-
1
-
-
14244272868
-
PHENIX: building new software for automated crystallographic structure determination
-
P.D. Adams, R.W. Grosse-Kunstleve, L.W. Hung, T.R. Ioerger, A.J. McCoy, N.W. Moriarty, R.J. Read, J.C. Sacchettini, N.K. Sauter, and T.C. Terwilliger PHENIX: building new software for automated crystallographic structure determination Acta Crystallogr. D Biol. Crystallogr. 58 2002 1948 1954
-
(2002)
Acta Crystallogr. D Biol. Crystallogr.
, vol.58
, pp. 1948-1954
-
-
Adams, P.D.1
Grosse-Kunstleve, R.W.2
Hung, L.W.3
Ioerger, T.R.4
McCoy, A.J.5
Moriarty, N.W.6
Read, R.J.7
Sacchettini, J.C.8
Sauter, N.K.9
Terwilliger, T.C.10
-
2
-
-
77955437093
-
A eubacterial riboswitch class that senses the coenzyme tetrahydrofolate
-
T.D. Ames, D.A. Rodionov, Z. Weinberg, and R.R. Breaker A eubacterial riboswitch class that senses the coenzyme tetrahydrofolate Chem. Biol. 17 2010 681 685
-
(2010)
Chem. Biol.
, vol.17
, pp. 681-685
-
-
Ames, T.D.1
Rodionov, D.A.2
Weinberg, Z.3
Breaker, R.R.4
-
3
-
-
9244225713
-
Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine
-
R.T. Batey, S.D. Gilbert, and R.K. Montange Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine Nature 432 2004 411 415
-
(2004)
Nature
, vol.432
, pp. 411-415
-
-
Batey, R.T.1
Gilbert, S.D.2
Montange, R.K.3
-
4
-
-
0019961116
-
ZTP (5-amino 4-imidazole carboxamide riboside 5′-triphosphate): a proposed alarmone for 10-formyl-tetrahydrofolate deficiency
-
B.R. Bochner, and B.N. Ames ZTP (5-amino 4-imidazole carboxamide riboside 5′-triphosphate): a proposed alarmone for 10-formyl-tetrahydrofolate deficiency Cell 29 1982 929 937
-
(1982)
Cell
, vol.29
, pp. 929-937
-
-
Bochner, B.R.1
Ames, B.N.2
-
5
-
-
84921482096
-
ZMP: a master regulator of one-carbon metabolism
-
G.S. Ducker, and J.D. Rabinowitz ZMP: a master regulator of one-carbon metabolism Mol. Cell 57 2015 203 204
-
(2015)
Mol. Cell
, vol.57
, pp. 203-204
-
-
Ducker, G.S.1
Rabinowitz, J.D.2
-
6
-
-
33748300801
-
Crystal structures of the thi-box riboswitch bound to thiamine pyrophosphate analogs reveal adaptive RNA-small molecule recognition
-
T.E. Edwards, and A.R. Ferre-D'Amare Crystal structures of the thi-box riboswitch bound to thiamine pyrophosphate analogs reveal adaptive RNA-small molecule recognition Structure 14 2006 1459 1468
-
(2006)
Structure
, vol.14
, pp. 1459-1468
-
-
Edwards, T.E.1
Ferre-D'Amare, A.R.2
-
7
-
-
58149138753
-
A structural basis for the recognition of 2′-deoxyguanosine by the purine riboswitch
-
A.L. Edwards, and R.T. Batey A structural basis for the recognition of 2′-deoxyguanosine by the purine riboswitch J. Mol. Biol. 385 2009 938 948
-
(2009)
J. Mol. Biol.
, vol.385
, pp. 938-948
-
-
Edwards, A.L.1
Batey, R.T.2
-
9
-
-
84906311591
-
Structural insights into recognition of c-di-AMP by the ydaO riboswitch
-
A. Gao, and A. Serganov Structural insights into recognition of c-di-AMP by the ydaO riboswitch Nat. Chem. Biol. 10 2014 787 792
-
(2014)
Nat. Chem. Biol.
, vol.10
, pp. 787-792
-
-
Gao, A.1
Serganov, A.2
-
10
-
-
80052602449
-
Long-range pseudoknot interactions dictate the regulatory response in the tetrahydrofolate riboswitch
-
L. Huang, S. Ishibe-Murakami, D.J. Patel, and A. Serganov Long-range pseudoknot interactions dictate the regulatory response in the tetrahydrofolate riboswitch Proc. Natl. Acad. Sci. USA 108 2011 14801 14806
-
(2011)
Proc. Natl. Acad. Sci. USA
, vol.108
, pp. 14801-14806
-
-
Huang, L.1
Ishibe-Murakami, S.2
Patel, D.J.3
Serganov, A.4
-
11
-
-
84911391431
-
Crystal structure of a c-di-AMP riboswitch reveals an internally pseudo-dimeric RNA
-
C.P. Jones, and A.R. Ferre-D'Amare Crystal structure of a c-di-AMP riboswitch reveals an internally pseudo-dimeric RNA EMBO J. 33 2014 2692 2703
-
(2014)
EMBO J
, vol.33
, pp. 2692-2703
-
-
Jones, C.P.1
Ferre-D'Amare, A.R.2
-
12
-
-
84928570713
-
GEMM-I riboswitches from Geobacter sense the bacterial second messenger cyclic AMP-GMP
-
C.A. Kellenberger, S.C. Wilson, S.F. Hickey, T.L. Gonzalez, Y. Su, Z.F. Hallberg, T.F. Brewer, A.T. Iavarone, H.K. Carlson, Y.F. Hsieh, and et al. GEMM-I riboswitches from Geobacter sense the bacterial second messenger cyclic AMP-GMP Proc. Natl. Acad. Sci. USA 112 2015 5383 5388
-
(2015)
Proc. Natl. Acad. Sci. USA
, vol.112
, pp. 5383-5388
-
-
Kellenberger, C.A.1
Wilson, S.C.2
Hickey, S.F.3
Gonzalez, T.L.4
Su, Y.5
Hallberg, Z.F.6
Brewer, T.F.7
Iavarone, A.T.8
Carlson, H.K.9
Hsieh, Y.F.10
-
13
-
-
36048942754
-
Guanine riboswitch variants from Mesoplasma florum selectively recognize 2′-deoxyguanosine
-
J.N. Kim, A. Roth, and R.R. Breaker Guanine riboswitch variants from Mesoplasma florum selectively recognize 2′-deoxyguanosine Proc. Natl. Acad. Sci. USA 104 2007 16092 16097
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, pp. 16092-16097
-
-
Kim, J.N.1
Roth, A.2
Breaker, R.R.3
-
14
-
-
84921493496
-
An ancient riboswitch class in bacteria regulates purine biosynthesis and one-carbon metabolism
-
P.B. Kim, J.W. Nelson, and R.R. Breaker An ancient riboswitch class in bacteria regulates purine biosynthesis and one-carbon metabolism Mol. Cell 57 2015 317 328
-
(2015)
Mol. Cell
, vol.57
, pp. 317-328
-
-
Kim, P.B.1
Nelson, J.W.2
Breaker, R.R.3
-
15
-
-
71449123530
-
Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch
-
N. Kulshina, N.J. Baird, and A.R. Ferre-D'Amare Recognition of the bacterial second messenger cyclic diguanylate by its cognate riboswitch Nat. Struct. Mol. Biol. 16 2009 1212 1217
-
(2009)
Nat. Struct. Mol. Biol.
, vol.16
, pp. 1212-1217
-
-
Kulshina, N.1
Baird, N.J.2
Ferre-D'Amare, A.R.3
-
16
-
-
0038210214
-
Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria
-
M. Mandal, B. Boese, J.E. Barrick, W.C. Winkler, and R.R. Breaker Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria Cell 113 2003 577 586
-
(2003)
Cell
, vol.113
, pp. 577-586
-
-
Mandal, M.1
Boese, B.2
Barrick, J.E.3
Winkler, W.C.4
Breaker, R.R.5
-
17
-
-
85011936067
-
Challenges of ligand identification for riboswitch candidates
-
M.M. Meyer, M.C. Hammond, Y. Salinas, A. Roth, N. Sudarsan, and R.R. Breaker Challenges of ligand identification for riboswitch candidates RNA Biol. 8 2011 5 10
-
(2011)
RNA Biol
, vol.8
, pp. 5-10
-
-
Meyer, M.M.1
Hammond, M.C.2
Salinas, Y.3
Roth, A.4
Sudarsan, N.5
Breaker, R.R.6
-
19
-
-
84887997976
-
Riboswitches in eubacteria sense the second messenger c-di-AMP
-
J.W. Nelson, N. Sudarsan, K. Furukawa, Z. Weinberg, J.X. Wang, and R.R. Breaker Riboswitches in eubacteria sense the second messenger c-di-AMP Nat. Chem. Biol. 9 2013 834 839
-
(2013)
Nat. Chem. Biol.
, vol.9
, pp. 834-839
-
-
Nelson, J.W.1
Sudarsan, N.2
Furukawa, K.3
Weinberg, Z.4
Wang, J.X.5
Breaker, R.R.6
-
20
-
-
84928789631
-
Control of bacterial exoelectrogenesis by c-AMP-GMP
-
J.W. Nelson, N. Sudarsan, G.E. Phillips, S. Stav, C.E. Lunse, P.J. McCown, and R.R. Breaker Control of bacterial exoelectrogenesis by c-AMP-GMP Proc. Natl. Acad. Sci. USA 112 2015 5389 5394
-
(2015)
Proc. Natl. Acad. Sci. USA
, vol.112
, pp. 5389-5394
-
-
Nelson, J.W.1
Sudarsan, N.2
Phillips, G.E.3
Stav, S.4
Lunse, C.E.5
McCown, P.J.6
Breaker, R.R.7
-
21
-
-
0346687595
-
The riboswitch control of bacterial metabolism
-
E. Nudler, and A.S. Mironov The riboswitch control of bacterial metabolism Trends Biochem. Sci. 29 2004 11 17
-
(2004)
Trends Biochem. Sci.
, vol.29
, pp. 11-17
-
-
Nudler, E.1
Mironov, A.S.2
-
22
-
-
4644366388
-
HKL2MAP: a graphical user interface for phasing with SHELX programs
-
T. Pape, and T.R. Schneider HKL2MAP: a graphical user interface for phasing with SHELX programs J. Appl. Crystallogr. 37 2004 843 844
-
(2004)
J. Appl. Crystallogr.
, vol.37
, pp. 843-844
-
-
Pape, T.1
Schneider, T.R.2
-
23
-
-
84908063090
-
Themes and variations in riboswitch structure and function
-
A. Peselis, and A. Serganov Themes and variations in riboswitch structure and function Biochim. Biophys. Acta 1839 2014 908 918
-
(2014)
Biochim. Biophys. Acta
, vol.1839
, pp. 908-918
-
-
Peselis, A.1
Serganov, A.2
-
24
-
-
65649131534
-
Preparation and crystallization of riboswitch-ligand complexes
-
O. Pikovskaya, A.A. Serganov, A. Polonskaia, A. Serganov, and D.J. Patel Preparation and crystallization of riboswitch-ligand complexes Methods Mol. Biol. 540 2009 115 128
-
(2009)
Methods Mol. Biol.
, vol.540
, pp. 115-128
-
-
Pikovskaya, O.1
Serganov, A.A.2
Polonskaia, A.3
Serganov, A.4
Patel, D.J.5
-
25
-
-
80052967464
-
Structural principles of nucleoside selectivity in a 2′-deoxyguanosine riboswitch
-
O. Pikovskaya, A. Polonskaia, D.J. Patel, and A. Serganov Structural principles of nucleoside selectivity in a 2′-deoxyguanosine riboswitch Nat. Chem. Biol. 7 2011 748 755
-
(2011)
Nat. Chem. Biol.
, vol.7
, pp. 748-755
-
-
Pikovskaya, O.1
Polonskaia, A.2
Patel, D.J.3
Serganov, A.4
-
26
-
-
84906313473
-
c-di-AMP binds the ydaO riboswitch in two pseudo-symmetry-related pockets
-
A. Ren, and D.J. Patel c-di-AMP binds the ydaO riboswitch in two pseudo-symmetry-related pockets Nat. Chem. Biol. 10 2014 780 786
-
(2014)
Nat. Chem. Biol.
, vol.10
, pp. 780-786
-
-
Ren, A.1
Patel, D.J.2
-
27
-
-
84927695413
-
Structural basis for molecular discrimination by a 3′,3′-cGAMP Sensing Riboswitch
-
A. Ren, X.C. Wang, C.A. Kellenberger, K.R. Rajashankar, R.A. Jones, M.C. Hammond, and D.J. Patel Structural basis for molecular discrimination by a 3′,3′-cGAMP Sensing Riboswitch Cell Rep. 11 2015 1 12
-
(2015)
Cell Rep
, vol.11
, pp. 1-12
-
-
Ren, A.1
Wang, X.C.2
Kellenberger, C.A.3
Rajashankar, K.R.4
Jones, R.A.5
Hammond, M.C.6
Patel, D.J.7
-
28
-
-
84861405805
-
Metabolite recognition principles and molecular mechanisms underlying riboswitch function
-
A. Serganov, and D.J. Patel Metabolite recognition principles and molecular mechanisms underlying riboswitch function Annu. Rev. Biophys. 41 2012 343 370
-
(2012)
Annu. Rev. Biophys.
, vol.41
, pp. 343-370
-
-
Serganov, A.1
Patel, D.J.2
-
29
-
-
84872543206
-
A decade of riboswitches
-
A. Serganov, and E. Nudler A decade of riboswitches Cell 152 2013 17 24
-
(2013)
Cell
, vol.152
, pp. 17-24
-
-
Serganov, A.1
Nudler, E.2
-
30
-
-
10644250950
-
Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs
-
A. Serganov, Y.R. Yuan, O. Pikovskaya, A. Polonskaia, L. Malinina, A.T. Phan, C. Hobartner, R. Micura, R.R. Breaker, and D.J. Patel Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs Chem. Biol. 11 2004 1729 1741
-
(2004)
Chem. Biol.
, vol.11
, pp. 1729-1741
-
-
Serganov, A.1
Yuan, Y.R.2
Pikovskaya, O.3
Polonskaia, A.4
Malinina, L.5
Phan, A.T.6
Hobartner, C.7
Micura, R.8
Breaker, R.R.9
Patel, D.J.10
-
31
-
-
33745635350
-
Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch
-
A. Serganov, A. Polonskaia, A.T. Phan, R.R. Breaker, and D.J. Patel Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch Nature 441 2006 1167 1171
-
(2006)
Nature
, vol.441
, pp. 1167-1171
-
-
Serganov, A.1
Polonskaia, A.2
Phan, A.T.3
Breaker, R.R.4
Patel, D.J.5
-
32
-
-
62249156218
-
Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch
-
A. Serganov, L. Huang, and D.J. Patel Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch Nature 458 2009 233 237
-
(2009)
Nature
, vol.458
, pp. 233-237
-
-
Serganov, A.1
Huang, L.2
Patel, D.J.3
-
33
-
-
71449108155
-
Structural basis of ligand binding by a c-di-GMP riboswitch
-
K.D. Smith, S.V. Lipchock, T.D. Ames, J. Wang, R.R. Breaker, and S.A. Strobel Structural basis of ligand binding by a c-di-GMP riboswitch Nat. Struct. Mol. Biol. 16 2009 1218 1223
-
(2009)
Nat. Struct. Mol. Biol.
, vol.16
, pp. 1218-1223
-
-
Smith, K.D.1
Lipchock, S.V.2
Ames, T.D.3
Wang, J.4
Breaker, R.R.5
Strobel, S.A.6
-
34
-
-
47749152941
-
Riboswitches in eubacteria sense the second messenger cyclic di-GMP
-
N. Sudarsan, E.R. Lee, Z. Weinberg, R.H. Moy, J.N. Kim, K.H. Link, and R.R. Breaker Riboswitches in eubacteria sense the second messenger cyclic di-GMP Science 321 2008 411 413
-
(2008)
Science
, vol.321
, pp. 411-413
-
-
Sudarsan, N.1
Lee, E.R.2
Weinberg, Z.3
Moy, R.H.4
Kim, J.N.5
Link, K.H.6
Breaker, R.R.7
-
35
-
-
33744469562
-
Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand
-
S. Thore, M. Leibundgut, and N. Ban Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand Science 312 2006 1208 1211
-
(2006)
Science
, vol.312
, pp. 1208-1211
-
-
Thore, S.1
Leibundgut, M.2
Ban, N.3
-
36
-
-
80054074740
-
The structure of a tetrahydrofolate-sensing riboswitch reveals two ligand binding sites in a single aptamer
-
J.J. Trausch, P. Ceres, F.E. Reyes, and R.T. Batey The structure of a tetrahydrofolate-sensing riboswitch reveals two ligand binding sites in a single aptamer Structure 19 2011 1413 1423
-
(2011)
Structure
, vol.19
, pp. 1413-1423
-
-
Trausch, J.J.1
Ceres, P.2
Reyes, F.E.3
Batey, R.T.4
-
37
-
-
27144527479
-
Regulation of bacterial gene expression by riboswitches
-
W.C. Winkler, and R.R. Breaker Regulation of bacterial gene expression by riboswitches Annu. Rev. Microbiol. 59 2005 487 517
-
(2005)
Annu. Rev. Microbiol.
, vol.59
, pp. 487-517
-
-
Winkler, W.C.1
Breaker, R.R.2
-
38
-
-
0037206833
-
Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression
-
W. Winkler, A. Nahvi, and R.R. Breaker Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression Nature 419 2002 952 956
-
(2002)
Nature
, vol.419
, pp. 952-956
-
-
Winkler, W.1
Nahvi, A.2
Breaker, R.R.3
|