-
1
-
-
0025580878
-
The numerous modified nucleotides in eukaryotic ribosomal RNA
-
Maden B.E.H. The numerous modified nucleotides in eukaryotic ribosomal RNA. Prog. Nucl. Acid Res. Mol. Biol. 39:1990;241-300.
-
(1990)
Prog. Nucl. Acid Res. Mol. Biol.
, vol.39
, pp. 241-300
-
-
Maden, B.E.H.1
-
2
-
-
0037029086
-
Ribosomal RNA pseudouridines and pseudouridine synthases
-
Ofengand J. Ribosomal RNA pseudouridines and pseudouridine synthases. FEBS Letters. 514:2002;17-25.
-
(2002)
FEBS Letters
, vol.514
, pp. 17-25
-
-
Ofengand, J.1
-
3
-
-
0031581856
-
Mapping to nucleotide resolution of pseudouridine residues in large subunit ribosomal RNAs from representative eukaryotes, archaebacteria, mitochondria and chloroplasts
-
Ofengand J., Bakin A. Mapping to nucleotide resolution of pseudouridine residues in large subunit ribosomal RNAs from representative eukaryotes, archaebacteria, mitochondria and chloroplasts. J. Mol. Biol. 266:1997;246-268.
-
(1997)
J. Mol. Biol.
, vol.266
, pp. 246-268
-
-
Ofengand, J.1
Bakin, A.2
-
4
-
-
0028088197
-
The single pseudouridine residue in Escherichia coli 16 S RNA is located at position 516
-
Bakin A., Kowalak J.A., McCloskey J.A., Ofengand J. The single pseudouridine residue in Escherichia coli 16 S RNA is located at position 516. Nucl. Acids Res. 22:1994;3681-3684.
-
(1994)
Nucl. Acids Res.
, vol.22
, pp. 3681-3684
-
-
Bakin, A.1
Kowalak, J.A.2
Mccloskey, J.A.3
Ofengand, J.4
-
5
-
-
0029883720
-
Structural characterization of U*-1915 in domain IV from Escherichia coli 23 S ribosomal RNA as 3-methylpseudouridine
-
Kowalak J.A., Bruenger E., Hashizume T., Peltier J.M., Ofengand J., McCloskey J.A. Structural characterization of U*-1915 in domain IV from Escherichia coli 23 S ribosomal RNA as 3-methylpseudouridine. Nucl. Acids Res. 24:1996;688-693.
-
(1996)
Nucl. Acids Res.
, vol.24
, pp. 688-693
-
-
Kowalak, J.A.1
Bruenger, E.2
Hashizume, T.3
Peltier, J.M.4
Ofengand, J.5
Mccloskey, J.A.6
-
6
-
-
0035805213
-
Crystal structure of the ribosome at 5.5 Å resolution
-
Yusupov M.M., Yusupova G.Z., Baucom A., Lieberman K., Earnest T.N., Cate J.H.D., Noller H.F. Crystal structure of the ribosome at 5.5 Å resolution. Science. 292:2001;883-896.
-
(2001)
Science
, vol.292
, pp. 883-896
-
-
Yusupov, M.M.1
Yusupova, G.Z.2
Baucom, A.3
Lieberman, K.4
Earnest, T.N.5
Cate, J.H.D.6
Noller, H.F.7
-
7
-
-
0034657608
-
Unique structural and stabilizing roles for the individual pseudouridine residues in the 1920 region of Escherichia coli 23 S rRNA
-
Meroueh M., Grohar P.J., Qiu J., SantaLucia J. Jr, Scaringe S.A., Chow C.S. Unique structural and stabilizing roles for the individual pseudouridine residues in the 1920 region of Escherichia coli 23 S rRNA. Nucl. Acids Res. 28:2000;2975-2983.
-
(2000)
Nucl. Acids Res.
, vol.28
, pp. 2975-2983
-
-
Meroueh, M.1
Grohar, P.J.2
Qiu, J.3
Santalucia Jr., J.4
Scaringe, S.A.5
Chow, C.S.6
-
8
-
-
0029832294
-
Identification of new RNA modifying enzymes by iterative genome search using known modifying enzymes as probes
-
Gustafsson C., Reid R., Greene P.J., Santi D.V. Identification of new RNA modifying enzymes by iterative genome search using known modifying enzymes as probes. Nucl. Acids Res. 24:1996;3756-3762.
-
(1996)
Nucl. Acids Res.
, vol.24
, pp. 3756-3762
-
-
Gustafsson, C.1
Reid, R.2
Greene, P.J.3
Santi, D.V.4
-
9
-
-
0029945504
-
Pseudouridine synthases: Four families of enzymes containing a putative uridine-binding motif also conserved in dUTPases and dCTP deaminases
-
Koonin E.V. Pseudouridine synthases: four families of enzymes containing a putative uridine-binding motif also conserved in dUTPases and dCTP deaminases. Nucl. Acids Res. 24:1996;2411-2415.
-
(1996)
Nucl. Acids Res.
, vol.24
, pp. 2411-2415
-
-
Koonin, E.V.1
-
10
-
-
0038475918
-
A novel unanticipated type of pseudouridine synthase with homologs in bacteria, archae and eukarya
-
Kaya Y., Ofengand J. A novel unanticipated type of pseudouridine synthase with homologs in bacteria, archae and eukarya. RNA. 9:2003;711-721.
-
(2003)
RNA
, vol.9
, pp. 711-721
-
-
Kaya, Y.1
Ofengand, J.2
-
11
-
-
0035163770
-
Identification and site of action of the remaining four pseudouridine synthases in Escherichia coli
-
Del Campo M., Kaya Y., Ofengand J. Identification and site of action of the remaining four pseudouridine synthases in Escherichia coli. RNA. 7:2001;1603-1615.
-
(2001)
RNA
, vol.7
, pp. 1603-1615
-
-
Del Campo, M.1
Kaya, Y.2
Ofengand, J.3
-
12
-
-
0032506248
-
Identification of two Escherichia coli pseudouridine synthases that show multisite specificity for 23 S RNA
-
Huang L., Ku J., Pookanjanatavip M., Gu X., Wang D., Greene P.J., Santi D.V. Identification of two Escherichia coli pseudouridine synthases that show multisite specificity for 23 S RNA. Biochemistry. 37:1998;15951-15957.
-
(1998)
Biochemistry
, vol.37
, pp. 15951-15957
-
-
Huang, L.1
Ku, J.2
Pookanjanatavip, M.3
Gu, X.4
Wang, D.5
Greene, P.J.6
Santi, D.V.7
-
13
-
-
0031787478
-
A pseudouridine synthase required for the formation of two universally conserved pseudouridines in ribosomal RNA is essential for normal growth of Escherichia coli
-
Raychaudhuri S., Conrad J., Hall B.G., Ofengand J. A pseudouridine synthase required for the formation of two universally conserved pseudouridines in ribosomal RNA is essential for normal growth of Escherichia coli. RNA. 4:1998;1407-1417.
-
(1998)
RNA
, vol.4
, pp. 1407-1417
-
-
Raychaudhuri, S.1
Conrad, J.2
Hall, B.G.3
Ofengand, J.4
-
14
-
-
0033794542
-
Isolation and properties of Escherichia coli 23 S-rRNA pseudouridine 1911, 1915, 1917 synthase (RluD)
-
Wrzesinski J., Bakin A., Ofengand J., Lane B.G. Isolation and properties of Escherichia coli 23 S-rRNA pseudouridine 1911, 1915, 1917 synthase (RluD). IUBMB Life. 50:2000;33-37.
-
(2000)
IUBMB Life
, vol.50
, pp. 33-37
-
-
Wrzesinski, J.1
Bakin, A.2
Ofengand, J.3
Lane, B.G.4
-
15
-
-
0034961963
-
A second function for pseudouridine synthases: A point mutant of RluD unable to form pseudouridines 1911, 1915 and 1917 in Escherichia coli 23 S ribosomal RNA restores growth to an RluD-minus strain
-
Gutgsell N.S., Del Campo M., Raychaudhuri S., Ofengand J. A second function for pseudouridine synthases: a point mutant of RluD unable to form pseudouridines 1911, 1915 and 1917 in Escherichia coli 23 S ribosomal RNA restores growth to an RluD-minus strain. RNA. 7:2001;990-998.
-
(2001)
RNA
, vol.7
, pp. 990-998
-
-
Gutgsell, N.S.1
Del Campo, M.2
Raychaudhuri, S.3
Ofengand, J.4
-
16
-
-
0141880634
-
Pseudouridines and pseudouridine synthases of the ribosome
-
Ofengand J., Malhorta A., Remme J., Gutgsell N.S., Del Campo M., Jean-Charles S., et al. Pseudouridines and pseudouridine synthases of the ribosome. Cold Spring Harbor Symp. Quant. Biol. 66:2001;147-159.
-
(2001)
Cold Spring Harbor Symp. Quant. Biol.
, vol.66
, pp. 147-159
-
-
Ofengand, J.1
Malhorta, A.2
Remme, J.3
Gutgsell, N.S.4
Del Campo, M.5
Jean-Charles, S.6
-
17
-
-
0033987499
-
The structural basis for tRNA recognition and pseudouridine formation by pseudouridine synthase I
-
Foster P.G., Huang L., Santi D.V., Stroud R.M. The structural basis for tRNA recognition and pseudouridine formation by pseudouridine synthase I. Nature Struct. Biol. 7:2000;23-27.
-
(2000)
Nature Struct. Biol.
, vol.7
, pp. 23-27
-
-
Foster, P.G.1
Huang, L.2
Santi, D.V.3
Stroud, R.M.4
-
18
-
-
0035966271
-
Co-crystal structure of a tRNA Ψ55 pseudouridine synthase: Nucleotide flipping by an RNA-modifying enzyme
-
Hoang C., Ferré-D'Amaré A.R. Co-crystal structure of a tRNA Ψ55 pseudouridine synthase: nucleotide flipping by an RNA-modifying enzyme. Cell. 71:2001;929-939.
-
(2001)
Cell
, vol.71
, pp. 929-939
-
-
Hoang, C.1
Ferré-D'amaré, A.R.2
-
19
-
-
0036242421
-
Structure of the 16 S rRNA pseudouridine synthase RsuA bound to uracil and UMP
-
Sivaraman J., Sauvé V., Larocque R., Stura E.A., Schrag J.D., Cygler M., Matte A. Structure of the 16 S rRNA pseudouridine synthase RsuA bound to uracil and UMP. Nature Struct. Biol. 9:2002;353-358.
-
(2002)
Nature Struct. Biol.
, vol.9
, pp. 353-358
-
-
Sivaraman, J.1
Sauvé, V.2
Larocque, R.3
Stura, E.A.4
Schrag, J.D.5
Cygler, M.6
Matte, A.7
-
21
-
-
0032488657
-
A conserved aspartate of tRNA pseudouridine synthase is essential for activity and a probable nucleophillic catalyst
-
Huang L., Pookanjanatavip M., Gu X., Santi D.V. A conserved aspartate of tRNA pseudouridine synthase is essential for activity and a probable nucleophillic catalyst. Biochemistry. 37:1998;344-351.
-
(1998)
Biochemistry
, vol.37
, pp. 344-351
-
-
Huang, L.1
Pookanjanatavip, M.2
Gu, X.3
Santi, D.V.4
-
22
-
-
0033435203
-
The mechanism of pseudouridine synthase I as deduced from its interaction with 5-fluorouracil-tRNA
-
Gu Z., Liu Y., Santi D.V. The mechanism of pseudouridine synthase I as deduced from its interaction with 5-fluorouracil-tRNA. Proc. Natl Acad. Sci. USA. 96:1999;14270-14275.
-
(1999)
Proc. Natl Acad. Sci. USA
, vol.96
, pp. 14270-14275
-
-
Gu, Z.1
Liu, Y.2
Santi, D.V.3
-
23
-
-
0036242429
-
Chips off the old block
-
Mueller E.G. Chips off the old block. Nature Struct. Biol. 9:2002;320-322.
-
(2002)
Nature Struct. Biol.
, vol.9
, pp. 320-322
-
-
Mueller, E.G.1
-
24
-
-
0000120520
-
ProDom: Automated clustering of homologous domains
-
Servant F., Bru C., Carrere S., Courcelle E., Gouzy J., Peyruc D., Kahn D. ProDom: automated clustering of homologous domains. Brief. Bioinformat. 3:2002;246-251.
-
(2002)
Brief. Bioinformat.
, vol.3
, pp. 246-251
-
-
Servant, F.1
Bru, C.2
Carrere, S.3
Courcelle, E.4
Gouzy, J.5
Peyruc, D.6
Kahn, D.7
-
25
-
-
0033046425
-
Novel predicted RNA-binding domains associated with the translation machinery
-
Aravind L., Koonin E.V. Novel predicted RNA-binding domains associated with the translation machinery. J. Mol. Evol. 48:1999;291-302.
-
(1999)
J. Mol. Evol.
, vol.48
, pp. 291-302
-
-
Aravind, L.1
Koonin, E.V.2
-
27
-
-
0027440362
-
Protein structure comparison by alignment of distance matrices
-
Holm L., Sander C. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233:1993;123-138.
-
(1993)
J. Mol. Biol.
, vol.233
, pp. 123-138
-
-
Holm, L.1
Sander, C.2
-
28
-
-
0034622568
-
Functional importance of motif I of pseudouridine synthases: Mutagenesis of aligned lysine and proline residues
-
Spedaliere C.J., Hamilton C.S., Mueller E.G. Functional importance of motif I of pseudouridine synthases: mutagenesis of aligned lysine and proline residues. Biochemistry. 39:2000;9459-9465.
-
(2000)
Biochemistry
, vol.39
, pp. 9459-9465
-
-
Spedaliere, C.J.1
Hamilton, C.S.2
Mueller, E.G.3
-
29
-
-
0029402597
-
The pseudouridine residues of ribosomal RNA
-
Ofengand J., Bakin A., Wrzesinski J., Nurse K., Lane B.G. The pseudouridine residues of ribosomal RNA. Biochem. Cell Biol. 73:1995;915-924.
-
(1995)
Biochem. Cell Biol.
, vol.73
, pp. 915-924
-
-
Ofengand, J.1
Bakin, A.2
Wrzesinski, J.3
Nurse, K.4
Lane, B.G.5
-
30
-
-
0026319199
-
Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons
-
Nicholls A., Sharp K.A., Honig B. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins: Struct. Funct. Genet. 11:1991;281-296.
-
(1991)
Proteins: Struct. Funct. Genet.
, vol.11
, pp. 281-296
-
-
Nicholls, A.1
Sharp, K.A.2
Honig, B.3
-
31
-
-
0023851755
-
Purification, structure and properties of Escherichia coli tRNA pseudouridine synthase I
-
Kammen H.O., Marvel C.C., Hardy L., Penhoet E.E. Purification, structure and properties of Escherichia coli tRNA pseudouridine synthase I. J. Biol. Chem. 263:1988;2255-2263.
-
(1988)
J. Biol. Chem.
, vol.263
, pp. 2255-2263
-
-
Kammen, H.O.1
Marvel, C.C.2
Hardy, L.3
Penhoet, E.E.4
-
32
-
-
0033516555
-
Functional effect of deletion and mutation of the Escherichia coli ribosomal RNA and tRNA pseudouridine synthase RluA
-
Raychaudhuri S., Niu L., Conrad J., Lane B.G., Ofengand J. Functional effect of deletion and mutation of the Escherichia coli ribosomal RNA and tRNA pseudouridine synthase RluA. J. Biol. Chem. 274:1999;18880-18886.
-
(1999)
J. Biol. Chem.
, vol.274
, pp. 18880-18886
-
-
Raychaudhuri, S.1
Niu, L.2
Conrad, J.3
Lane, B.G.4
Ofengand, J.5
-
33
-
-
0033529594
-
Critical aspartic acid residues in pseudouridine synthases
-
Ramamurthy V., Swann S.L., Paulson J.L., Spedaliere C.J., Mueller E.G. Critical aspartic acid residues in pseudouridine synthases. J. Biol. Chem. 274:1999;22225-22230.
-
(1999)
J. Biol. Chem.
, vol.274
, pp. 22225-22230
-
-
Ramamurthy, V.1
Swann, S.L.2
Paulson, J.L.3
Spedaliere, C.J.4
Mueller, E.G.5
-
35
-
-
0029163563
-
RNA chaperones and the RNA folding problem
-
Herschlag D. RNA chaperones and the RNA folding problem. J. Biol. Chem. 270:1995;20871-20874.
-
(1995)
J. Biol. Chem.
, vol.270
, pp. 20871-20874
-
-
Herschlag, D.1
-
36
-
-
0035945586
-
Genome sequence of the enterohaemorrhagic Escherichia coli O157:H7
-
Perna N.T., Plunkett G. III, Burland V., Mau B., Glasner J.D., Rose D.J., et al. Genome sequence of the enterohaemorrhagic Escherichia coli O157:H7. Nature. 409:2001;529-533.
-
(2001)
Nature
, vol.409
, pp. 529-533
-
-
Perna, N.T.1
Plunkett III, G.2
Burland, V.3
Mau, B.4
Glasner, J.D.5
Rose, D.J.6
-
37
-
-
0025262173
-
Selenomethionyl proteins produced for analysis by multiwavelength anaomalous diffraction (MAD): A vehicle for direct determination of three-dimensional structure
-
Hendrickson W.A., Horton J.R., LeMaster D.M. Selenomethionyl proteins produced for analysis by multiwavelength anaomalous diffraction (MAD): a vehicle for direct determination of three-dimensional structure. EMBO J. 9:1990;1665-1672.
-
(1990)
EMBO J.
, vol.9
, pp. 1665-1672
-
-
Hendrickson, W.A.1
Horton, J.R.2
Lemaster, D.M.3
-
38
-
-
0031936811
-
Comparative studies of protein crystallization by vapour-diffusion and microbatch techniques
-
Chayen N.E. Comparative studies of protein crystallization by vapour-diffusion and microbatch techniques. Acta Crystallog. sect. D. 54:1998;8-15.
-
(1998)
Acta Crystallog. sect. D
, vol.54
, pp. 8-15
-
-
Chayen, N.E.1
-
39
-
-
0031059866
-
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. 276:1997;307-326.
-
(1997)
Methods Enzymol.
, vol.276
, pp. 307-326
-
-
Otwinowski, Z.1
Minor, W.2
-
42
-
-
0032964481
-
Automated protein model building combined with iterative structure refinement
-
Perrakis A., Morris R., Lamzin V.S. Automated protein model building combined with iterative structure refinement. Nature Struct. Biol. 6:1999;458-463.
-
(1999)
Nature Struct. Biol.
, vol.6
, pp. 458-463
-
-
Perrakis, A.1
Morris, R.2
Lamzin, V.S.3
-
43
-
-
84889120137
-
Improved methods for building protein models in electron density maps and the location of errors in these models
-
Jones T.A., Zou J.-Y., Cowan S., Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallog. sect. A. 47:1991;100-119.
-
(1991)
Acta Crystallog. sect. A
, vol.47
, pp. 100-119
-
-
Jones, T.A.1
Zou, J.-Y.2
Cowan, S.3
Kjeldgaard, M.4
-
44
-
-
3543012707
-
Crystallography and 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., et al. Crystallography and NMR system: a new software suite for macromolecular structure determination. Acta Crystallog. sect. D. 54:1998;905-921.
-
(1998)
Acta Crystallog. sect. D
, 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
-
45
-
-
0033954256
-
The Protein Data Bank
-
Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., et al. The Protein Data Bank. Nucl. Acids Res. 28:2000;235-242.
-
(2000)
Nucl. Acids Res.
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
-
46
-
-
0033119938
-
Further additions to Molscript version 1.4, including reading and contouring of electron density maps
-
Esnouf R.M. Further additions to Molscript version 1.4, including reading and contouring of electron density maps. Acta Crystallog. sect. D. 55:1999;938-940.
-
(1999)
Acta Crystallog. sect. D
, vol.55
, pp. 938-940
-
-
Esnouf, R.M.1
-
47
-
-
0026244229
-
MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
-
Kraulis P. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallog. 24:1991;946-950.
-
(1991)
J. Appl. Crystallog.
, vol.24
, pp. 946-950
-
-
Kraulis, P.1
-
48
-
-
0030815133
-
Raster3D: Photorealistic molecular graphics
-
Merrit E.A., Bacon D.J. Raster3D: photorealistic molecular graphics. Methods Enzymol. 277:1997;505-524.
-
(1997)
Methods Enzymol.
, vol.277
, pp. 505-524
-
-
Merrit, E.A.1
Bacon, D.J.2
-
50
-
-
0042121237
-
Multiple sequence alignment with the Clustal series of programs
-
Chenna R., Sugawara H., Koike T., Lopez R., Gibson T.J., Higgins D.G., Thompson J.D. Multiple sequence alignment with the Clustal series of programs. Nucl. Acids Res. 31:2003;3497-3500.
-
(2003)
Nucl. Acids Res.
, vol.31
, pp. 3497-3500
-
-
Chenna, R.1
Sugawara, H.2
Koike, T.3
Lopez, R.4
Gibson, T.J.5
Higgins, D.G.6
Thompson, J.D.7
|