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Volumn 11, Issue 12, 2004, Pages 1186-1191

The role of modifications in codon discrimination by tRNALysUUU

Author keywords

[No Author keywords available]

Indexed keywords

LYSINE TRANSFER RNA;

EID: 16544395239     PISSN: 15459993     EISSN: 15459985     Source Type: Journal    
DOI: 10.1038/nsmb861     Document Type: Article
Times cited : (280)

References (45)
  • 1
    • 0038403669 scopus 로고    scopus 로고
    • Insights into the decoding mechanism from recent ribosome structures
    • Ogle, J.M., Carter, A.P. & Ramakrishnan, V. Insights into the decoding mechanism from recent ribosome structures. Trends Biochem. Sci. 28, 259-266 (2003).
    • (2003) Trends Biochem. Sci. , vol.28 , pp. 259-266
    • Ogle, J.M.1    Carter, A.P.2    Ramakrishnan, V.3
  • 2
    • 0035805229 scopus 로고    scopus 로고
    • Recognition of cognate transfer RNA by the 30S ribosomal subunit
    • Ogle, J.M. et al. Recognition of cognate transfer RNA by the 30S ribosomal subunit. Science 292, 897-902 (2001).
    • (2001) Science 292 , pp. 897-902
    • Ogle, J.M.1
  • 3
    • 0037184536 scopus 로고    scopus 로고
    • Selection of tRNA by the ribosome requires a transition from an open to a closed form
    • Ogle, J.M., Murphy, F.V., Tarry, M.J. & Ramakrishnan, V. Selection of tRNA by the ribosome requires a transition from an open to a closed form. Cell 111, 721-732 (2002).
    • (2002) Cell , vol.111 , pp. 721-732
    • Ogle, J.M.1    Murphy, F.V.2    Tarry, M.J.3    Ramakrishnan, V.4
  • 4
    • 0013936167 scopus 로고
    • Codon-anticodon pairing: The wobble hypothesis
    • Crick, F.H.C. Codon-anticodon pairing: the wobble hypothesis. J. Mol. Biol. 19, 548-555 (1966).
    • (1966) J. Mol. Biol. , vol.19 , pp. 548-555
    • Crick, F.H.C.1
  • 5
    • 1242309517 scopus 로고    scopus 로고
    • Decoding the genome: A modified view
    • Agris, P.F. Decoding the genome: a modified view. Nucleic Acids Res. 32, 223-238 (2004).
    • (2004) Nucleic Acids Res , vol.32 , pp. 223-238
    • Agris, P.F.1
  • 8
    • 0037053384 scopus 로고    scopus 로고
    • Accurate translation of the genetic code depends on tRNA modified nucleosides
    • Yarian, C. et al. Accurate translation of the genetic code depends on tRNA modified nucleosides. J. Biol. Chem. 277, 16391-16395 (2002).
    • (2002) J. Biol. Chem. , vol.277 , pp. 16391-16395
    • Yarian, C.1
  • 9
    • 0035801515 scopus 로고    scopus 로고
    • Improvement of reading frame maintenance is a common function for several tRNA modifications
    • Urbonavicius, J., Qian, Q., Durand, J.M., Hagervall, T.G. & Bjork, G.R. Improvement of reading frame maintenance is a common function for several tRNA modifications. EMBO J. 20, 4863-4873 (2001).
    • (2001) EMBO J , vol.20 , pp. 4863-4873
    • Urbonavicius, J.1    Qian, Q.2    Durand, J.M.3    Hagervall, T.G.4    Bjork, G.R.5
  • 11
    • 0002495140 scopus 로고
    • (eds. Soll, D. & RajBhandary, U.), American Society for Microbiology, Washington, DC
    • Bjork, G.R. In tRNA: Structure, Biosynthesis and Function (eds. Soll, D. & RajBhandary, U.) 165-205 (American Society for Microbiology, Washington, DC, 1995).
    • (1995) In Trna: Structure, Biosynthesis and Function , pp. 165-205
    • Bjork, G.R.1
  • 12
    • 0031023569 scopus 로고    scopus 로고
    • Identification of 2'-hydroxyl groups required for interaction of a tRNA anticodon stem-loop region with the ribosome
    • von Ahsen, U., Green, R., Schroeder, R. & Noller, H.F. Identification of 2'-hydroxyl groups required for interaction of a tRNA anticodon stem-loop region with the ribosome. RNA 3, 49-56 (1997).
    • (1997) RNA , vol.3 , pp. 49-56
    • Von Ahsen, U.1    Green, R.2    Schroeder, R.3    Noller, H.F.4
  • 13
    • 0036809730 scopus 로고    scopus 로고
    • Universally conserved interactions between the ribosome and the anticodon stem-loop of A site tRNA important for translocation
    • Phelps, S.S., Jerinic, O. & Joseph, S. Universally conserved interactions between the ribosome and the anticodon stem-loop of A site tRNA important for translocation. Mol. Cell 10, 799-807 (2002).
    • (2002) Mol. Cell , vol.10 , pp. 799-807
    • Phelps, S.S.1    Jerinic, O.2    Joseph, S.3
  • 15
    • 0034619418 scopus 로고    scopus 로고
    • Functional anticodon architecture of human tRNALys3 includes disruption of intraloop hydrogen bonding by the naturally occurring amino acid modification, t6A
    • 6A. Biochemistry 39, 13396-13404 (2000).
    • (2000) Biochemistry , vol.39 , pp. 13396-13404
    • Stuart, J.W.1
  • 16
    • 0033744175 scopus 로고    scopus 로고
    • The crystal structure of HIV reverse-transcription primer tRNA(Lys,3) shows a canonical anticodon loop
    • Benas, P. et al. The crystal structure of HIV reverse-transcription primer tRNA(Lys,3) shows a canonical anticodon loop. RNA 6, 1347-1355 (2000).
    • (2000) RNA , vol.6 , pp. 1347-1355
    • Benas, P.1
  • 17
    • 0017165207 scopus 로고
    • Studies of the complex between transfer RNAs with complementary anticodons
    • Grosjean, H., Soll, D. & Crothers, D.M. Studies of the complex between transfer RNAs with complementary anticodons. J. Mol. Biol. 103, 499-519 (1976).
    • (1976) J. Mol. Biol. , vol.103 , pp. 499-519
    • Grosjean, H.1    Soll, D.2    Crothers, D.M.3
  • 18
    • 0347623198 scopus 로고    scopus 로고
    • Purine bases at position 37 of tRNA stabilize codon-anticodon interaction in the ribosomal A site by stacking and Mg2+-dependent interactions
    • 2+-dependent interactions. RNA 10, 90-101 (2004).
    • (2004) RNA , vol.10 , pp. 90-101
    • Konevega, A.L.1
  • 19
    • 0033534369 scopus 로고    scopus 로고
    • Cross-strand purine-pyrimidine stack and sheared purine pyrimidine pairing in the human HIV-1 reverse transcriptase inhibitors
    • Chou, S.-H. & Tseng, Y.-Y. Cross-strand purine-pyrimidine stack and sheared purine pyrimidine pairing in the human HIV-1 reverse transcriptase inhibitors. J. Mol. Biol. 285, 41-48 (1999).
    • (1999) J. Mol. Biol. , vol.285 , pp. 41-48
    • Chou, S.-H.1    Tseng, Y.-Y.2
  • 20
    • 0029100233 scopus 로고
    • Predicting thermodynamic properties of RNA
    • Serra, M.J. & Turner, D.H. Predicting thermodynamic properties of RNA. Methods Enzymol. 259, 242-261 (1995).
    • (1995) Methods Enzymol , vol.259 , pp. 242-261
    • Serra, M.J.1    Turner, D.H.2
  • 22
    • 0037015077 scopus 로고    scopus 로고
    • Specificity of RNA-RNA helix recognition
    • Battle, D.J. & Doudna, J.A. Specificity of RNA-RNA helix recognition. Proc. Natl. Acad. Sci. USA 99, 11676-11681 (2002).
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 11676-11681
    • Battle, D.J.1    Doudna, J.A.2
  • 23
    • 0026343194 scopus 로고
    • Wobble position modified nucleosides evolved to select transfer RNA codon recognition: A modified-wobble hypothesis
    • Agris, P.F. Wobble position modified nucleosides evolved to select transfer RNA codon recognition: a modified-wobble hypothesis. Biochemistry 73, 1345-1349 (1991).
    • (1991) Biochemistry , vol.73 , pp. 1345-1349
    • Agris, P.F.1
  • 24
    • 0000075467 scopus 로고
    • Improved free-energy parameters for predictions of RNA duplex stability
    • Freier, S.M. et al. Improved free-energy parameters for predictions of RNA duplex stability. Proc. Natl. Acad. Sci. USA 83, 9373-9377 (1986).
    • (1986) Proc. Natl. Acad. Sci. USA , vol.83 , pp. 9373-9377
    • Freier, S.M.1
  • 25
    • 0034680364 scopus 로고    scopus 로고
    • Hypermodified nucleosides in the anticodon of tRNALys stabilize a canonical U-turn structure
    • Lys stabilize a canonical U-turn structure. Biochemistry 39, 12575-12584 (2000).
    • (2000) Biochemistry , vol.39 , pp. 12575-12584
    • Sundaram, M.1    Durant, P.C.2    Davis, D.R.3
  • 26
    • 0002365884 scopus 로고
    • (eds. Soll, D. & RajBhandary, U., American Society for Microbiology, Washington, DC
    • Yokoyama, S. & Nishimura, S. In tRNA: Structure, Biosynthesis, and Function (eds. Soll, D. & RajBhandary, U.) 207-223 (American Society for Microbiology, Washington, DC, 1995).
    • (1995) Trna: Structure, Biosynthesis, and Function , pp. 207-223
    • Yokoyama, S.1    Nishimura, S.2
  • 27
    • 0345531141 scopus 로고    scopus 로고
    • Roles of 5-substituents of tRNA wobble uridines in the rec-ognition of purine-ending codons
    • Takai, K. & Yokoyama, S. Roles of 5-substituents of tRNA wobble uridines in the rec-ognition of purine-ending codons. Nucleic Acids Res. 31, 6383-6391 (2003).
    • (2003) Nucleic Acids Res , vol.31 , pp. 6383-6391
    • Takai, K.1    Yokoyama, S.2
  • 28
    • 0033600832 scopus 로고    scopus 로고
    • Singly and bifurcated hydrogen-bonded base-pairs in tRNA anticodon hairpins and ribozymes
    • Auffinger, P. & Westhof, E. Singly and bifurcated hydrogen-bonded base-pairs in tRNA anticodon hairpins and ribozymes. J. Mol. Biol. 292, 467-483 (1999).
    • (1999) J. Mol. Biol. , vol.292 , pp. 467-483
    • Auffinger, P.1    Westhof, E.2
  • 29
    • 0032500312 scopus 로고    scopus 로고
    • Energetic superiority of two-center hydrogen bonding relative to three-center hydrogen bonding in a model system
    • Yang, J. & Gellman, S.H. Energetic superiority of two-center hydrogen bonding relative to three-center hydrogen bonding in a model system. J. Am. Chem. Soc. 120, 9090-9091 (1998).
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 9090-9091
    • Yang, J.1    Gellman, S.H.2
  • 30
    • 0018086876 scopus 로고
    • Stacking of Crick wobble pair and Watson-Crick pair: Stability rules of G-U pairs at ends of helical stems in tRNAs and the relation to codon- anticodon wobble interaction
    • Mizuno, H. & Sundaralingam, M. Stacking of Crick wobble pair and Watson-Crick pair: stability rules of G-U pairs at ends of helical stems in tRNAs and the relation to codon- anticodon wobble interaction. Nucleic Acids Res. 5, 4451-4461 (1978).
    • (1978) Nucleic Acids Res , vol.5 , pp. 4451-4461
    • Mizuno, H.1    Sundaralingam, M.2
  • 31
    • 0034254780 scopus 로고    scopus 로고
    • Nuclear magnetic resonance spectroscopy and molecular modeling reveal that different hydrogen bonding patterns are possible for GU pairs: One hydrogen bond for each G U pair in r(GGCGUGCC)2 and two for each G U pair in r(GAGUGCUC)2
    • Chen, X., McDowell, J.A., Kierzek, R., Krugh, T.R. & Turner, D.H. Nuclear magnetic resonance spectroscopy and molecular modeling reveal that different hydrogen bonding patterns are possible for GU pairs: one hydrogen bond for each G U pair in r(GGCGUGCC)2 and two for each G U pair in r(GAGUGCUC)2. Biochemistry 39, 8970-8982 (2000).
    • (2000) Biochemistry , vol.39 , pp. 8970-8982
    • Chen, X.1    McDowell, J.A.2    Kierzek, R.3    Krugh, T.R.4    Turner, D.H.5
  • 32
    • 0034923932 scopus 로고    scopus 로고
    • Fidelity of aminoacyl-tRNA selection on the ribosome: Kinetic and structural mechanisms
    • Rodnina, M.V. & Wintermeyer, W. Fidelity of aminoacyl-tRNA selection on the ribosome: kinetic and structural mechanisms. Annu. Rev. Biochem. 70, 415-435 (2001).
    • (2001) Annu. Rev. Biochem. , vol.70 , pp. 415-435
    • Rodnina, M.V.1    Wintermeyer, W.2
  • 33
    • 0035919727 scopus 로고    scopus 로고
    • Crystal structure of the 30 S ribosomal subunit from Thermus thermophilus: Purification, crystallization and structure determination
    • Clemons, W.M. Jr. et al. Crystal structure of the 30 S ribosomal subunit from Thermus thermophilus: purification, crystallization and structure determination. J. Mol. Biol. 310, 827-843 (2001).
    • (2001) J. Mol. Biol. , vol.310 , pp. 827-843
    • Clemons, W.M.1
  • 34
    • 0006021423 scopus 로고
    • Total chemical synthesis of a 77-nucleotide-long RNA sequence having methionine-acceptance activity
    • Ogilvie, K.K., Usman, N., Nicoghosian, K. & Cedergren, R.J. Total chemical synthesis of a 77-nucleotide-long RNA sequence having methionine-acceptance activity. Proc. Natl. Acad. Sci. USA 85, 5764-5768 (1988).
    • (1988) Proc. Natl. Acad. Sci. USA , vol.85 , pp. 5764-5768
    • Ogilvie, K.K.1    Usman, N.2    Nicoghosian, K.3    Cedergren, R.J.4
  • 35
    • 0028915734 scopus 로고
    • Site-selected introduction of modified purine and pyrimidine ribonu- cleosides into RNA by automated phosphoramidite chemistry
    • Agris, P.F. et al. Site-selected introduction of modified purine and pyrimidine ribonu- cleosides into RNA by automated phosphoramidite chemistry. Biochimie 77, 125-134 (1995).
    • (1995) Biochimie , vol.77 , pp. 125-134
    • Agris, P.F.1
  • 36
    • 0031266354 scopus 로고    scopus 로고
    • A sequencing method for RNA oli- gonucleotides based on mass spectrometry
    • Faulstich, K., Worner, K., Brill, H. & Engels, J.W. A sequencing method for RNA oli- gonucleotides based on mass spectrometry. Anal. Chem. 69, 4349-4353 (1997).
    • (1997) Anal. Chem. , vol.69 , pp. 4349-4353
    • Faulstich, K.1    Worner, K.2    Brill, H.3    Engels, J.W.4
  • 37
    • 0031059866 scopus 로고    scopus 로고
    • 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. 276A, 307-326 (1997).
    • (1997) Methods Enzymol , vol.276A , pp. 307-326
    • Otwinowski, Z.1    Minor, W.2
  • 38
    • 0001614694 scopus 로고    scopus 로고
    • STRATEGY: A program to optimize the starting spindle angle and scan range for X-ray data collection
    • Ravelli, R.B.G., Sweet, R.M., Skinner, J.M., Duisenberg, A.J.M. & Kroon, J. STRATEGY: a program to optimize the starting spindle angle and scan range for X-ray data collection. J. Appl. Cryst. 30, 551-554 (1997).
    • (1997) J. Appl. Cryst. , vol.30 , pp. 551-554
    • Ravelli, R.B.G.1    Sweet, R.M.2    Skinner, J.M.3    Duisenberg, A.J.M.4    Kroon, J.5
  • 39
    • 3543012707 scopus 로고    scopus 로고
    • Crystallography & NMR System: A new software suite for macromo- lecular structure determination
    • Brunger, A.T. et al. Crystallography & NMR System: a new software suite for macromo- lecular structure determination. Acta Crystallogr. D54, 905-921 (1998).
    • (1998) Acta Crystallogr. , vol.D54 , pp. 905-921
    • Brunger, A.T.1
  • 40
    • 0032215320 scopus 로고    scopus 로고
    • Databases in protein crystallography
    • Kleywegt, G.J. & Jones, T.A. Databases in protein crystallography. Acta Crystallogr. D54, 1119-1131 (1998).
    • (1998) Acta Crystallogr. , vol.D54 , pp. 1119-1131
    • Kleywegt, G.J.1    Jones, T.A.2
  • 41
    • 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 Crystallogr. A47, 110-119 (1991).
    • (1991) Acta Crystallogr. , vol.A47 , pp. 110-119
    • Jones, T.A.1    Zou, J.Y.2    Cowan, S.W.3    Kjeldgaard, M.4
  • 42
    • 0028103275 scopus 로고
    • Number 4. The CCP4 suite: Programs for protein crystallography
    • Collaborative Computational Project, Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D50, 760-763 (1994).
    • (1994) Acta Crystallogr. , vol.D50 , pp. 760-763
  • 43
    • 0029881007 scopus 로고    scopus 로고
    • MOLMOL: A program for display and analysis of macromolecular structures
    • Koradi, R., Billeter, M. & Wuthrich, K. MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graph. 14, 51-55 (1996).
    • (1996) J. Mol. Graph. , vol.14 , pp. 51-55
    • Koradi, R.1    Billeter, M.2    Wuthrich, K.3
  • 44
    • 0036008503 scopus 로고    scopus 로고
    • A genetic algorithm for the identification of conformationally invariant regions in protein molecules
    • Schneider, T.R. A genetic algorithm for the identification of conformationally invariant regions in protein molecules. Acta Crystallogr. D58, 195-208 (2002).
    • (2002) Acta Crystallogr. , vol.D58 , pp. 195-208
    • Schneider, T.R.1
  • 45
    • 0242396923 scopus 로고    scopus 로고
    • 3DNA: A software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures
    • Lu, X.J. & Olson, W.K. 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res. 31, 5108-5121 (2003).
    • (2003) Nucleic Acids Res , vol.31 , pp. 5108-5121
    • Lu, X.J.1    Olson, W.K.2


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