메뉴 건너뛰기




Volumn 328, Issue 2, 2003, Pages 395-408

Amino acid discrimination by a class I aminoacyl-tRNA synthetase specified by negative determinants

Author keywords

Electrostatics; Hydrogen bonding; Molecular evolution; QSI, 5 O N (L Glu)sulfamoyl adenosine; RS, tRNA synthetase; Substrate specificity; Water mediated interactions

Indexed keywords

ALPHA CARBOXYLATE; AMIDE; AMINO ACID; AMINO ACID TRANSFER RNA LIGASE; ARGININE; CARBOXYLIC ACID DERIVATIVE; GLUTAMIC ACID; OXYGEN; TRANSFER RNA; UNCLASSIFIED DRUG;

EID: 0037466332     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(03)00305-X     Document Type: Article
Times cited : (87)

References (49)
  • 1
    • 0033782994 scopus 로고    scopus 로고
    • Aminoacyl-tRNA synthesis
    • Ibba M., Söll D. Aminoacyl-tRNA synthesis. Annu. Rev. Biochem. 69:2000;617-650.
    • (2000) Annu. Rev. Biochem. , vol.69 , pp. 617-650
    • Ibba, M.1    Söll, D.2
  • 2
    • 0015378783 scopus 로고
    • The frequency of errors in protein biosynthesis
    • Loftfield R.B., Vanderjagt D. The frequency of errors in protein biosynthesis. Biochem. J. 128:1972;1353-1356.
    • (1972) Biochem. J. , vol.128 , pp. 1353-1356
    • Loftfield, R.B.1    Vanderjagt, D.2
  • 3
    • 0035812828 scopus 로고    scopus 로고
    • Uniform binding of aminoacyl-tRNAs to elongation factor Tu by thermodynamic compensation
    • LaRiviere F.J., Wolfson A.D., Uhlenbeck O.C. Uniform binding of aminoacyl-tRNAs to elongation factor Tu by thermodynamic compensation. Science. 294:2001;165-168.
    • (2001) Science , vol.294 , pp. 165-168
    • LaRiviere, F.J.1    Wolfson, A.D.2    Uhlenbeck, O.C.3
  • 4
    • 0033551859 scopus 로고    scopus 로고
    • Insights into editing from an Ile-tRNA synthetase structure with tRNAIle and mupirocin
    • Silvian L.F., Wang J., Steitz T.A. Insights into editing from an Ile-tRNA synthetase structure with tRNAIle and mupirocin. Science. 285:1999;1074-1077.
    • (1999) Science , vol.285 , pp. 1074-1077
    • Silvian, L.F.1    Wang, J.2    Steitz, T.A.3
  • 5
    • 0028305036 scopus 로고
    • Mutational isolation of a sieve for editing in a transfer RNA synthetase
    • Schmidt E., Schimmel P.R. Mutational isolation of a sieve for editing in a transfer RNA synthetase. Science. 264:1994;265-267.
    • (1994) Science , vol.264 , pp. 265-267
    • Schmidt, E.1    Schimmel, P.R.2
  • 6
    • 0032562571 scopus 로고    scopus 로고
    • 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., et al. Enzyme structure with two catalytic sites for double-sieve selection of substrate. Science. 280:1998;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
  • 7
    • 0034657687 scopus 로고    scopus 로고
    • The 2 Å crystal structure of leucyl-tRNA synthetase and its complex with a leucyl-adenylate analogue
    • Cusack S., Yaremchuk A., Tukalo M. The 2 Å crystal structure of leucyl-tRNA synthetase and its complex with a leucyl-adenylate analogue. EMBO J. 19:2000;2351-2361.
    • (2000) EMBO J. , vol.19 , pp. 2351-2361
    • Cusack, S.1    Yaremchuk, A.2    Tukalo, M.3
  • 9
    • 0027480763 scopus 로고
    • Proofreading and the evolution of a methyl donor function. Cyclization of methionine to S-methyl homocysteine thiolactone by Escherichia coli methionyl-tRNA synthetase
    • Jakubowski H. Proofreading and the evolution of a methyl donor function. Cyclization of methionine to S-methyl homocysteine thiolactone by Escherichia coli methionyl-tRNA synthetase. J. Biol. Chem. 268:1993;6549-6553.
    • (1993) J. Biol. Chem. , vol.268 , pp. 6549-6553
    • Jakubowski, H.1
  • 11
    • 0029643793 scopus 로고
    • Tryptophanyl-tRNA synthetase crystal structure reveals an unexpected homology to tyrosyl-tRNA synthetase
    • Doublié S., Bricogne G., Gilmore G., Carter C.W. Tryptophanyl-tRNA synthetase crystal structure reveals an unexpected homology to tyrosyl-tRNA synthetase. Structure. 3:1995;17-31.
    • (1995) Structure , vol.3 , pp. 17-31
    • Doublié, S.1    Bricogne, G.2    Gilmore, G.3    Carter, C.W.4
  • 12
    • 0024406896 scopus 로고
    • Structure of tyrosyl-tRNA synthetase refined at 2.3 Å resolution. Interaction of the enzyme with the tyrosyl adenylate intermediate
    • Brick P., Bhat T.N., Blow D. Structure of tyrosyl-tRNA synthetase refined at 2.3 Å resolution. Interaction of the enzyme with the tyrosyl adenylate intermediate. J. Mol. Biol. 208:1989;83-98.
    • (1989) J. Mol. Biol. , vol.208 , pp. 83-98
    • Brick, P.1    Bhat, T.N.2    Blow, D.3
  • 13
    • 0035793701 scopus 로고    scopus 로고
    • How methionyl-tRNA synthetase creates its amino acid recognition pocket upon L-methionine binding
    • Serre L., Verdon G., Choinowski T., Hervouet N., Risler J.L., Zelwer C. How methionyl-tRNA synthetase creates its amino acid recognition pocket upon L-methionine binding. J. Mol. Biol. 306:2001;863-876.
    • (2001) J. Mol. Biol. , vol.306 , pp. 863-876
    • Serre, L.1    Verdon, G.2    Choinowski, T.3    Hervouet, N.4    Risler, J.L.5    Zelwer, C.6
  • 15
    • 0037013921 scopus 로고    scopus 로고
    • Structural origins of amino acid selection without editing by cysteinyl-tRNA synthetase
    • Newberry K.J., Hou Y.-M., Perona J.J. Structural origins of amino acid selection without editing by cysteinyl-tRNA synthetase. EMBO J. 21:2002;2778-2787.
    • (2002) EMBO J. , vol.21 , pp. 2778-2787
    • Newberry, K.J.1    Hou, Y.-M.2    Perona, J.J.3
  • 18
    • 0025744320 scopus 로고
    • Structural basis of anticodon loop recognition by glutaminyl-tRNA synthetase
    • Rould M.A., Perona J.J., Steitz T.A. Structural basis of anticodon loop recognition by glutaminyl-tRNA synthetase. Nature. 352:1991;213-218.
    • (1991) Nature , vol.352 , pp. 213-218
    • Rould, M.A.1    Perona, J.J.2    Steitz, T.A.3
  • 19
    • 0027165755 scopus 로고
    • Structural basis for transfer RNA aminoacylation by E. coli glutaminyl-tRNA synthetase
    • Perona J.J., Rould M.A., Steitz T.A. Structural basis for transfer RNA aminoacylation by E. coli glutaminyl-tRNA synthetase. Biochemistry. 32:1993;8758-8771.
    • (1993) Biochemistry , vol.32 , pp. 8758-8771
    • Perona, J.J.1    Rould, M.A.2    Steitz, T.A.3
  • 20
    • 0018826793 scopus 로고
    • The glutaminyl-tRNA synthetase of Escherichia coli. Purification, structure and function relationship
    • Kern D., Potier S., Lapointe J., Boulanger Y. The glutaminyl-tRNA synthetase of Escherichia coli. Purification, structure and function relationship. Biochim. Biophys. Acta. 607:1980;65-80.
    • (1980) Biochim. Biophys. Acta , vol.607 , pp. 65-80
    • Kern, D.1    Potier, S.2    Lapointe, J.3    Boulanger, Y.4
  • 21
    • 0012886315 scopus 로고
    • Doctoral thesis, Department of Molecular Biophysics and Biochemistry, Yale University
    • Gln complex. Doctoral thesis, Department of Molecular Biophysics and Biochemistry, Yale University.
    • (1990) Gln Complex
    • Perona, J.J.1
  • 22
    • 0031977170 scopus 로고    scopus 로고
    • A cognate tRNA specific conformational change in glutaminyl-tRNA synthetase and its implication for specificity
    • Mandal A.K., Bhattacharyya A., Bhattacharyya S., Bhattacharyya T., Roy S. A cognate tRNA specific conformational change in glutaminyl-tRNA synthetase and its implication for specificity. Protein Sci. 7:1998;1046-1051.
    • (1998) Protein Sci. , vol.7 , pp. 1046-1051
    • Mandal, A.K.1    Bhattacharyya, A.2    Bhattacharyya, S.3    Bhattacharyya, T.4    Roy, S.5
  • 23
    • 0025887667 scopus 로고
    • Gln are major recognition elements for E. coli glutaminyl-tRNA synthetase
    • Gln are major recognition elements for E. coli glutaminyl-tRNA synthetase. Nature. 352:1991;258-260.
    • (1991) Nature , vol.352 , pp. 258-260
    • Jahn, M.1    Rogers, M.J.2    Söll, D.3
  • 24
    • 0029902187 scopus 로고    scopus 로고
    • Interactions between tRNA identity nucleotides and their recognition sites in glutaminyl-tRNA synthetase determine the cognate amino acid affinity of the enzyme
    • Ibba M., Hong K.-W., Sherman J.M., Sever S., Söll D. Interactions between tRNA identity nucleotides and their recognition sites in glutaminyl-tRNA synthetase determine the cognate amino acid affinity of the enzyme. Proc. Natl Acad. Sci. USA. 93:1996;6953-6958.
    • (1996) Proc. Natl Acad. Sci. USA , vol.93 , pp. 6953-6958
    • Ibba, M.1    Hong, K.-W.2    Sherman, J.M.3    Sever, S.4    Söll, D.5
  • 25
    • 0029877579 scopus 로고    scopus 로고
    • Transfer RNA-dependent cognate amino acid recognition by an aminoacyl-tRNA synthetase
    • Hong K.-W., Ibba M., Weygand-Durasevic I., Rogers M.J., Thomann H.-U., Söll D. Transfer RNA-dependent cognate amino acid recognition by an aminoacyl-tRNA synthetase. EMBO J. 15:1996;1983-1991.
    • (1996) EMBO J. , vol.15 , pp. 1983-1991
    • Hong, K.-W.1    Ibba, M.2    Weygand-Durasevic, I.3    Rogers, M.J.4    Thomann, H.-U.5    Söll, D.6
  • 26
    • 0032493330 scopus 로고    scopus 로고
    • Gln mediates tRNA-dependent amino acid recognition by glutaminyl-tRNA synthetase
    • Gln mediates tRNA-dependent amino acid recognition by glutaminyl-tRNA synthetase. Biochemistry. 37:1998;9836-9842.
    • (1998) Biochemistry , vol.37 , pp. 9836-9842
    • Liu, J.1    Ibba, M.2    Hong, K.-W.3    Söll, D.4
  • 27
    • 0033609150 scopus 로고    scopus 로고
    • Progress toward the evolution of an organism with an expanded genetic code
    • Liu D.R., Schultz P.G. Progress toward the evolution of an organism with an expanded genetic code. Proc. Natl Acad. Sci. USA. 96:1999;4780-4785.
    • (1999) Proc. Natl Acad. Sci. USA , vol.96 , pp. 4780-4785
    • Liu, D.R.1    Schultz, P.G.2
  • 28
    • 0035956903 scopus 로고    scopus 로고
    • Twenty-first aminoacyl-tRNA synthetase-suppressor tRNA pairs for possible use in site-specific incorporation of amino acid analogues into proteins in eukaryotes and in eubacteria
    • Kowal A.K., Kohrer C., RajBhandary U.L. Twenty-first aminoacyl-tRNA synthetase-suppressor tRNA pairs for possible use in site-specific incorporation of amino acid analogues into proteins in eukaryotes and in eubacteria. Proc. Natl Acad. Sci. USA. 98:2001;2268-2273.
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , pp. 2268-2273
    • Kowal, A.K.1    Kohrer, C.2    RajBhandary, U.L.3
  • 30
    • 0025875873 scopus 로고
    • Occurrence of bifurcated three-center hydrogen-bonds in proteins
    • Preissner R., Egner U., Saenger W. Occurrence of bifurcated three-center hydrogen-bonds in proteins. FEBS Letters. 288:1991;192-196.
    • (1991) FEBS Letters , vol.288 , pp. 192-196
    • Preissner, R.1    Egner, U.2    Saenger, W.3
  • 31
    • 0029873183 scopus 로고    scopus 로고
    • Ground state conformations and entropic and enthalpic factors in the efficiency of intramolecular and enzymatic reactions. 1. Cyclic anhydride formation by substituted glutarates, succinate, and 3,6-endoxo-Δ4-tetrahydrophthalate monophenyl esters
    • Lightstone F.C., Bruice T.C. Ground state conformations and entropic and enthalpic factors in the efficiency of intramolecular and enzymatic reactions. 1. Cyclic anhydride formation by substituted glutarates, succinate, and 3,6-endoxo-Δ4-tetrahydrophthalate monophenyl esters. J. Am. Chem. Soc. 118:1996;2595-2605.
    • (1996) J. Am. Chem. Soc. , vol.118 , pp. 2595-2605
    • Lightstone, F.C.1    Bruice, T.C.2
  • 32
    • 3643114575 scopus 로고    scopus 로고
    • Universal rules and idiosyncratic features in tRNA identity
    • Giegé R., Sissler M., Florentz C. Universal rules and idiosyncratic features in tRNA identity. Nucl. Acids Res. 26:1998;5017-5035.
    • (1998) Nucl. Acids Res. , vol.26 , pp. 5017-5035
    • Giegé, R.1    Sissler, M.2    Florentz, C.3
  • 34
    • 0027372621 scopus 로고
    • Tandem binding in crystals of a trp repressor/operator half-site complex
    • Lawson C.L., Carey J. Tandem binding in crystals of a trp repressor/operator half-site complex. Nature. 366:1993;178-182.
    • (1993) Nature , vol.366 , pp. 178-182
    • Lawson, C.L.1    Carey, J.2
  • 35
    • 0032844737 scopus 로고    scopus 로고
    • Gene descent, duplication, and horizontal transfer in the evolution of glutamyl- and glutaminyl-tRNA synthetases
    • Brown J.R., Doolittle W.F. Gene descent, duplication, and horizontal transfer in the evolution of glutamyl- and glutaminyl-tRNA synthetases. J. Mol. Evol. 49:1999;485-495.
    • (1999) J. Mol. Evol. , vol.49 , pp. 485-495
    • Brown, J.R.1    Doolittle, W.F.2
  • 36
    • 0037415750 scopus 로고    scopus 로고
    • ATP binding by glutamyl-tRNA synthetase is switched to the productive mode by tRNA binding
    • Sekine S., Nureki O., Dubois D.Y., Bernier S., Chenevert R., LaPointe J., et al. ATP binding by glutamyl-tRNA synthetase is switched to the productive mode by tRNA binding. EMBO J. 22:2003;676-688.
    • (2003) EMBO J. , vol.22 , pp. 676-688
    • Sekine, S.1    Nureki, O.2    Dubois, D.Y.3    Bernier, S.4    Chenevert, R.5    LaPointe, J.6
  • 37
    • 0023840230 scopus 로고
    • OmpT encodes the Escherichia coli outer membrane protease that cleaves T7 RNA polymerase during purification
    • Grodberg J., Dunn J.J. OmpT encodes the Escherichia coli outer membrane protease that cleaves T7 RNA polymerase during purification. J. Bacteriol. 170:1988;1245-1258.
    • (1988) J. Bacteriol. , vol.170 , pp. 1245-1258
    • Grodberg, J.1    Dunn, J.J.2
  • 39
    • 0033015536 scopus 로고    scopus 로고
    • An engineered class I transfer RNA with a class II tertiary fold
    • Nissan T.A., Oliphant B.O., Perona J.J. An engineered class I transfer RNA with a class II tertiary fold. RNA. 5:1999;434-445.
    • (1999) RNA , vol.5 , pp. 434-445
    • Nissan, T.A.1    Oliphant, B.O.2    Perona, J.J.3
  • 40
    • 0023720026 scopus 로고
    • Gln and its use in crystallization of the glutaminyl-tRNA synthetase-tRNAGln complex
    • Gln and its use in crystallization of the glutaminyl-tRNA synthetase-tRNAGln complex. J. Mol. Biol. 202:1988;121-126.
    • (1988) J. Mol. Biol. , vol.202 , pp. 121-126
    • Perona, J.J.1    Swanson, R.2    Steitz, T.A.3    Söll, D.4
  • 41
    • 0034098420 scopus 로고    scopus 로고
    • Tertiary core rearrangements in a tight-binding transfer RNA aptamer
    • Bullock T.L., Sherlin L.D., Perona J.J. Tertiary core rearrangements in a tight-binding transfer RNA aptamer. Nature Struct. Biol. 7:2000;497-504.
    • (2000) Nature Struct. Biol. , vol.7 , pp. 497-504
    • Bullock, T.L.1    Sherlin, L.D.2    Perona, J.J.3
  • 43
    • 0023651444 scopus 로고
    • Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates
    • Milligan J.F., Groebe D.R., Witherell G.W., Uhlenbeck O.C. Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucl. Acids Res. 21:1987;8783-8798.
    • (1987) Nucl. Acids Res. , vol.21 , pp. 8783-8798
    • Milligan, J.F.1    Groebe, D.R.2    Witherell, G.W.3    Uhlenbeck, O.C.4
  • 44
    • 0027991544 scopus 로고
    • In vitro transcription: Preparative RNA yields in analytical scale reactions
    • Pokrovskaya I.D., Gurevich V.V. In vitro transcription: preparative RNA yields in analytical scale reactions. Anal. Biochem. 220:1994;420-423.
    • (1994) Anal. Biochem. , vol.220 , pp. 420-423
    • Pokrovskaya, I.D.1    Gurevich, V.V.2
  • 45
    • 0034595508 scopus 로고    scopus 로고
    • Influence of transfer RNA tertiary structure on aminoacylation efficiency by glutaminyl and cysteinyl-tRNA synthetases
    • Sherlin L.D., Bullock T.L., Newberry K.J., Lipman R.S., Hou Y.-M., Beijer B., et al. Influence of transfer RNA tertiary structure on aminoacylation efficiency by glutaminyl and cysteinyl-tRNA synthetases. J. Mol. Biol. 299:2000;431-446.
    • (2000) J. Mol. Biol. , vol.299 , pp. 431-446
    • Sherlin, L.D.1    Bullock, T.L.2    Newberry, K.J.3    Lipman, R.S.4    Hou, Y.-M.5    Beijer, B.6
  • 46
    • 0028103275 scopus 로고
    • The CCP4 suite: Programs for protein crystallography
    • The CCP4 suite: programs for protein crystallography. Acta Crystallog. sect. D. 50:1994;760-763.
    • (1994) Acta Crystallog. sect. D , vol.50 , pp. 760-763
  • 47
    • 0023140814 scopus 로고
    • Crystallographic R-factor refinement by molecular dynamics
    • Brunger A.T., Kuriyan J., Karplus M. Crystallographic R-factor refinement by molecular dynamics. Science. 235:1987;458-460.
    • (1987) Science , vol.235 , pp. 458-460
    • Brunger, A.T.1    Kuriyan, J.2    Karplus, M.3
  • 48
    • 84889120137 scopus 로고
    • 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.W., 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;110-119.
    • (1991) Acta Crystallog. sect. A , vol.47 , pp. 110-119
    • Jones, T.A.1    Zou, J.Y.2    Cowan, S.W.3    Kjeldgaard, M.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.