-
1
-
-
0001918945
-
Location and distribution of modified nucleotides in tRNA
-
Grosjean H, Benne R, editors, Washington: ASM Press;
-
Auffinger P, Westhof E. Location and distribution of modified nucleotides in tRNA. In: Grosjean H, Benne R, editors. Modification and editing of RNA. Washington: ASM Press; 1998. pp 569-576.
-
(1998)
Modification and editing of RNA
, pp. 569-576
-
-
Auffinger, P.1
Westhof, E.2
-
2
-
-
33644875540
-
-
Dunin-Horkawicz S, Czerwoniec A, Gajda MJ, Feder M, Grosjean H, Bujnicki JM. MODOMICS: a database of RNA modification pathways. Nucleic Acids Res 2006;34(Database issue):D145-D149.
-
Dunin-Horkawicz S, Czerwoniec A, Gajda MJ, Feder M, Grosjean H, Bujnicki JM. MODOMICS: a database of RNA modification pathways. Nucleic Acids Res 2006;34(Database issue):D145-D149.
-
-
-
-
3
-
-
0031804156
-
Compilation of tRNA sequences and sequences of tRNA genes
-
Sprinzl M, Horn C, Brown M, Ioudovitch A, Steinberg S. Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res 1998;26:148-153.
-
(1998)
Nucleic Acids Res
, vol.26
, pp. 148-153
-
-
Sprinzl, M.1
Horn, C.2
Brown, M.3
Ioudovitch, A.4
Steinberg, S.5
-
4
-
-
0000238430
-
Molecular mechanism of codon recognition by tRNA species with modified uridine in the first position of the anticodon
-
Yokoyama S, Watanabe T, Murao K, Ishikura H, Yamaizumi Z, Nishimura S, Miyazawa T. Molecular mechanism of codon recognition by tRNA species with modified uridine in the first position of the anticodon. Proc Natl Acad Sci USA 1985;82:4905-4909.
-
(1985)
Proc Natl Acad Sci USA
, vol.82
, pp. 4905-4909
-
-
Yokoyama, S.1
Watanabe, T.2
Murao, K.3
Ishikura, H.4
Yamaizumi, Z.5
Nishimura, S.6
Miyazawa, T.7
-
5
-
-
34249870122
-
Mechanism for expanding the decoding capacity of transfer RNAs by modification of uridines
-
Weixlbaumer A, Murphy FVt, Dziergowska A, Malkiewicz A, Vendeix FA, Agris PF, Ramakrishnan V. Mechanism for expanding the decoding capacity of transfer RNAs by modification of uridines. Nat Struct Mol Biol 2007;14:498-502.
-
(2007)
Nat Struct Mol Biol
, vol.14
, pp. 498-502
-
-
Weixlbaumer, A.1
Murphy, F.V.2
Dziergowska, A.3
Malkiewicz, A.4
Vendeix, F.A.5
Agris, P.F.6
Ramakrishnan, V.7
-
6
-
-
33846269602
-
tRNA's wobble decoding of the genome: 40 years of modification
-
Agris PF, Vendeix FA, Graham WD. tRNA's wobble decoding of the genome: 40 years of modification. J Mol Biol 2007;366:1-13.
-
(2007)
J Mol Biol
, vol.366
, pp. 1-13
-
-
Agris, P.F.1
Vendeix, F.A.2
Graham, W.D.3
-
7
-
-
0029894141
-
NMR studies of the effects of the 5′-phosphate group on conformational properties of 5- methylaminomethyluridine found in the first position of the anticodon of Escherichia coli tRNA(Arg)4
-
Sakamoto K, Kawai G, Watanabe S, Niimi T, Hayashi N, Muto Y, Watanabe K, Satoh T, Sekine M, Yokoyama S. NMR studies of the effects of the 5′-phosphate group on conformational properties of 5- methylaminomethyluridine found in the first position of the anticodon of Escherichia coli tRNA(Arg)4. Biochemistry 1996;35:6533-6538.
-
(1996)
Biochemistry
, vol.35
, pp. 6533-6538
-
-
Sakamoto, K.1
Kawai, G.2
Watanabe, S.3
Niimi, T.4
Hayashi, N.5
Muto, Y.6
Watanabe, K.7
Satoh, T.8
Sekine, M.9
Yokoyama, S.10
-
8
-
-
0032553438
-
Reduced misreading of asparagine codons by Escherichia coli tRNALys with hypomodified derivatives of 5-methylaminomethyl-2-thiouridine in the wobble position
-
Hagervall TG, Pomerantz SC, McCloskey JA. Reduced misreading of asparagine codons by Escherichia coli tRNALys with hypomodified derivatives of 5-methylaminomethyl-2-thiouridine in the wobble position. J Mol Biol 1998;284:33-42.
-
(1998)
J Mol Biol
, vol.284
, pp. 33-42
-
-
Hagervall, T.G.1
Pomerantz, S.C.2
McCloskey, J.A.3
-
9
-
-
0345531141
-
Roles of 5-substituents of tRNA wobble uridines in the recognition of purine-ending codons
-
Takai K, Yokoyama S. Roles of 5-substituents of tRNA wobble uridines in the recognition of purine-ending codons. Nucleic Acids Res 2003;31:6383-6391.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 6383-6391
-
-
Takai, K.1
Yokoyama, S.2
-
10
-
-
0021941805
-
Antisuppressor mutation in Escherichia coli defective in biosynthesis of 5-methylaminomethyl-2- thiouridine
-
Sullivan MA, Cannon JF, Webb FH, Bock RM. Antisuppressor mutation in Escherichia coli defective in biosynthesis of 5-methylaminomethyl-2- thiouridine. J Bacteriol 1985;161:368-376.
-
(1985)
J Bacteriol
, vol.161
, pp. 368-376
-
-
Sullivan, M.A.1
Cannon, J.F.2
Webb, F.H.3
Bock, R.M.4
-
11
-
-
0037417771
-
MnmA and IscS are required for in vitro 2-thiouridine biosynthesis in Escherichia coli
-
Kambampati R, Lauhon CT. MnmA and IscS are required for in vitro 2-thiouridine biosynthesis in Escherichia coli. Biochemistry 2003;42:1109-1117.
-
(2003)
Biochemistry
, vol.42
, pp. 1109-1117
-
-
Kambampati, R.1
Lauhon, C.T.2
-
12
-
-
29544452864
-
Mechanistic insights into sulfur relay by multiple sulfur mediators involved in thiouridine biosynthesis at tRNA wobble positions
-
Ikeuchi Y, Shigi N, Kato J, Nishimura A, Suzuki T. Mechanistic insights into sulfur relay by multiple sulfur mediators involved in thiouridine biosynthesis at tRNA wobble positions. Mol Cell 2006;21:97-108.
-
(2006)
Mol Cell
, vol.21
, pp. 97-108
-
-
Ikeuchi, Y.1
Shigi, N.2
Kato, J.3
Nishimura, A.4
Suzuki, T.5
-
13
-
-
32044441001
-
Structural basis for sulfur relay to RNA mediated by heterohexameric TusBCD complex
-
Numata T, Fukai S, Ikeuchi Y, Suzuki T, Nureki O. Structural basis for sulfur relay to RNA mediated by heterohexameric TusBCD complex. Structure 2006;14:357-366.
-
(2006)
Structure
, vol.14
, pp. 357-366
-
-
Numata, T.1
Fukai, S.2
Ikeuchi, Y.3
Suzuki, T.4
Nureki, O.5
-
14
-
-
0020511286
-
The role of 2-methylthio-N6- isopentenyladenosine in readthrough and suppression of nonsense codons in Escherichia coli
-
Petrullo LA, Gallagher PJ, Elseviers D. The role of 2-methylthio-N6- isopentenyladenosine in readthrough and suppression of nonsense codons in Escherichia coli. Mol Gen Genet 1983;190:289-294.
-
(1983)
Mol Gen Genet
, vol.190
, pp. 289-294
-
-
Petrullo, L.A.1
Gallagher, P.J.2
Elseviers, D.3
-
15
-
-
0033573089
-
The Escherichia coli trmE (mnmE) gene, involved in tRNA modification, codes for an evolutionarily conserved GTPase with unusual biochemical properties
-
Cabedo H, Macian F, Villarroya M, Escudero JC, Martinez-Vicente M, Knecht E, Armengod ME. The Escherichia coli trmE (mnmE) gene, involved in tRNA modification, codes for an evolutionarily conserved GTPase with unusual biochemical properties. EMBO J 1999;18:7063-7076.
-
(1999)
EMBO J
, vol.18
, pp. 7063-7076
-
-
Cabedo, H.1
Macian, F.2
Villarroya, M.3
Escudero, J.C.4
Martinez-Vicente, M.5
Knecht, E.6
Armengod, M.E.7
-
16
-
-
0035449350
-
Translational misreading: A tRNA modification counteracts a +2 ribosomal frameshift
-
Bregeon D, Colot V, Radman M, Taddei F. Translational misreading: a tRNA modification counteracts a +2 ribosomal frameshift. Genes Dev 2001;15:2295-2306.
-
(2001)
Genes Dev
, vol.15
, pp. 2295-2306
-
-
Bregeon, D.1
Colot, V.2
Radman, M.3
Taddei, F.4
-
17
-
-
33845672606
-
Further insights into the tRNA modification process controlled by proteins MnmE and GidA of Escherichia coli
-
Yim L, Moukadiri I, Bjork GR, Armengod ME. Further insights into the tRNA modification process controlled by proteins MnmE and GidA of Escherichia coli Nucleic Acids Res 2006;34:5892-5905.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 5892-5905
-
-
Yim, L.1
Moukadiri, I.2
Bjork, G.R.3
Armengod, M.E.4
-
18
-
-
0023664535
-
Transfer RNA(5-methylaminomethyl-2-thiouridine) -methyltransferase from Escherichia coli K-12 has two enzymatic activities
-
Hagervall TG, Edmonds CG, McCloskey JA, Bjork GR. Transfer RNA(5-methylaminomethyl-2-thiouridine) -methyltransferase from Escherichia coli K-12 has two enzymatic activities. J Biol Chem 1987;262:8488-8495.
-
(1987)
J Biol Chem
, vol.262
, pp. 8488-8495
-
-
Hagervall, T.G.1
Edmonds, C.G.2
McCloskey, J.A.3
Bjork, G.R.4
-
19
-
-
3343024377
-
Identification of a bifunctional enzyme MnmC involved in the biosynthesis of a hypermodified uridine in the wobble position of tRNA
-
Bujnicki JM, Oudjama Y, Roovers M, Owczarek S, Caillet J, Droogmans L. Identification of a bifunctional enzyme MnmC involved in the biosynthesis of a hypermodified uridine in the wobble position of tRNA. RNA 2004;10:1236-1242.
-
(2004)
RNA
, vol.10
, pp. 1236-1242
-
-
Bujnicki, J.M.1
Oudjama, Y.2
Roovers, M.3
Owczarek, S.4
Caillet, J.5
Droogmans, L.6
-
20
-
-
12544259245
-
Mitochondria-specific RNA-modifying enzymes responsible for the biosynthesis of the wobble base in mitochondrial tRNAs. Implications for the molecular pathogenesis of human mitochondrial diseases
-
Umeda N, Suzuki T, Yukawa M, Ohya Y, Shindo H, Watanabe K, Suzuki T. Mitochondria-specific RNA-modifying enzymes responsible for the biosynthesis of the wobble base in mitochondrial tRNAs. Implications for the molecular pathogenesis of human mitochondrial diseases. J Biol Chem 2005;280:1613-1624.
-
(2005)
J Biol Chem
, vol.280
, pp. 1613-1624
-
-
Umeda, N.1
Suzuki, T.2
Yukawa, M.3
Ohya, Y.4
Shindo, H.5
Watanabe, K.6
Suzuki, T.7
-
21
-
-
0345826117
-
Functional diversity of the rhodanese homology domain: The Escherichia coli ybbB gene encodes a selenophosphate-dependent tRNA 2-selenouridine synthase
-
Wolfe MD, Ahmed F, Lacourciere GM, Lauhon CT, Stadtman TC, Larson TJ. Functional diversity of the rhodanese homology domain: the Escherichia coli ybbB gene encodes a selenophosphate-dependent tRNA 2-selenouridine synthase. J Biol Chem 2004;279:1801-1809.
-
(2004)
J Biol Chem
, vol.279
, pp. 1801-1809
-
-
Wolfe, M.D.1
Ahmed, F.2
Lacourciere, G.M.3
Lauhon, C.T.4
Stadtman, T.C.5
Larson, T.J.6
-
22
-
-
20044392729
-
A "gain of function" mutation in a protein mediates production of novel modified nucleosides
-
Chen P, Crain PF, Nasvall SJ, Pomerantz SC, Bjork GR. A "gain of function" mutation in a protein mediates production of novel modified nucleosides. EMBO J 2005;24:1842-1851.
-
(2005)
EMBO J
, vol.24
, pp. 1842-1851
-
-
Chen, P.1
Crain, P.F.2
Nasvall, S.J.3
Pomerantz, S.C.4
Bjork, G.R.5
-
23
-
-
33747125139
-
Snapshots of tRNA sulphuration via an adenylated intermediate
-
Numata T, Ikeuchi Y, Fukai S, Suzuki T, Nureki O. Snapshots of tRNA sulphuration via an adenylated intermediate. Nature 2006;442:419-424.
-
(2006)
Nature
, vol.442
, pp. 419-424
-
-
Numata, T.1
Ikeuchi, Y.2
Fukai, S.3
Suzuki, T.4
Nureki, O.5
-
24
-
-
13244284641
-
The structure of the TrmE GTP-binding protein and its implications for tRNA modification
-
Scrima A, Vetter IR, Armengod ME, Wittinghofer A. The structure of the TrmE GTP-binding protein and its implications for tRNA modification. EMBO J 2005;24:23-33.
-
(2005)
EMBO J
, vol.24
, pp. 23-33
-
-
Scrima, A.1
Vetter, I.R.2
Armengod, M.E.3
Wittinghofer, A.4
-
25
-
-
33745520400
-
Dimerisation-dependent GTPase reaction of MnmE: How potassium acts as GTPase-activating element
-
Scrima A, Wittinghofer A. Dimerisation-dependent GTPase reaction of MnmE: how potassium acts as GTPase-activating element. EMBO J 2006;25:2940-2951.
-
(2006)
EMBO J
, vol.25
, pp. 2940-2951
-
-
Scrima, A.1
Wittinghofer, A.2
-
26
-
-
0043123216
-
GeneSilico protein structure prediction meta-server
-
Kurowski MA, Bujnicki JM. GeneSilico protein structure prediction meta-server. Nucleic Acids Res 2003;31:3305-3307.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3305-3307
-
-
Kurowski, M.A.1
Bujnicki, J.M.2
-
27
-
-
0242362160
-
A "Frankenstein's monster" approach to comparative modeling: Merging the finest fragments of fold-recognition models and iterative model refinement aided by 3D structure evaluation
-
Kosinski J, Cymerman IA, Feder M, Kurowski MA, Sasin JM, Bujnicki JM. A "Frankenstein's monster" approach to comparative modeling: merging the finest fragments of fold-recognition models and iterative model refinement aided by 3D structure evaluation. Proteins 2003;53(Suppl. 6):369-379.
-
(2003)
Proteins
, vol.53
, Issue.SUPPL. 6
, pp. 369-379
-
-
Kosinski, J.1
Cymerman, I.A.2
Feder, M.3
Kurowski, M.A.4
Sasin, J.M.5
Bujnicki, J.M.6
-
28
-
-
30344466041
-
FRankenstein becomes a cyborg: The automatic recombination and realignment of fold recognition models in CASP6
-
Kosinski J, Gajda MJ, Cymerman IA, Kurowski MA, Pawlowski M, Boniecki M, Obarska A, Papaj G, Sroczynska-Obuchowicz P, Tkaczuk KL, Sniezynska P, Sasin JM, Augustyn A, Bujnicki JM, Feder M. FRankenstein becomes a cyborg: the automatic recombination and realignment of fold recognition models in CASP6. Proteins 2005;61(Suppl. 7):106-113.
-
(2005)
Proteins
, vol.61
, Issue.SUPPL. 7
, pp. 106-113
-
-
Kosinski, J.1
Gajda, M.J.2
Cymerman, I.A.3
Kurowski, M.A.4
Pawlowski, M.5
Boniecki, M.6
Obarska, A.7
Papaj, G.8
Sroczynska-Obuchowicz, P.9
Tkaczuk, K.L.10
Sniezynska, P.11
Sasin, J.M.12
Augustyn, A.13
Bujnicki, J.M.14
Feder, M.15
-
29
-
-
0037406141
-
Can correct protein models be identified?
-
Wallner B, Elofsson A. Can correct protein models be identified? Protein Sci 2003;12:1073-1086.
-
(2003)
Protein Sci
, vol.12
, pp. 1073-1086
-
-
Wallner, B.1
Elofsson, A.2
-
30
-
-
3242877198
-
-
Sasin JM, Bujnicki JM. COLORADO3D, a web server for the visual analysis of protein structures. Nucleic Acids Res 2004;32(Web Server issue):W586-W589.
-
Sasin JM, Bujnicki JM. COLORADO3D, a web server for the visual analysis of protein structures. Nucleic Acids Res 2004;32(Web Server issue):W586-W589.
-
-
-
-
31
-
-
17444372787
-
Improved prediction of protein-protein binding sites using a support vector machines approach
-
Bradford JR, Westhead DR. Improved prediction of protein-protein binding sites using a support vector machines approach. Bioinformatics 2005;21:1487-1494.
-
(2005)
Bioinformatics
, vol.21
, pp. 1487-1494
-
-
Bradford, J.R.1
Westhead, D.R.2
-
32
-
-
0037442962
-
HADDOCK: A protein-protein docking approach based on biochemical or biophysical information
-
Dominguez C, Boelens R, Bonvin AM. HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J Am Chem Soc 2003;125:1731-1737.
-
(2003)
J Am Chem Soc
, vol.125
, pp. 1731-1737
-
-
Dominguez, C.1
Boelens, R.2
Bonvin, A.M.3
-
33
-
-
0032566485
-
Chromatographic determination of flavin derivatives in baker's yeast
-
Gliszczynska A, Koziolowa A. Chromatographic determination of flavin derivatives in baker's yeast. J Chromatogr A 1998;822:59-66.
-
(1998)
J Chromatogr A
, vol.822
, pp. 59-66
-
-
Gliszczynska, A.1
Koziolowa, A.2
-
34
-
-
0034780030
-
Peons: A neural-network-based consensus predictor that improves fold recognition
-
Lundstrom J, Rychlewski L, Bujnicki J, Elofsson A. Peons: a neural-network-based consensus predictor that improves fold recognition. Protein Sci 2001;10:2354-2362.
-
(2001)
Protein Sci
, vol.10
, pp. 2354-2362
-
-
Lundstrom, J.1
Rychlewski, L.2
Bujnicki, J.3
Elofsson, A.4
-
35
-
-
0033302662
-
6-adenine DNA methylation
-
6-adenine DNA methylation. In Silico Biol 1999;1:175-182.
-
(1999)
In Silico Biol
, vol.1
, pp. 175-182
-
-
Bujnicki, J.M.1
-
36
-
-
0036142291
-
The crystal structure of spermidine synthase with a multisubstrate adduct inhibitor
-
Korolev S, Ikeguchi Y, Skarina T, Beasley S, Arrowsmith C, Edwards A, Joachimiak A, Pegg AE, Savchenko A. The crystal structure of spermidine synthase with a multisubstrate adduct inhibitor. Nat Struct Biol 2002;9:27-31.
-
(2002)
Nat Struct Biol
, vol.9
, pp. 27-31
-
-
Korolev, S.1
Ikeguchi, Y.2
Skarina, T.3
Beasley, S.4
Arrowsmith, C.5
Edwards, A.6
Joachimiak, A.7
Pegg, A.E.8
Savchenko, A.9
-
37
-
-
20544464874
-
Crystal structure of heterotetrameric sarcosine oxidase from Corynebacterium sp. U-96
-
Ida K, Moriguchi T, Suzuki H. Crystal structure of heterotetrameric sarcosine oxidase from Corynebacterium sp. U-96. Biochem Biophys Res Commun 2005;333:359-366.
-
(2005)
Biochem Biophys Res Commun
, vol.333
, pp. 359-366
-
-
Ida, K.1
Moriguchi, T.2
Suzuki, H.3
-
38
-
-
27844530636
-
Natural history of S-adenosylmethionine-binding proteins
-
Kozbial PZ, Mushegian AR. Natural history of S-adenosylmethionine-binding proteins. BMC Struct Biol 2005;5:19.
-
(2005)
BMC Struct Biol
, vol.5
, pp. 19
-
-
Kozbial, P.Z.1
Mushegian, A.R.2
-
39
-
-
0034746572
-
Structure of the N6-adenine DNA methyltransferase M.TaqI in complex with DNA and a cofactor analog
-
Goedecke K, Pignot M, Goody RS, Scheidig AJ, Weinhold E. Structure of the N6-adenine DNA methyltransferase M.TaqI in complex with DNA and a cofactor analog. Nat Struct Biol 2001;8:121-125.
-
(2001)
Nat Struct Biol
, vol.8
, pp. 121-125
-
-
Goedecke, K.1
Pignot, M.2
Goody, R.S.3
Scheidig, A.J.4
Weinhold, E.5
-
40
-
-
0028204489
-
Sculpting proteins interactively: Continual energy minimization embedded in a graphical modeling system
-
Surles MC, Richardson JS, Richardson DC, Brooks-FP J. Sculpting proteins interactively: continual energy minimization embedded in a graphical modeling system. Protein Sci 1994;3:198-210.
-
(1994)
Protein Sci
, vol.3
, pp. 198-210
-
-
Surles, M.C.1
Richardson, J.S.2
Richardson, D.C.3
Brooks-FP, J.4
-
42
-
-
34547829268
-
Functional specialization of domains tandemly duplicated within 16S rRNA methyltransferase RsmC
-
Sunita S, Purta E, Durawa M, Tkaczuk KL, Swaathi J, Bujnicki JM, Sivaraman J. Functional specialization of domains tandemly duplicated within 16S rRNA methyltransferase RsmC. Nucleic Acids Res 2007;35:4264-4274.
-
(2007)
Nucleic Acids Res
, vol.35
, pp. 4264-4274
-
-
Sunita, S.1
Purta, E.2
Durawa, M.3
Tkaczuk, K.L.4
Swaathi, J.5
Bujnicki, J.M.6
Sivaraman, J.7
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