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Volumn 290, Issue 33, 2015, Pages 20032-20043

NMR-based structural analysis of threonylcarbamoyl-AMP synthase and its substrate interactions

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; BINDING SITES; BIOCHEMISTRY; BIOSYNTHESIS; ESCHERICHIA COLI; SUBSTRATES;

EID: 84939645471     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M114.631242     Document Type: Article
Times cited : (12)

References (51)
  • 2
    • 0001918945 scopus 로고    scopus 로고
    • (Grosjean, H., and Benne, R., eds) American Society for Microbiology, Washington, D. C.
    • Auffinger, P., and Westhof, P. (1998) in Modification and Editing of RNA (Grosjean, H., and Benne, R., eds) pp. 569-576, American Society for Microbiology, Washington, D. C.
    • (1998) Modification and Editing of RNA , pp. 569-576
    • Auffinger, P.1    Westhof, P.2
  • 4
    • 0028943560 scopus 로고
    • Posttranscriptionally modified nucleosides in transfer RNA: Their locations and frequencies
    • Grosjean, H., Sprinzl, M., and Steinberg, S. (1995) Posttranscriptionally modified nucleosides in transfer RNA: their locations and frequencies. Biochimie 77, 139-141
    • (1995) Biochimie , vol.77 , pp. 139-141
    • Grosjean, H.1    Sprinzl, M.2    Steinberg, S.3
  • 5
    • 0031985443 scopus 로고    scopus 로고
    • Structural requirements for enzymatic formation of threonylcarbamoyladenosine (t6A) in tRNA: An in vivo study with Xenopus laevis oocytes
    • Morin, A., Auxilien, S., Senger, B., Tewari, R., and Grosjean, H. (1998) Structural requirements for enzymatic formation of threonylcarbamoyladenosine (t6A) in tRNA: an in vivo study with Xenopus laevis oocytes. RNA 4, 24-37
    • (1998) RNA , vol.4 , pp. 24-37
    • Morin, A.1    Auxilien, S.2    Senger, B.3    Tewari, R.4    Grosjean, H.5
  • 6
    • 0017064254 scopus 로고
    • The involvement of the anticodon adjacent modified nucleoside N-(9-(β-D-ribofuranosyl)-purine-6-ylcarbamoyl)-threonine in the biological function of E. coli tRNAIle
    • Miller, J. P., Hussain, Z., and Schweizer, M. P. (1976) The involvement of the anticodon adjacent modified nucleoside N-(9-(β-D-ribofuranosyl)-purine-6-ylcarbamoyl)-threonine in the biological function of E. coli tRNAIle. Nucleic Acids Res. 3, 1185-1201
    • (1976) Nucleic Acids Res , vol.3 , pp. 1185-1201
    • Miller, J.P.1    Hussain, Z.2    Schweizer, M.P.3
  • 7
    • 0019355045 scopus 로고
    • Effect of threonylcarbamoyl modification (t6A) in yeast tRNA Arg III on codon-anticodon and anticodon-anticodon interactions. A thermodynamic and kinetic evaluation
    • Weissenbach, J., and Grosjean, H. (1981) Effect of threonylcarbamoyl modification (t6A) in yeast tRNA Arg III on codon-anticodon and anticodon-anticodon interactions. A thermodynamic and kinetic evaluation. Eur. J. Biochem. 116, 207-213
    • (1981) Eur. J. Biochem. , vol.116 , pp. 207-213
    • Weissenbach, J.1    Grosjean, H.2
  • 10
    • 84857367382 scopus 로고    scopus 로고
    • Human tRNA(Lys3)UUU is pre-structured by natural modifications for cognate and wobble codon binding through Keto-Enol tautomerism
    • Vendeix, F. A., Murphy, F. V., 4th, Cantara, W. A., Leszczyńska, G., Gustilo, E. M., Sproat, B., Malkiewicz, A., and Agris, P. F. (2012) Human tRNA(Lys3)UUU is pre-structured by natural modifications for cognate and wobble codon binding through Keto-Enol tautomerism. J. Mol. Biol. 416, 467-485
    • (2012) J. Mol. Biol. , vol.416 , pp. 467-485
    • Vendeix, F.A.1    Murphy, F.V.2    Cantara, W.A.3    Leszczyńska, G.4    Gustilo, E.M.5    Sproat, B.6    Malkiewicz, A.7    Agris, P.F.8
  • 11
    • 0026343194 scopus 로고
    • Wobble position modified nucleosides evolved to select transfer RNA codon recognition: A modified-wobble hypothesis
    • Agris, P. F. (1991) Wobble position modified nucleosides evolved to select transfer RNA codon recognition: a modified-wobble hypothesis. Biochimie 73, 1345-1349
    • (1991) Biochimie , vol.73 , pp. 1345-1349
    • Agris, P.F.1
  • 12
    • 0015278178 scopus 로고
    • Minor components in transfer RNA: Their characterization, location, and function
    • Nishimura, S. (1972) Minor components in transfer RNA: their characterization, location, and function. Prog. Nucleic Acids Res. Mol. Biol. 12, 49-85
    • (1972) Prog. Nucleic Acids Res. Mol. Biol. , vol.12 , pp. 49-85
    • Nishimura, S.1
  • 13
    • 73549090572 scopus 로고    scopus 로고
    • The Sua5 protein is essential for normal translational regulation in yeast
    • Lin, C. A., Ellis, S. R., and True, H. L. (2010) The Sua5 protein is essential for normal translational regulation in yeast. Mol. Cell. Biol. 30, 354-363
    • (2010) Mol. Cell. Biol. , vol.30 , pp. 354-363
    • Lin, C.A.1    Ellis, S.R.2    True, H.L.3
  • 16
    • 84859994582 scopus 로고    scopus 로고
    • Biosynthesis of threonylcarbamoyl adenosine (t6A), a universal tRNA nucleoside
    • Deutsch, C., El Yacoubi, B., de Crécy-Lagard, V., and Iwata-Reuyl, D. (2012) Biosynthesis of threonylcarbamoyl adenosine (t6A), a universal tRNA nucleoside. J. Biol. Chem. 287, 13666-13673
    • (2012) J. Biol. Chem. , vol.287 , pp. 13666-13673
    • Deutsch, C.1    El Yacoubi, B.2    De Crécy-Lagard, V.3    Iwata-Reuyl, D.4
  • 17
    • 84868529691 scopus 로고    scopus 로고
    • Mechanism of N6-threonylcarbamoyladenonsine (t6A) biosynthesis: Isolation and characterization of the intermediate threonylcarbamoyl-AMP
    • Lauhon, C. T. (2012) Mechanism of N6-threonylcarbamoyladenonsine (t6A) biosynthesis: isolation and characterization of the intermediate threonylcarbamoyl-AMP. Biochemistry 51, 8950-8963
    • (2012) Biochemistry , vol.51 , pp. 8950-8963
    • Lauhon, C.T.1
  • 23
    • 79952280840 scopus 로고    scopus 로고
    • The highly conserved KEOPS/EKC complex is essential for a universal tRNA modification, t6A
    • Srinivasan, M., Mehta, P., Yu, Y., Prugar, E., Koonin, E. V., Karzai, A. W., and Sternglanz, R. (2011) The highly conserved KEOPS/EKC complex is essential for a universal tRNA modification, t6A. EMBO J. 30, 873-881
    • (2011) EMBO J , vol.30 , pp. 873-881
    • Srinivasan, M.1    Mehta, P.2    Yu, Y.3    Prugar, E.4    Koonin, E.V.5    Karzai, A.W.6    Sternglanz, R.7
  • 25
    • 84860390106 scopus 로고    scopus 로고
    • YrdC exhibits properties expected of a subunit for a tRNA threonylcarbamoyl transferase
    • Harris, K. A., Jones, V., Bilbille, Y., Swairjo, M. A., and Agris, P. F. (2011) YrdC exhibits properties expected of a subunit for a tRNA threonylcarbamoyl transferase. RNA 17, 1678-1687
    • (2011) RNA , vol.17 , pp. 1678-1687
    • Harris, K.A.1    Jones, V.2    Bilbille, Y.3    Swairjo, M.A.4    Agris, P.F.5
  • 26
    • 84890067053 scopus 로고    scopus 로고
    • Functional assignment of KEOPS/EKC complex subunits in the biosynthesis of the universal t6A tRNA modification
    • Perrochia, L., Guetta, D., Hecker, A., Forterre, P., and Basta, T. (2013) Functional assignment of KEOPS/EKC complex subunits in the biosynthesis of the universal t6A tRNA modification. Nucleic Acids Res. 41, 9484-9499
    • (2013) Nucleic Acids Res , vol.41 , pp. 9484-9499
    • Perrochia, L.1    Guetta, D.2    Hecker, A.3    Forterre, P.4    Basta, T.5
  • 27
    • 0034491066 scopus 로고    scopus 로고
    • The structure of the yrdC gene product from Escherichia coli reveals a new fold and suggests a role in RNA binding
    • Teplova, M., Tereshko, V., Sanishvili, R., Joachimiak, A., Bushueva, T., Anderson, W. F., and Egli, M. (2000) The structure of the yrdC gene product from Escherichia coli reveals a new fold and suggests a role in RNA binding. Protein Sci. 9, 2557-2566
    • (2000) Protein Sci , vol.9 , pp. 2557-2566
    • Teplova, M.1    Tereshko, V.2    Sanishvili, R.3    Joachimiak, A.4    Bushueva, T.5    Anderson, W.F.6    Egli, M.7
  • 28
    • 0036780778 scopus 로고    scopus 로고
    • Crystal structure of the YciO protein from Escherichia coli
    • Jia, J., Lunin, V. V., Sauvé, V., Huang, L. W., Matte, A., and Cygler, M. (2002) Crystal structure of the YciO protein from Escherichia coli. Proteins 49, 139-141
    • (2002) Proteins , vol.49 , pp. 139-141
    • Jia, J.1    Lunin, V.V.2    Sauvé, V.3    Huang, L.W.4    Matte, A.5    Cygler, M.6
  • 31
    • 65649135871 scopus 로고    scopus 로고
    • Practical protocols for production of very high yields of recombinant proteins using Escherichia coli
    • Sivashanmugam, A., Murray, V., Cui, C., Zhang, Y., Wang, J., and Li, Q. (2009) Practical protocols for production of very high yields of recombinant proteins using Escherichia coli. Protein Sci. 18, 936-948
    • (2009) Protein Sci , vol.18 , pp. 936-948
    • Sivashanmugam, A.1    Murray, V.2    Cui, C.3    Zhang, Y.4    Wang, J.5    Li, Q.6
  • 32
    • 68349093958 scopus 로고    scopus 로고
    • TALOS+: A hybrid method for predicting protein backbone torsion angles from NMR chemical shifts
    • Shen, Y., Delaglio, F., Cornilescu, G., and Bax, A. (2009) TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts. J. Biomol. NMR 44, 213-223
    • (2009) J. Biomol. NMR , vol.44 , pp. 213-223
    • Shen, Y.1    Delaglio, F.2    Cornilescu, G.3    Bax, A.4
  • 33
    • 0032042263 scopus 로고    scopus 로고
    • Measurement of J and dipolar couplings from simplified two-dimensional NMR spectra
    • Ottiger, M., Delaglio, F., and Bax, A. (1998) Measurement of J and dipolar couplings from simplified two-dimensional NMR spectra. J. Magn. Reson. 131, 373-378
    • (1998) J. Magn. Reson. , vol.131 , pp. 373-378
    • Ottiger, M.1    Delaglio, F.2    Bax, A.3
  • 34
    • 0029400480 scopus 로고
    • NMRPipe: A multidimensional spectral processing system based on UNIX pipes
    • Delaglio, F., Grzesiek, S., Vuister, G. W., Zhu, G., Pfeifer, J., and Bax, A. (1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR 6, 277-293
    • (1995) J. Biomol. NMR , vol.6 , pp. 277-293
    • Delaglio, F.1    Grzesiek, S.2    Vuister, G.W.3    Zhu, G.4    Pfeifer, J.5    Bax, A.6
  • 35
    • 84871444338 scopus 로고    scopus 로고
    • University of California, San Francisco, CA
    • Goddard, T. D., and Kneller, D. G. (2008) SPARKY 3. University of California, San Francisco, CA
    • (2008) SPARKY 3
    • Goddard, T.D.1    Kneller, D.G.2
  • 36
    • 4644259437 scopus 로고    scopus 로고
    • Using NMRView to visualize and analyze the NMR spectra of macromolecules
    • Johnson, B. A. (2004) Using NMRView to visualize and analyze the NMR spectra of macromolecules. Methods Mol. Biol. 278, 313-352
    • (2004) Methods Mol. Biol. , vol.278 , pp. 313-352
    • Johnson, B.A.1
  • 38
    • 4644340524 scopus 로고    scopus 로고
    • Automated NMR structure calculation with CYANA
    • Güntert, P. (2004) Automated NMR structure calculation with CYANA. Methods Mol. Biol 278, 353-378
    • (2004) Methods Mol. Biol , vol.278 , pp. 353-378
    • Güntert, P.1
  • 41
    • 33847079676 scopus 로고    scopus 로고
    • Evaluating protein structures determined by structural genomics consortia
    • Bhattacharya, A., Tejero, R., and Montelione, G. T. (2007) Evaluating protein structures determined by structural genomics consortia. Proteins 66, 778-795
    • (2007) Proteins , vol.66 , pp. 778-795
    • Bhattacharya, A.1    Tejero, R.2    Montelione, G.T.3
  • 43
    • 0037442962 scopus 로고    scopus 로고
    • HADDOCK: A protein-protein docking approach based on biochemical or biophysical information
    • Dominguez, C., Boelens, R., and Bonvin, A. M. (2003) HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J. Am. Chem. Soc. 125, 1731-1737
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 1731-1737
    • Dominguez, C.1    Boelens, R.2    Bonvin, A.M.3
  • 45
    • 0000009443 scopus 로고
    • Rapid Comparison of Protein Structures
    • McLachlan, A. D. (1982) Rapid Comparison of Protein Structures. Acta Crystallogr. Sect. A 38, 871-873
    • (1982) Acta Crystallogr. Sect. A , vol.38 , pp. 871-873
    • McLachlan, A.D.1
  • 47
    • 0242669339 scopus 로고    scopus 로고
    • Slow diffusion of macromolecular assemblies by a new pulsed field gradient NMR method
    • Ferrage, F., Zoonens, M., Warschawski, D. E., Popot, J.-L., and Bodenhausen, G. (2003) Slow diffusion of macromolecular assemblies by a new pulsed field gradient NMR method. J. Am. Chem. Soc. 125, 2541-2545
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 2541-2545
    • Ferrage, F.1    Zoonens, M.2    Warschawski, D.E.3    Popot, J.-L.4    Bodenhausen, G.5
  • 48
    • 0032879507 scopus 로고    scopus 로고
    • R-factor, free R, and complete cross-validation for dipolar coupling refinement of NMR structures
    • Clore, G. M., and Garrett, D. S. (1999) R-factor, free R, and complete cross-validation for dipolar coupling refinement of NMR structures. J. Am. Chem. Soc. 121, 9008-9012
    • (1999) J. Am. Chem. Soc. , vol.121 , pp. 9008-9012
    • Clore, G.M.1    Garrett, D.S.2
  • 49
    • 0030339738 scopus 로고    scopus 로고
    • AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR
    • Laskowski, R. A., Rullmannn, J. A., MacArthur, M. W., Kaptein, R., and Thornton, J. M. (1996) AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J. Biomol. NMR 8, 477-486
    • (1996) J. Biomol. NMR , vol.8 , pp. 477-486
    • Laskowski, R.A.1    Rullmannn, J.A.2    MacArthur, M.W.3    Kaptein, R.4    Thornton, J.M.5
  • 51
    • 0029881007 scopus 로고    scopus 로고
    • MOLMOL: A program for display and analysis of macromolecular structures
    • Koradi, R., Billeter, M., and Wüthrich, K. (1996) MOLMOL: A program for display and analysis of macromolecular structures. J. Mol. Graph. 14, 51-55
    • (1996) J. Mol. Graph. , vol.14 , pp. 51-55
    • Koradi, R.1    Billeter, M.2    Wüthrich, K.3


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