of a second metal ion required for nucleophile activation in the step of exon ligation. Comparison with similar experiments using group I introns suggests a two-metal ion mechanism as a paradigm for large ribozymes.
-
(2007)
Chem Biol
, vol.14
, pp. 607-612
-
-
Gordon, P.M.1
Fong, R.2
Piccirilli, J.A.3
-
8
-
-
24944569654
-
Functional identification of catalytic metal ion binding sites within RNA
-
Hougland J.L., Kravchuk A.V., Herschlag D., and Piccirilli J.A. Functional identification of catalytic metal ion binding sites within RNA. PLoS Biol 3 (2005) 1536-1548
-
(2005)
PLoS Biol
, vol.3
, pp. 1536-1548
-
-
Hougland, J.L.1
Kravchuk, A.V.2
Herschlag, D.3
Piccirilli, J.A.4
-
9
-
-
0032404048
-
Defining functional groups, core structural features and inter-domain tertiary contacts essential for group II intron self-splicing: a NAIM analysis
-
Boudvillain M., and Pyle A.M. Defining functional groups, core structural features and inter-domain tertiary contacts essential for group II intron self-splicing: a NAIM analysis. EMBO J 17 (1998) 7091-7104
-
(1998)
EMBO J
, vol.17
, pp. 7091-7104
-
-
Boudvillain, M.1
Pyle, A.M.2
-
10
-
-
70449416220
-
The identity of the nucleophile substitution may influence metal interactions with the cleavage site of the minimal hammerhead ribozyme
-
A study indicating that results from nucleotide modifications have to be interpreted with care as the change in local environment might alter the general mechanism.
-
Osborne E.M., Ward W.L., Ruehle M.Z., and DeRose V.J. The identity of the nucleophile substitution may influence metal interactions with the cleavage site of the minimal hammerhead ribozyme. Biochemistry 48 (2009) 10654-10664. A study indicating that results from nucleotide modifications have to be interpreted with care as the change in local environment might alter the general mechanism.
-
(2009)
Biochemistry
, vol.48
, pp. 10654-10664
-
-
Osborne, E.M.1
Ward, W.L.2
Ruehle, M.Z.3
DeRose, V.J.4
-
11
-
-
47649130326
-
The different role of high-affinity and low-affinity metal ions in cleavage by a tertiary stabilized cis hammerhead ribozyme from tobacco ringspot virus
-
Kisseleva N., Khvorova A., Westhof E., Schiemann O., and Wolfson A.D. The different role of high-affinity and low-affinity metal ions in cleavage by a tertiary stabilized cis hammerhead ribozyme from tobacco ringspot virus. Oligonucleotides 18 (2008) 101-110
-
(2008)
Oligonucleotides
, vol.18
, pp. 101-110
-
-
Kisseleva, N.1
Khvorova, A.2
Westhof, E.3
Schiemann, O.4
Wolfson, A.D.5
-
12
-
-
85013257546
-
Characterizing multiple metal ion binding sites within a ribozyme by cadmium-induced EPR silencing
-
Kisseleva N., Kraut S., Jaschke A., and Schiemann O. Characterizing multiple metal ion binding sites within a ribozyme by cadmium-induced EPR silencing. HFSP J 1 (2007) 127-136
-
(2007)
HFSP J
, vol.1
, pp. 127-136
-
-
Kisseleva, N.1
Kraut, S.2
Jaschke, A.3
Schiemann, O.4
-
13
-
-
0037028557
-
Structural analysis of metal ion ligation to nucleotides and nucleic acids using pulsed EPR spectroscopy
-
Hoogstraten C.G., Grant C.V., Horton T.E., DeRose V.J., and Britt R.D. Structural analysis of metal ion ligation to nucleotides and nucleic acids using pulsed EPR spectroscopy. J Am Chem Soc 124 (2002) 834-842
-
(2002)
J Am Chem Soc
, vol.124
, pp. 834-842
-
-
Hoogstraten, C.G.1
Grant, C.V.2
Horton, T.E.3
DeRose, V.J.4
Britt, R.D.5
-
14
-
-
0025998488
-
Role of divalent metal ions in the hammerhead RNA cleavage reaction
-
Dahm S.C., and Uhlenbeck O.C. Role of divalent metal ions in the hammerhead RNA cleavage reaction. Biochemistry 30 (1991) 9464-9469
-
(1991)
Biochemistry
, vol.30
, pp. 9464-9469
-
-
Dahm, S.C.1
Uhlenbeck, O.C.2
-
15
-
-
33749267488
-
Extraordinary rates of transition metal ion-mediated ribozyme catalysis
-
Roychowdhury-Saha M., and Burke D.H. Extraordinary rates of transition metal ion-mediated ribozyme catalysis. RNA 12 (2006) 1846-1852
-
(2006)
RNA
, vol.12
, pp. 1846-1852
-
-
Roychowdhury-Saha, M.1
Burke, D.H.2
-
16
-
-
0001101248
-
Hydrolysis of nucleoside phosphates. 8. General considerations on transphosphorylations - mechanism of the metal ion-facilitated dephosphorylation of nucleoside 5′-triphosphates, including promotion of ATP dephosphorylation by addition of adenosine 5′-monophosphate
-
Sigel H., Hofstetter F., Martin R.B., Milburn R.M., Scheller-Krattiger V., and Scheller K.H. Hydrolysis of nucleoside phosphates. 8. General considerations on transphosphorylations - mechanism of the metal ion-facilitated dephosphorylation of nucleoside 5′-triphosphates, including promotion of ATP dephosphorylation by addition of adenosine 5′-monophosphate. J Am Chem Soc 106 (1984) 7935-7946
-
(1984)
J Am Chem Soc
, vol.106
, pp. 7935-7946
-
-
Sigel, H.1
Hofstetter, F.2
Martin, R.B.3
Milburn, R.M.4
Scheller-Krattiger, V.5
Scheller, K.H.6
-
17
-
-
0001340347
-
Mechanistic aspects of the metal ion promoted hydrolysis of nucleoside 5′-triphosphates (NTPs)
-
Sigel H. Mechanistic aspects of the metal ion promoted hydrolysis of nucleoside 5′-triphosphates (NTPs). Coord Chem Rev 100 (1990) 453-539
-
(1990)
Coord Chem Rev
, vol.100
, pp. 453-539
-
-
Sigel, H.1
-
18
-
-
41749109563
-
Crystal structure of a self-spliced group II intron
-
First crystal structure of a complete group II intron ribozyme. Two metal ions are found in the catalytic core being indicative of a two-metal ion mechanism.
-
Toor N., Keating K.S., Taylor S.D., and Pyle A.M. Crystal structure of a self-spliced group II intron. Science 320 (2008) 77-82. First crystal structure of a complete group II intron ribozyme. Two metal ions are found in the catalytic core being indicative of a two-metal ion mechanism.
-
(2008)
Science
, vol.320
, pp. 77-82
-
-
Toor, N.1
Keating, K.S.2
Taylor, S.D.3
Pyle, A.M.4
-
19
-
-
67349123194
-
Comparative enzymology and structural biology of RNA self-cleavage
-
Fedor M.J. Comparative enzymology and structural biology of RNA self-cleavage. Ann Rev Biophys 38 (2009) 271-299
-
(2009)
Ann Rev Biophys
, vol.38
, pp. 271-299
-
-
Fedor, M.J.1
-
21
-
-
0001940219
-
Have ATP and related purine nucleotides played a role in early evolution? ATP, its own 'enzyme' in metal ion facilitated hydrolysis
-
Sigel H. Have ATP and related purine nucleotides played a role in early evolution? ATP, its own 'enzyme' in metal ion facilitated hydrolysis. Inorg Chim Acta 198-200 (1992) 1-11
-
(1992)
Inorg Chim Acta
, vol.198-200
, pp. 1-11
-
-
Sigel, H.1
-
22
-
-
63649098099
-
Threshold occupancy and specific cation binding modes in the hammerhead ribozyme active site are required for active conformation
-
Lee T.-S., Giambasu G.M., Sosa C.P., Martick M., Scott W.G., and York D.M. Threshold occupancy and specific cation binding modes in the hammerhead ribozyme active site are required for active conformation. J Mol Biol 388 (2009) 195-206
-
(2009)
J Mol Biol
, vol.388
, pp. 195-206
-
-
Lee, T.-S.1
Giambasu, G.M.2
Sosa, C.P.3
Martick, M.4
Scott, W.G.5
York, D.M.6
-
23
-
-
33745700326
-
Cations and hydration in catalytic RNA: molecular dynamics of the hepatitis delta virus ribozyme
-
Krasovska M.V., Sefcikova J., Reblova K., Schneider B., Walter N.G., and Sponer J. Cations and hydration in catalytic RNA: molecular dynamics of the hepatitis delta virus ribozyme. Biophys J 91 (2006) 626-638
-
(2006)
Biophys J
, vol.91
, pp. 626-638
-
-
Krasovska, M.V.1
Sefcikova, J.2
Reblova, K.3
Schneider, B.4
Walter, N.G.5
Sponer, J.6
-
24
-
-
52949104434
-
Metal ion specificities for folding and cleavage activity in the Schistosoma hammerhead ribozyme
-
Detailed FRET investigation of the effect of different metal ions on the folding and catalytic cleavage reaction of the tertiary stabilized Schistosoma hammerhead ribozyme, operating the effect on folding and cleavage.
-
Boots J.L., Canny M.D., Azimi E., and Pardi A. Metal ion specificities for folding and cleavage activity in the Schistosoma hammerhead ribozyme. RNA 14 (2008) 2212-2222. Detailed FRET investigation of the effect of different metal ions on the folding and catalytic cleavage reaction of the tertiary stabilized Schistosoma hammerhead ribozyme, operating the effect on folding and cleavage.
-
(2008)
RNA
, vol.14
, pp. 2212-2222
-
-
Boots, J.L.1
Canny, M.D.2
Azimi, E.3
Pardi, A.4
-
25
-
-
33749016245
-
HDV ribozyme activity in monovalent cations
-
Perrotta A.T., and Been M.D. HDV ribozyme activity in monovalent cations. Biochemistry 45 (2006) 11357-11365
-
(2006)
Biochemistry
, vol.45
, pp. 11357-11365
-
-
Perrotta, A.T.1
Been, M.D.2
-
26
-
-
33847691104
-
Structural roles of monovalent cations in the HDV ribozyme
-
Ke A., Ding F., Batchelor J.D., and Doudna J.A. Structural roles of monovalent cations in the HDV ribozyme. Structure 15 (2007) 281-287
-
(2007)
Structure
, vol.15
, pp. 281-287
-
-
Ke, A.1
Ding, F.2
Batchelor, J.D.3
Doudna, J.A.4
-
27
-
-
34247560640
-
A single nucleotide linked to a switch in metal ion reactivity preference in the HDV ribozymes
-
2+ in catalysis.
-
2+ in catalysis.
-
(2007)
Biochemistry
, vol.46
, pp. 5124-5130
-
-
Perrotta, A.T.1
Been, M.D.2
-
28
-
-
41949138497
-
Solvent structure and hammerhead ribozyme catalysis
-
Martick M., Lee T.-S., York D.M., and Scott W.G. Solvent structure and hammerhead ribozyme catalysis. Chem Biol 15 (2008) 332-342
-
(2008)
Chem Biol
, vol.15
, pp. 332-342
-
-
Martick, M.1
Lee, T.-S.2
York, D.M.3
Scott, W.G.4
-
29
-
-
0043009734
-
Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity
-
Khvorova A., Lescoute A., Westhof E., and Jayasena S.D. Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity. Nat Struct Biol 10 (2003) 708-712
-
(2003)
Nat Struct Biol
, vol.10
, pp. 708-712
-
-
Khvorova, A.1
Lescoute, A.2
Westhof, E.3
Jayasena, S.D.4
-
30
-
-
0142105383
-
Peripheral regions of natural hammerhead ribozymes greatly increase their self-cleavage activity
-
De la Pena M., Gago S., and Flores R. Peripheral regions of natural hammerhead ribozymes greatly increase their self-cleavage activity. EMBO J 22 (2003) 5561-5570
-
(2003)
EMBO J
, vol.22
, pp. 5561-5570
-
-
De la Pena, M.1
Gago, S.2
Flores, R.3
-
31
-
-
21244480925
-
Group II intron ribozymes and metal ions - a delicate relationship
-
Sigel R.K.O. Group II intron ribozymes and metal ions - a delicate relationship. Eur J Inorg Chem 12 (2005) 2281-2292
-
(2005)
Eur J Inorg Chem
, vol.12
, pp. 2281-2292
-
-
Sigel, R.K.O.1
-
32
-
-
34250631912
-
Group II introns: structure, folding and splicing mechanism
-
Fedorova O., and Zingler N. Group II introns: structure, folding and splicing mechanism. Biol Chem 388 (2007) 665-678
-
(2007)
Biol Chem
, vol.388
, pp. 665-678
-
-
Fedorova, O.1
Zingler, N.2
-
33
-
-
48149099082
-
Divalent metal ions tune the self-splicing reaction of the yeast mitochondrial group II intron Sc.ai5γ
-
2+ binding sites within the active structure.
-
2+ binding sites within the active structure.
-
(2008)
J Biol Inorg Chem
, vol.13
, pp. 1025-1036
-
-
Erat, M.C.1
Sigel, R.K.O.2
-
35
-
-
71949084158
-
2+ on single molecule folding of a group II intron ribozyme
-
2+, the intron folds into two distinct subpopulations that do not interchange.
-
2+, the intron folds into two distinct subpopulations that do not interchange.
-
(2009)
Angew Chem Int Ed
, vol.48
, pp. 9739-9742
-
-
Steiner, M.1
Rueda, D.2
Sigel RKO3
-
36
-
-
0030476765
-
Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme
-
Scott W.G., Murray J.B., Arnold J.R.P., Stoddard B.L., and Klug A. Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme. Science 274 (1996) 2065-2069
-
(1996)
Science
, vol.274
, pp. 2065-2069
-
-
Scott, W.G.1
Murray, J.B.2
Arnold, J.R.P.3
Stoddard, B.L.4
Klug, A.5
-
37
-
-
0033860560
-
Capture and visualization of a catalytic RNA enzyme-product complex using crystal lattice trapping and X-ray holographic reconstruction
-
Murray J.B., Szoke H., Szoke A., and Scott W.G. Capture and visualization of a catalytic RNA enzyme-product complex using crystal lattice trapping and X-ray holographic reconstruction. Mol Cell 5 (2000) 279-287
-
(2000)
Mol Cell
, vol.5
, pp. 279-287
-
-
Murray, J.B.1
Szoke, H.2
Szoke, A.3
Scott, W.G.4
-
38
-
-
58149280561
-
a shifts through metals: potential relevance to ribozyme chemistry
-
a shifts in model systems and transferring it to ribozymes.
-
a shifts in model systems and transferring it to ribozymes.
-
(2008)
Chem Biodivers
, vol.5
, pp. 1455-1474
-
-
Lippert, B.1
-
39
-
-
50649098884
-
a
-
a into the physiological pH range with the electrostatic effects of different metal ions on the VS ribozyme.
-
a into the physiological pH range with the electrostatic effects of different metal ions on the VS ribozyme.
-
(2008)
RNA
, vol.14
, pp. 1942-1949
-
-
Smith, M.D.1
Mehdizadeh, R.2
Olive, J.E.3
Collins, R.A.4
-
40
-
-
4544273058
-
Two metal ions coordinated to a purine residue tolerate each other well!
-
Knobloch B., Sigel R.K.O., Lippert B., and Sigel H. Two metal ions coordinated to a purine residue tolerate each other well!. Angew Chem Int Ed 43 (2004) 3793-3795
-
(2004)
Angew Chem Int Ed
, vol.43
, pp. 3793-3795
-
-
Knobloch, B.1
Sigel, R.K.O.2
Lippert, B.3
Sigel, H.4
-
41
-
-
55549085243
-
Mechanistic characterization of the HDV genomic ribozyme: solvent isotope effects and proton inventories in the absence of divalent metal ions support C75 as the general acid
-
A thorough and detailed study on proton transfers taking part in the catalytic steps of the HDV genomic ribozyme.
-
Cerrone-Szakal A.L., Siegfried N.A., and Bevilacqua P.C. Mechanistic characterization of the HDV genomic ribozyme: solvent isotope effects and proton inventories in the absence of divalent metal ions support C75 as the general acid. J Am Chem Soc 130 (2008) 14504-14520. A thorough and detailed study on proton transfers taking part in the catalytic steps of the HDV genomic ribozyme.
-
(2008)
J Am Chem Soc
, vol.130
, pp. 14504-14520
-
-
Cerrone-Szakal, A.L.1
Siegfried, N.A.2
Bevilacqua, P.C.3
-
42
-
-
26944448948
-
Nucleoside 5′-triphosphates: self-association, acid-base, and metal ion-binding properties in solution
-
Sigel H., and Griesser R. Nucleoside 5′-triphosphates: self-association, acid-base, and metal ion-binding properties in solution. Chem Soc Rev 34 (2005) 875-900
-
(2005)
Chem Soc Rev
, vol.34
, pp. 875-900
-
-
Sigel, H.1
Griesser, R.2
-
43
-
-
84899742655
-
Complex formation of Nickel(II) and related metal ions with sugar residues, nucleobases, phosphates, nucleotides, and nucleic acids
-
Sigel R.K.O., and Sigel H. Complex formation of Nickel(II) and related metal ions with sugar residues, nucleobases, phosphates, nucleotides, and nucleic acids. Met Ions Life Sci 2 (2007) 109-180
-
(2007)
Met Ions Life Sci
, vol.2
, pp. 109-180
-
-
Sigel, R.K.O.1
Sigel, H.2
-
44
-
-
0001056524
-
Solution structures of nucleotide-metal ion complexes. Isomeric equilibria
-
Sigel H., and Song B. Solution structures of nucleotide-metal ion complexes. Isomeric equilibria. Met Ions Biol Syst 32 (1996) 135-206
-
(1996)
Met Ions Biol Syst
, vol.32
, pp. 135-206
-
-
Sigel, H.1
Song, B.2
-
45
-
-
38149014107
-
2+ ions coordinated to domain 6 of a group II intron ribozyme
-
2+ ions coordinated to domain 6 of a group II intron ribozyme. Inorg Chem 46 (2007) 11224-11234
-
(2007)
Inorg Chem
, vol.46
, pp. 11224-11234
-
-
Erat, M.C.1
Sigel, R.K.O.2
-
47
-
-
54749153656
-
Capturing hammerhead ribozyme structures in action by modulating general base catalysis
-
Chi Y.-I., Martick M., Lares M., Kim R., Scott W.G., and Kim S.-H. Capturing hammerhead ribozyme structures in action by modulating general base catalysis. PLoS Biol 6 (2008) e234-e1234
-
(2008)
PLoS Biol
, vol.6
-
-
Chi, Y.-I.1
Martick, M.2
Lares, M.3
Kim, R.4
Scott, W.G.5
Kim, S.-H.6
-
48
-
-
33947296922
-
On the discriminating behavior of metal ions and ligands with regard to their biological significance
-
Sigel H., and McCormick D.B. On the discriminating behavior of metal ions and ligands with regard to their biological significance. Acc Chem Res 3 (1970) 201-208
-
(1970)
Acc Chem Res
, vol.3
, pp. 201-208
-
-
Sigel, H.1
McCormick, D.B.2
-
49
-
-
19744375331
-
Metal ion-binding properties of (N3)-deprotonated uridine, thymidine, and related pyrimidine nucleosides in aqueous solution
-
Knobloch B., Linert W., and Sigel H. Metal ion-binding properties of (N3)-deprotonated uridine, thymidine, and related pyrimidine nucleosides in aqueous solution. Proc Natl Acad Sci U S A 102 (2005) 7459-7464
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, pp. 7459-7464
-
-
Knobloch, B.1
Linert, W.2
Sigel, H.3
-
50
-
-
52949139200
-
Acid-base properties of ribose versus 2′-deoxyribose nucleotides
-
Mucha A., Knobloch B., Jeżowska-Bojczuk M., Kozłowski H., and Sigel R.K.O. Acid-base properties of ribose versus 2′-deoxyribose nucleotides. Chem Eur J 14 (2008) 6663-6671
-
(2008)
Chem Eur J
, vol.14
, pp. 6663-6671
-
-
Mucha, A.1
Knobloch, B.2
Jezowska-Bojczuk, M.3
Kozłowski, H.4
Sigel, R.K.O.5
|