-
1
-
-
0033782994
-
Aminoacyl-tRNA synthesis
-
Ibba, M. and Söll, D. (2000) Aminoacyl-tRNA synthesis. Annu. Rev. Biochem., 69, 617-650.
-
(2000)
Annu. Rev. Biochem.
, vol.69
, pp. 617-650
-
-
Ibba, M.1
Söll, D.2
-
2
-
-
41849117355
-
From one amino acid to another: tRNA-dependent amino acid biosynthesis
-
Sheppard, K., Yuan, J., Hohn, M.J., Jester, B., Devine, K.M. and Söll, D. (2008) From one amino acid to another: tRNA-dependent amino acid biosynthesis. Nucleic Acids Res., 36, 1813-1825.
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. 1813-1825
-
-
Sheppard, K.1
Yuan, J.2
Hohn, M.J.3
Jester, B.4
Devine, K.M.5
Söll, D.6
-
3
-
-
0022449958
-
Gln1 in vitro
-
Lapointe, J., Duplain, L. and Proulx, M. (1986) A single glutamyl-tRNA synthetase aminoacylates tRNAGlu and tRNAGln in Bacillus subtilis and efficiently misacylates Escherichia coli tRNAGln1 in vitro. J. Bacteriol., 165, 88-93.
-
(1986)
J. Bacteriol.
, vol.165
, pp. 88-93
-
-
Lapointe, J.1
Duplain, L.2
Proulx, M.3
-
4
-
-
0014324873
-
Transfer RNA as a cofactor coupling amino acid synthesis with that of protein
-
Wilcox, M. and Nirenberg, M. (1968) Transfer RNA as a cofactor coupling amino acid synthesis with that of protein. Proc. Natl Acad. Sci. USA, 61, 229-236.
-
(1968)
Proc. Natl Acad. Sci. USA
, vol.61
, pp. 229-236
-
-
Wilcox, M.1
Nirenberg, M.2
-
5
-
-
0029781454
-
tRNA-dependent asparagine formation
-
Curnow, A.W., Ibba, M. and Söll, D. (1996) tRNA-dependent asparagine formation. Nature, 382, 589-590.
-
(1996)
Nature
, vol.382
, pp. 589-590
-
-
Curnow, A.W.1
Ibba, M.2
Söll, D.3
-
6
-
-
0030811296
-
Existence of two distinct aspartyl-tRNA synthetases in Thermus thermophilus. Structural and biochemical properties of the two enzymes
-
Becker, H.D., Reinbolt, J., Kreutzer, R., Giegé, R. and Kern, D. (1997) Existence of two distinct aspartyl-tRNA synthetases in Thermus thermophilus. Structural and biochemical properties of the two enzymes. Biochemistry, 36, 8785-8797.
-
(1997)
Biochemistry
, vol.36
, pp. 8785-8797
-
-
Becker, H.D.1
Reinbolt, J.2
Kreutzer, R.3
Giegé, R.4
Kern, D.5
-
7
-
-
0030613553
-
Glu-tRNAGln amidotransferase: a novel heterotrimeric enzyme required for correct decoding of glutamine codons during translation
-
Curnow, A.W., Hong, K., Yuan, R., Kim, S., Martins, O., Winkler, W., Henkin, T.M. and Söll, D. (1997) Glu-tRNAGln amidotransferase: a novel heterotrimeric enzyme required for correct decoding of glutamine codons during translation. Proc. Natl Acad. Sci. USA, 94, 11819-11826.
-
(1997)
Proc. Natl Acad. Sci. USA
, vol.94
, pp. 11819-11826
-
-
Curnow, A.W.1
Hong, K.2
Yuan, R.3
Kim, S.4
Martins, O.5
Winkler, W.6
Henkin, T.M.7
Söll, D.8
-
8
-
-
0034618571
-
Domain-specific recruitment of amide amino acids for protein synthesis
-
Tumbula, D.L., Becker, H.D., Chang, W.Z. and Söll, D. (2000) Domain-specific recruitment of amide amino acids for protein synthesis. Nature, 407, 106-110.
-
(2000)
Nature
, vol.407
, pp. 106-110
-
-
Tumbula, D.L.1
Becker, H.D.2
Chang, W.Z.3
Söll, D.4
-
9
-
-
0042388199
-
When contemporary aminoacyl-tRNA synthetases invent their cognate amino acid metabolism
-
Roy, H., Becker, H.D., Reinbolt, J. and Kern, D. (2003) When contemporary aminoacyl-tRNA synthetases invent their cognate amino acid metabolism. Proc. Natl Acad. Sci. USA, 100, 9837-9842.
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 9837-9842
-
-
Roy, H.1
Becker, H.D.2
Reinbolt, J.3
Kern, D.4
-
10
-
-
40649114689
-
Gln confines the amidotransferase GatCAB to asparaginyl-tRNAAsn formation
-
Sheppard, K., Sherrer, R.L. and Söll, D. (2008) Methanothermobacter thermautotrophicus tRNAGln confines the amidotransferase GatCAB to asparaginyl-tRNAAsn formation. J. Mol. Biol., 377, 845-853.
-
(2008)
J. Mol. Biol.
, vol.377
, pp. 845-853
-
-
Sheppard, K.1
Sherrer, R.L.2
Söll, D.3
-
11
-
-
33745596803
-
Ammonia channel couples glutaminase with transamidase reactions in GatCAB
-
Nakamura, A., Yao, M., Chimnaronk, S., Sakai, N. and Tanaka, I. (2006) Ammonia channel couples glutaminase with transamidase reactions in GatCAB. Science, 312, 1954-1958.
-
(2006)
Science
, vol.312
, pp. 1954-1958
-
-
Nakamura, A.1
Yao, M.2
Chimnaronk, S.3
Sakai, N.4
Tanaka, I.5
-
12
-
-
33745587780
-
Structural basis of RNA-dependent recruitment of glutamine to the genetic code
-
Oshikane, H., Sheppard, K., Fukai, S., Nakamura, Y., Ishitani, R., Numata, T., Sherrer, R.L., Feng, L., Schmitt, E., Panvert, M. et al. (2006) Structural basis of RNA-dependent recruitment of glutamine to the genetic code. Science, 312, 1950-1954.
-
(2006)
Science
, vol.312
, pp. 1950-1954
-
-
Oshikane, H.1
Sheppard, K.2
Fukai, S.3
Nakamura, Y.4
Ishitani, R.5
Numata, T.6
Sherrer, R.L.7
Feng, L.8
Schmitt, E.9
Panvert, M.10
-
13
-
-
33845632933
-
A single tRNA base pair mediates bacterial tRNA-dependent biosynthesis of asparagine
-
Bailly, M., Giannouli, S., Blaise, M., Stathopoulos, C., Kern, D. and Becker, H.D. (2006) A single tRNA base pair mediates bacterial tRNA-dependent biosynthesis of asparagine. Nucleic Acids Res., 34, 6083-6094.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 6083-6094
-
-
Bailly, M.1
Giannouli, S.2
Blaise, M.3
Stathopoulos, C.4
Kern, D.5
Becker, H.D.6
-
15
-
-
34247136211
-
Deinococcus glutaminyl-tRNA synthetase is a chimer between proteins from an ancient and the modern pathways of aminoacyl-tRNA formation
-
Deniziak, M., Sauter, C., Becker, H.D., Paulus, C.A., Giegé, R. and Kern, D. (2007) Deinococcus glutaminyl-tRNA synthetase is a chimer between proteins from an ancient and the modern pathways of aminoacyl-tRNA formation. Nucleic Acids Res., 35, 1421-1431.
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. 1421-1431
-
-
Deniziak, M.1
Sauter, C.2
Becker, H.D.3
Paulus, C.A.4
Giegé, R.5
Kern, D.6
-
16
-
-
40649101442
-
On the Evolution of the tRNA-dependent amidotransferases, GatCAB and GatDE
-
Sheppard, K. and Söll, D. (2008) On the Evolution of the tRNA-dependent amidotransferases, GatCAB and GatDE. J. Mol. Biol., 377, 831-844.
-
(2008)
J. Mol. Biol.
, vol.377
, pp. 831-844
-
-
Sheppard, K.1
Söll, D.2
-
17
-
-
26444567797
-
Structural basis for tRNA-dependent amidotransferase function
-
Schmitt, E., Panvert, M., Blanquet, S. and Mechulam, Y. (2005) Structural basis for tRNA-dependent amidotransferase function. Structure, 13, 1421-1433.
-
(2005)
Structure
, vol.13
, pp. 1421-1433
-
-
Schmitt, E.1
Panvert, M.2
Blanquet, S.3
Mechulam, Y.4
-
18
-
-
68149137734
-
Insights into tRNA-dependent amidotransferase evolution and catalysis from the structure of the Aquifex aeolicus enzyme
-
Wu, J., Bu, W., Sheppard, K., Kitabatake, M., Kwon, S.T., Söll, D. and Smith, J.L. (2009) Insights into tRNA-dependent amidotransferase evolution and catalysis from the structure of the Aquifex aeolicus enzyme. J. Mol. Biol., 391, 703-716.
-
(2009)
J. Mol. Biol.
, vol.391
, pp. 703-716
-
-
Wu, J.1
Bu, W.2
Sheppard, K.3
Kitabatake, M.4
Kwon, S.T.5
Söll, D.6
Smith, J.L.7
-
19
-
-
1842578348
-
A novel system for expressing recombinant proteins over a wide temperature range from 4 to 35 degrees C
-
Nakashima, N. and Tamura, T. (2004) A novel system for expressing recombinant proteins over a wide temperature range from 4 to 35 degrees C. Biotechnol. Bioeng., 86, 136-148.
-
(2004)
Biotechnol. Bioeng.
, vol.86
, pp. 136-148
-
-
Nakashima, N.1
Tamura, T.2
-
20
-
-
34249744662
-
The Helicobacter pylori amidotransferase GatCAB is equally efficient in glutamine-dependent transamidation of Asp-tRNAAsn and Glu-tRNAGln
-
Sheppard, K., Akochy, P.M., Salazar, J.C. and Söll, D. (2007) The Helicobacter pylori amidotransferase GatCAB is equally efficient in glutamine-dependent transamidation of Asp-tRNAAsn and Glu-tRNAGln. J. Biol. Chem., 282, 11866-11873.
-
(2007)
J. Biol. Chem.
, vol.282
, pp. 11866-11873
-
-
Sheppard, K.1
Akochy, P.M.2
Salazar, J.C.3
Söll, D.4
-
21
-
-
0001989874
-
Seeding techniques
-
second edition, Ducroix, A. and Giegé, R. (eds), IRL Press, Oxford
-
Stura, E.A. (2000) Seeding techniques. In Ducroix, A. and Giegé, R. (eds), Crystallization of Nucleic Acids and Proteins: A Practical Approach, second edition. IRL Press, Oxford, pp. 177-207.
-
(2000)
Crystallization of Nucleic Acids and Proteins: A Practical Approach
, pp. 177-207
-
-
Stura, E.A.1
-
22
-
-
0031059866
-
Processing of X-ray Diffraction Data Collected in Oscillation Mode
-
Carter, C.W.J. and Sweet, R.M. (eds), Academic Press, New York
-
Otwinowski, Z. and Minor, W. (1997) Processing of X-ray Diffraction Data Collected in Oscillation Mode. In Carter, C.W.J. and Sweet, R.M. (eds), Methods in Enzymology, Volume 276: Macromolecular Crystallography, part A. Academic Press, New York, pp. 307-326.
-
(1997)
Methods in Enzymology, Macromolecular Crystallography, part A
, vol.276
, pp. 307-326
-
-
Otwinowski, Z.1
Minor, W.2
-
24
-
-
33644872571
-
LAFIRE: software for automating the refinement process of protein-structure analysis
-
Yao, M., Zhou, Y. and Tanaka, I. (2006) LAFIRE: software for automating the refinement process of protein-structure analysis. Acta Crystallogr. Sect. D: Biol. Crystallogr., 62, 189-196.
-
(2006)
Acta Crystallogr. Sect. D: Biol. Crystallogr.
, vol.62
, pp. 189-196
-
-
Yao, M.1
Zhou, Y.2
Tanaka, I.3
-
25
-
-
33645136606
-
New algorithm for protein model building
-
Zyou, Y., Yao, M. and Tanaka, I. (2006) New algorithm for protein model building. J. Appl. Crystallogr., 39, 57-63.
-
(2006)
J. Appl. Crystallogr.
, vol.39
, pp. 57-63
-
-
Zyou, Y.1
Yao, M.2
Tanaka, I.3
-
26
-
-
3543012707
-
Crystallography & NMR system: A new software suite for macromolecular structure determination
-
Brünger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.S., Kuszewski, J., Nilges, M., Pannu, N.S. et al. (1998) Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. Sect. D: Biol. Crystallogr., 54, 905-921.
-
(1998)
Acta Crystallogr. Sect. D: Biol. Crystallogr.
, vol.54
, pp. 905-921
-
-
Brünger, A.T.1
Adams, P.D.2
Clore, G.M.3
DeLano, W.L.4
Gros, P.5
Grosse-Kunstleve, R.W.6
Jiang, J.S.7
Kuszewski, J.8
Nilges, M.9
Pannu, N.S.10
-
28
-
-
0003845223
-
The PyMOL Molecular Graphics System
-
DeLano Scientific, San Carlos, CA, USA
-
DeLano, W.L. (2002) The PyMOL Molecular Graphics System. The PyMOL Molecular Graphics System. DeLano Scientific, San Carlos, CA, USA.
-
(2002)
The PyMOL Molecular Graphics System
-
-
DeLano, W.L.1
-
29
-
-
0034512175
-
Small-angle X-ray scattering station at the SPring-8 RIKEN beamline
-
Fujisawa, T., Inoue, K., Oka, T., Iwamoto, H., Uruga, T., Kumasaka, T., Inoko, Y., Yagi, N., Yamamoto, M. and Ueki, T. (2000) Small-angle X-ray scattering station at the SPring-8 RIKEN beamline. J. Appl. Crystallogr., 33, 797-800.
-
(2000)
J. Appl. Crystallogr.
, vol.33
, pp. 797-800
-
-
Fujisawa, T.1
Inoue, K.2
Oka, T.3
Iwamoto, H.4
Uruga, T.5
Kumasaka, T.6
Inoko, Y.7
Yagi, N.8
Yamamoto, M.9
Ueki, T.10
-
30
-
-
0141484613
-
PRIMUS: a Windows PC-based system for small-angle scattering data analysis
-
Konarev, P.V., Volkov, V.V., Sokolova, A.V., Koch, M.H.J. and Svergun, D.I. (2003) PRIMUS: a Windows PC-based system for small-angle scattering data analysis. J. Appl. Crystallogr., 36, 1277-1282.
-
(2003)
J. Appl. Crystallogr.
, vol.36
, pp. 1277-1282
-
-
Konarev, P.V.1
Volkov, V.V.2
Sokolova, A.V.3
Koch, M.H.J.4
Svergun, D.I.5
-
31
-
-
0026910457
-
Determination of the regularization parameter in indirect-transform methods using perceptual criteria
-
Svergun, D.I. (1992) Determination of the regularization parameter in indirect-transform methods using perceptual criteria. J. Appl. Crystallogr., 25, 495-503.
-
(1992)
J. Appl. Crystallogr.
, vol.25
, pp. 495-503
-
-
Svergun, D.I.1
-
32
-
-
0029185933
-
CRYSOL-a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates
-
Svergun, D.I., Barberato, C. and Koch, M.H.J. (1995) CRYSOL-a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates. J. Appl. Crystallogr., 28, 768-773.
-
(1995)
J. Appl. Crystallogr.
, vol.28
, pp. 768-773
-
-
Svergun, D.I.1
Barberato, C.2
Koch, M.H.J.3
-
33
-
-
37549067728
-
Structure of the yeast tRNA m7G methylation complex
-
Leulliot, N., Chaillet, M., Durand, D., Ulryck, N., Blondeau, K. and van Tilbeurgh, H. (2008) Structure of the yeast tRNA m7G methylation complex. Structure, 16, 52-61.
-
(2008)
Structure
, vol.16
, pp. 52-61
-
-
Leulliot, N.1
Chaillet, M.2
Durand, D.3
Ulryck, N.4
Blondeau, K.5
van Tilbeurgh, H.6
-
34
-
-
42949099523
-
X-ray scattering study of activated Arp2/3 complex with bound actin-WCA
-
Boczkowska, M., Rebowski, G., Petoukhov, M.V., Hayes, D.B., Svergun, D.I. and Dominguez, R. (2008) X-ray scattering study of activated Arp2/3 complex with bound actin-WCA. Structure, 16, 695-704.
-
(2008)
Structure
, vol.16
, pp. 695-704
-
-
Boczkowska, M.1
Rebowski, G.2
Petoukhov, M.V.3
Hayes, D.B.4
Svergun, D.I.5
Dominguez, R.6
-
35
-
-
0033001996
-
Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing
-
Svergun, D.I. (1999) Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. Biophys. J., 76, 2879-2886.
-
(1999)
Biophys. J.
, vol.76
, pp. 2879-2886
-
-
Svergun, D.I.1
-
36
-
-
0037701585
-
Uniqueness of ab initio shape determination in small-angle scattering
-
Volkov, V.V. and Svergun, D.I. (2003) Uniqueness of ab initio shape determination in small-angle scattering. J. Appl. Crystallogr., 36, 860-864.
-
(2003)
J. Appl. Crystallogr.
, vol.36
, pp. 860-864
-
-
Volkov, V.V.1
Svergun, D.I.2
-
37
-
-
0035124442
-
Automated matching of high-and low-resolution structural models
-
Kozin, M.B. and Svergun, D.I. (2001) Automated matching of high-and low-resolution structural models. J. Appl. Crystallogr., 34, 33-41.
-
(2001)
J. Appl. Crystallogr.
, vol.34
, pp. 33-41
-
-
Kozin, M.B.1
Svergun, D.I.2
-
38
-
-
38649095230
-
Assays for transfer RNA-dependent amino acid biosynthesis
-
Sheppard, K., Akochy, P.M. and Söll, D. (2008) Assays for transfer RNA-dependent amino acid biosynthesis. Methods, 44, 139-145.
-
(2008)
Methods
, vol.44
, pp. 139-145
-
-
Sheppard, K.1
Akochy, P.M.2
Söll, D.3
-
39
-
-
3242662773
-
Growth inhibition of Escherichia coli during heterologous expression of Bacillus subtilis glutamyl-tRNA synthetase that catalyzes the formation of mischarged glutamyl-tRNA1Gln
-
Baick, J.W., Yoon, J.H., Namgoong, S., Söll, D., Kim, S.I., Eom, S.H. and Hong, K.W. (2004) Growth inhibition of Escherichia coli during heterologous expression of Bacillus subtilis glutamyl-tRNA synthetase that catalyzes the formation of mischarged glutamyl-tRNA1Gln. J. Microbiol., 42, 111-116.
-
(2004)
J. Microbiol.
, vol.42
, pp. 111-116
-
-
Baick, J.W.1
Yoon, J.H.2
Namgoong, S.3
Söll, D.4
Kim, S.I.5
Eom, S.H.6
Hong, K.W.7
-
40
-
-
0036792830
-
tRNomics: analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features
-
Marck, C. and Grosjean, H. (2002) tRNomics: analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features. RNA, 8, 1189-1232.
-
(2002)
RNA
, vol.8
, pp. 1189-1232
-
-
Marck, C.1
Grosjean, H.2
-
41
-
-
34548690780
-
Indirect readout of tRNA for aminoacylation
-
Perona, J.J. and Hou, Y.M. (2007) Indirect readout of tRNA for aminoacylation. Biochemistry, 46, 10419-10432.
-
(2007)
Biochemistry
, vol.46
, pp. 10419-10432
-
-
Perona, J.J.1
Hou, Y.M.2
-
42
-
-
35348989769
-
The transamidosome: a dynamic ribonucleoprotein particle dedicated to prokaryotic tRNA-dependent asparagine biosynthesis
-
Bailly, M., Blaise, M., Lorber, B., Becker, H.D. and Kern, D. (2007) The transamidosome: a dynamic ribonucleoprotein particle dedicated to prokaryotic tRNA-dependent asparagine biosynthesis. Mol. Cell, 28, 228-239.
-
(2007)
Mol. Cell
, vol.28
, pp. 228-239
-
-
Bailly, M.1
Blaise, M.2
Lorber, B.3
Becker, H.D.4
Kern, D.5
-
43
-
-
36048943978
-
Mechanism of a GatCAB amidotransferase: aspartyl-tRNA synthetase increases its affinity for Asp-tRNAAsn and novel aminoacyl-tRNA analogues are competitive inhibitors
-
Huot, J.L., Balg, C., Jahn, D., Moser, J., Émond, A., Blais, S.P., Chênevert, R. and Lapointe, J. (2007) Mechanism of a GatCAB amidotransferase: aspartyl-tRNA synthetase increases its affinity for Asp-tRNAAsn and novel aminoacyl-tRNA analogues are competitive inhibitors. Biochemistry, 46, 13190-13198.
-
(2007)
Biochemistry
, vol.46
, pp. 13190-13198
-
-
Huot, J.L.1
Balg, C.2
Jahn, D.3
Moser, J.4
Émond, A.5
Blais, S.P.6
Chênevert, R.7
Lapointe, J.8
-
44
-
-
0026429275
-
Asp
-
Ruff, M., Krishnaswamy, S., Boeglin, M., Poterszman, A., Mitschler, A., Podjarny, A., Rees, B., Thierry, J.C. and Moras, D. (1991) Class II aminoacyl transfer RNA synthetases: crystal structure of yeast aspartyl-tRNA synthetase complexed with tRNAAsp. Science, 252, 1682-1689.
-
(1991)
Science
, vol.252
, pp. 1682-1689
-
-
Ruff, M.1
Krishnaswamy, S.2
Boeglin, M.3
Poterszman, A.4
Mitschler, A.5
Podjarny, A.6
Rees, B.7
Thierry, J.C.8
Moras, D.9
-
45
-
-
0035119935
-
Structural basis for anticodon recognition by discriminating glutamyl-tRNA synthetase
-
Sekine, S., Nureki, O., Shimada, A., Vassylyev, D.G. and Yokoyama, S. (2001) Structural basis for anticodon recognition by discriminating glutamyl-tRNA synthetase. Nat. Struct. Biol., 8, 203-206.
-
(2001)
Nat. Struct. Biol.
, vol.8
, pp. 203-206
-
-
Sekine, S.1
Nureki, O.2
Shimada, A.3
Vassylyev, D.G.4
Yokoyama, S.5
-
46
-
-
0032562571
-
Enzyme structure with two catalytic sites for double-sieve selection of substrate
-
Nureki, O., Vassylyev, D.G., Tateno, M., Shimada, A., Nakama, T., Fukai, S., Konno, M., Hendrickson, T.L., Schimmel, P. and Yokoyama, S. (1998) Enzyme structure with two catalytic sites for double-sieve selection of substrate. Science, 280, 578-582.
-
(1998)
Science
, vol.280
, pp. 578-582
-
-
Nureki, O.1
Vassylyev, D.G.2
Tateno, M.3
Shimada, A.4
Nakama, T.5
Fukai, S.6
Konno, M.7
Hendrickson, T.L.8
Schimmel, P.9
Yokoyama, S.10
|