메뉴 건너뛰기




Volumn 32, Issue 3, 1998, Pages 362-380

Engineering an Mg2+ site to replace a structurally conserved arginine in the catalytic center of histidyl-tRNA synthetase by computer experiments

Author keywords

Aminoacyl tRNA synthetase; ATP; Molecular dynamics simulations; Mutagenesis

Indexed keywords

AMINO ACID ANALYSIS; AMINO ACID METABOLISM; AMINO ACID SEQUENCE; ARTICLE; CATALYSIS; COMPUTER ANALYSIS; ENZYME ACTIVITY; ESCHERICHIA COLI; GENETIC ENGINEERING; GEOMETRY; MUTAGENESIS; PRIORITY JOURNAL; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; ENZYMOLOGY; GENETICS; METABOLISM; MUTATION; NUCLEOTIDE SEQUENCE; PROTEIN ENGINEERING; THERMUS THERMOPHILUS;

EID: 0032528684     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19980815)32:3<362::AID-PROT11>3.0.CO;2-7     Document Type: Article
Times cited : (16)

References (45)
  • 1
    • 0025158208 scopus 로고
    • Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs
    • Eriani, G., Delarue, M., Poch, O., Gangloff, J., Moras, D. Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. Nature 347:203-206, 1990.
    • (1990) Nature , vol.347 , pp. 203-206
    • Eriani, G.1    Delarue, M.2    Poch, O.3    Gangloff, J.4    Moras, D.5
  • 2
    • 0026591001 scopus 로고
    • Structural and functional relationships between aminoacyl-tRNA synthetases
    • Moras, D. Structural and functional relationships between aminoacyl-tRNA synthetases. Trends Biochem. Sci. 17:159-164, 1992.
    • (1992) Trends Biochem. Sci. , vol.17 , pp. 159-164
    • Moras, D.1
  • 3
    • 0030962189 scopus 로고    scopus 로고
    • Structural and functional considerations of the aminoacylation reaction
    • Arnez, J.G., Moras, D. Structural and functional considerations of the aminoacylation reaction. Trends Biochem. Sci. 22:211-216, 1997.
    • (1997) Trends Biochem. Sci. , vol.22 , pp. 211-216
    • Arnez, J.G.1    Moras, D.2
  • 4
    • 0029127816 scopus 로고
    • Crystal structure of histidyl-tRNA synthetase from E. coli complexed with histidyl-adenylate
    • Arnez, J.G., Harris, D.C., Mitschler, A., Rees, B., Francklyn, C.S., Moras, D. Crystal structure of histidyl-tRNA synthetase from E. coli complexed with histidyl-adenylate. EMBOJ. 14:4143-4155, 1995.
    • (1995) EMBOJ. , vol.14 , pp. 4143-4155
    • Arnez, J.G.1    Harris, D.C.2    Mitschler, A.3    Rees, B.4    Francklyn, C.S.5    Moras, D.6
  • 5
  • 7
    • 0026019625 scopus 로고
    • Structural basis for the 3′-5′ exonuclease activity of Escherichia coli DNA polymerase I: A two metal ion mechanism
    • Beese, L.S., Steitz, T.A. Structural basis for the 3′-5′ exonuclease activity of Escherichia coli DNA polymerase I: A two metal ion mechanism. EMBO J. 10:25-33, 1991.
    • (1991) EMBO J. , vol.10 , pp. 25-33
    • Beese, L.S.1    Steitz, T.A.2
  • 8
    • 0029410817 scopus 로고
    • Structure-energy analysis of the role of metal ions in phosphodiester bond hydrolysis by DNA polymerase I
    • Fothergill, M., Goodman, M.F., Petruska, J., Warshel, A. Structure-energy analysis of the role of metal ions in phosphodiester bond hydrolysis by DNA polymerase I. J. Am. Chem. Soc. 117:11619-11627, 1995.
    • (1995) J. Am. Chem. Soc. , vol.117 , pp. 11619-11627
    • Fothergill, M.1    Goodman, M.F.2    Petruska, J.3    Warshel, A.4
  • 9
    • 0028084909 scopus 로고
    • The active site of yeast aspartyl-tRNA synthetase: Structural and functional aspects of the aminoacylation reaction
    • Cavarelli, J., Eriani, G., Rees, B., et al. The active site of yeast aspartyl-tRNA synthetase: Structural and functional aspects of the aminoacylation reaction. EMBO J. 13:327-337, 1994.
    • (1994) EMBO J. , vol.13 , pp. 327-337
    • Cavarelli, J.1    Eriani, G.2    Rees, B.3
  • 10
    • 0028104763 scopus 로고
    • Synthesis and recognition of aspartyl-adenylate by Thermus thermophilus aspartyl-tRNA synthetase
    • Poterszman, A., Delarue, M., Thierry, J.-C., Moras, D. Synthesis and recognition of aspartyl-adenylate by Thermus thermophilus aspartyl-tRNA synthetase. J. Mol. Biol. 244:158-167, 1994.
    • (1994) J. Mol. Biol. , vol.244 , pp. 158-167
    • Poterszman, A.1    Delarue, M.2    Thierry, J.-C.3    Moras, D.4
  • 12
    • 0000111252 scopus 로고
    • Humidity-controlled reversible structure transition of disodium adenosine 5′-triphosphate between dihydrate and trihydrate in a single crystal state
    • Sugawara, Y., Kamiya, N., Iwasaki, H., Ito, T., Satow, Y.J. Humidity-controlled reversible structure transition of disodium adenosine 5′-triphosphate between dihydrate and trihydrate in a single crystal state. Am. Chem. Soc. 113: 5440, 1991.
    • (1991) Am. Chem. Soc. , vol.113 , pp. 5440
    • Sugawara, Y.1    Kamiya, N.2    Iwasaki, H.3    Ito, T.4    Satow, Y.J.5
  • 13
    • 0022428143 scopus 로고
    • Crystal structure of the alpha, beta, gamma-tridentate manganese complex of adenosine 5′-triphosphate cocrystallized with 2,2′-dipyridylamine
    • Sabat, M., Cini, R., Haromy, T., Sundaralingam, M. Crystal structure of the alpha, beta, gamma-tridentate manganese complex of adenosine 5′-triphosphate cocrystallized with 2,2′-dipyridylamine. Biochemistry 24:7827-7833, 1985.
    • (1985) Biochemistry , vol.24 , pp. 7827-7833
    • Sabat, M.1    Cini, R.2    Haromy, T.3    Sundaralingam, M.4
  • 15
    • 0028854420 scopus 로고
    • Metalloantibody design
    • Roberts, V.A., Getzoff, E.D. Metalloantibody design. FASEB J. 9:94-100, 1995.
    • (1995) FASEB J. , vol.9 , pp. 94-100
    • Roberts, V.A.1    Getzoff, E.D.2
  • 16
    • 0029016430 scopus 로고    scopus 로고
    • Protein design: Novel metal-binding sites
    • Regan, L. Protein design: Novel metal-binding sites. Trends Biochem. Sci. 20:280-285, 1996.
    • (1996) Trends Biochem. Sci. , vol.20 , pp. 280-285
    • Regan, L.1
  • 17
    • 0030220211 scopus 로고    scopus 로고
    • Metalloprotein design
    • Hellinga, H. Metalloprotein design. Curr. Opin. Biotech. 7:437-441, 1996.
    • (1996) Curr. Opin. Biotech. , vol.7 , pp. 437-441
    • Hellinga, H.1
  • 18
    • 0030801175 scopus 로고    scopus 로고
    • Engineering metal-binding sites in proteins
    • Lu, Y., Valentine, J.S. Engineering metal-binding sites in proteins. Curr. Opin. Struct. Biol. 7:495-500, 1997.
    • (1997) Curr. Opin. Struct. Biol. , vol.7 , pp. 495-500
    • Lu, Y.1    Valentine, J.S.2
  • 19
    • 0031104643 scopus 로고    scopus 로고
    • Construction and characterization of a magnesium-binding site in cytochrome c peroxidase: Toward a novel manganese peroxidase
    • Yeung, B.K.S., Wang, X., Sigman, J.A., Petillo, P.A., Lu, Y. Construction and characterization of a magnesium-binding site in cytochrome c peroxidase: Toward a novel manganese peroxidase. Chem. Biol. 4:215-222, 1997.
    • (1997) Chem. Biol. , vol.4 , pp. 215-222
    • Yeung, B.K.S.1    Wang, X.2    Sigman, J.A.3    Petillo, P.A.4    Lu, Y.5
  • 21
    • 0030934790 scopus 로고    scopus 로고
    • Crystal structure of the activation of histidine by Thermus thermophilus histidyl-tRNA synthetase
    • Åberg, A., Yaremchuk, A., Tukalo, M., Rasmussen, B., Cusack, S. Crystal structure of the activation of histidine by Thermus thermophilus histidyl-tRNA synthetase. Biochemistry 36:3084-3094, 1997.
    • (1997) Biochemistry , vol.36 , pp. 3084-3094
    • Åberg, A.1    Yaremchuk, A.2    Tukalo, M.3    Rasmussen, B.4    Cusack, S.5
  • 22
    • 0041784950 scopus 로고    scopus 로고
    • An all-atom empirical potential for molecular modelling and dynamics study of proteins
    • MacKerell, A.D., Bashford, D., Bellott, M., et al. An all-atom empirical potential for molecular modelling and dynamics study of proteins. J. Phys. Chem. B 102:3586-3616, 1998.
    • (1998) J. Phys. Chem. B , vol.102 , pp. 3586-3616
    • MacKerell, A.D.1    Bashford, D.2    Bellott, M.3
  • 23
  • 24
    • 0000036869 scopus 로고    scopus 로고
    • Simulation of activation free energies in molecular systems
    • Neria, E., Fischer, S., Karplus, M. Simulation of activation free energies in molecular systems. J. Chem. Phys. 105: 1902-1921, 1996.
    • (1996) J. Chem. Phys. , vol.105 , pp. 1902-1921
    • Neria, E.1    Fischer, S.2    Karplus, M.3
  • 25
    • 0030574785 scopus 로고    scopus 로고
    • Accurate calculation of the dielectric constant of water from simulations of a microscopic droplet in vacuum
    • Simonson, T. Accurate calculation of the dielectric constant of water from simulations of a microscopic droplet in vacuum. Chem. Phys. Lett. 250:450-454, 1996.
    • (1996) Chem. Phys. Lett. , vol.250 , pp. 450-454
    • Simonson, T.1
  • 26
    • 0022068152 scopus 로고
    • Active site dynamics in proteins: A stochastic boundary molecular dynamics approach
    • Brooks III, C., Brünger, A.T., Karplus, M. Active site dynamics in proteins: A stochastic boundary molecular dynamics approach. Biopolymers 24:843-865, 1985.
    • (1985) Biopolymers , vol.24 , pp. 843-865
    • Brooks III, C.1    Brünger, A.T.2    Karplus, M.3
  • 27
    • 0031561292 scopus 로고    scopus 로고
    • Continuum treatment of long-range interactions in free energy calculations. Application to protein-ligand binding
    • Simonson, T., Archontis, G., Karplus, M. Continuum treatment of long-range interactions in free energy calculations. Application to protein-ligand binding. J. Phys. Chem. B. 101:8349-8362, 1997.
    • (1997) J. Phys. Chem. B. , vol.101 , pp. 8349-8362
    • Simonson, T.1    Archontis, G.2    Karplus, M.3
  • 28
    • 33646940952 scopus 로고
    • Numerical integration of the cartesian equations of motion for a system with constraints: Molecular dynamics of n-alkanes
    • Ryckaert, J., Ciccotti, G., Berendsen, H. Numerical integration of the cartesian equations of motion for a system with constraints: Molecular dynamics of n-alkanes. J. Comp. Phys. 23:327-341, 1977.
    • (1977) J. Comp. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.1    Ciccotti, G.2    Berendsen, H.3
  • 31
    • 84986512474 scopus 로고
    • CHARMM: A program for macromolecular energy minimization and molecular dynamics calculations
    • Brooks, B., Bruccoleri, R., Olafson, B., States, D., Swaminathan, S., Karplus, M. CHARMM: A program for macromolecular energy minimization and molecular dynamics calculations. J. Comp. Chem. 4:187-217, 1983.
    • (1983) J. Comp. Chem. , vol.4 , pp. 187-217
    • Brooks, B.1    Bruccoleri, R.2    Olafson, B.3    States, D.4    Swaminathan, S.5    Karplus, M.6
  • 32
    • 0029115487 scopus 로고
    • Zinc binding in proteins and in solution: A simple but accurate nonbonded representation
    • Stote, R., Karplus, M. Zinc binding in proteins and in solution: A simple but accurate nonbonded representation. Proteins 23:12-31, 1995.
    • (1995) Proteins , vol.23 , pp. 12-31
    • Stote, R.1    Karplus, M.2
  • 33
    • 0032488817 scopus 로고    scopus 로고
    • Specific amino acid recognition by aspartyl-tRNA synthetase studied by free energy simulations
    • Archontis, G., Simonson, T., Moras, D., Karplus, M. Specific amino acid recognition by aspartyl-tRNA synthetase studied by free energy simulations. J. Mol. Biol. 275:823-846.
    • J. Mol. Biol. , vol.275 , pp. 823-846
    • Archontis, G.1    Simonson, T.2    Moras, D.3    Karplus, M.4
  • 35
    • 0030782840 scopus 로고    scopus 로고
    • Influence of magnesium ions on duplex DNA structural, dynamic, and solvation properties
    • MacKerell, A.D. Influence of magnesium ions on duplex DNA structural, dynamic, and solvation properties. J. Phys. Chem. B. 101:646-650, 1997.
    • (1997) J. Phys. Chem. B. , vol.101 , pp. 646-650
    • MacKerell, A.D.1
  • 37
    • 0344341365 scopus 로고
    • Water-water and ion-water potential functions including terms for many-body effects
    • Lybrand, T., Kollman, P. Water-water and ion-water potential functions including terms for many-body effects. J. Chem. Phys. 83:2923-2933, 1985.
    • (1985) J. Chem. Phys. , vol.83 , pp. 2923-2933
    • Lybrand, T.1    Kollman, P.2
  • 38
    • 0029091055 scopus 로고
    • Crystal structure of glycyl-tRNA synthetase from Thermus thermophilus: New functional domains and substrate specificity
    • Logan, D.T., Mazauric, M.H., Kern, D., Moras, D. Crystal structure of glycyl-tRNA synthetase from Thermus thermophilus: New functional domains and substrate specificity. EMBO J. 14:4156-4167, 1995.
    • (1995) EMBO J. , vol.14 , pp. 4156-4167
    • Logan, D.T.1    Mazauric, M.H.2    Kern, D.3    Moras, D.4
  • 39
    • 0029643954 scopus 로고
    • The crystal structure of the lysyl-tRNA synthetase (LysU) from Escherichia coli
    • Onesti, S., Miller, A.D., Brick, P. The crystal structure of the lysyl-tRNA synthetase (LysU) from Escherichia coli. Structure 3:163-176, 1995.
    • (1995) Structure , vol.3 , pp. 163-176
    • Onesti, S.1    Miller, A.D.2    Brick, P.3
  • 41
    • 6344260593 scopus 로고
    • An all-atom empirical energy force-field for the study of nucleic acids
    • MacKerell, A.D., Wiorkiewicz-Kuczera, J., Karplus, M. An all-atom empirical energy force-field for the study of nucleic acids. J. Am. Chem. Soc. 117:11946-11975, 1995.
    • (1995) J. Am. Chem. Soc. , vol.117 , pp. 11946-11975
    • MacKerell, A.D.1    Wiorkiewicz-Kuczera, J.2    Karplus, M.3
  • 43
    • 0026244229 scopus 로고
    • MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
    • Kraulis, P.J. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24:946-950, 1991.
    • (1991) J. Appl. Crystallogr. , vol.24 , pp. 946-950
    • Kraulis, P.J.1
  • 44
    • 0000913086 scopus 로고
    • A fast algorithm for rendering space-filling molecule pictures
    • Bacon, D.J., Anderson, W.F. A fast algorithm for rendering space-filling molecule pictures. J. Mol. Graphics 6:219-220, 1988.
    • (1988) J. Mol. Graphics , vol.6 , pp. 219-220
    • Bacon, D.J.1    Anderson, W.F.2
  • 45
    • 0028057108 scopus 로고
    • Raster 3D: A program for photorealistic molecular graphics
    • Merritt, E.A., Murphy, M.E.P. Raster 3D: A program for photorealistic molecular graphics. Acta Crystallogr. D50: 869-873, 1994.
    • (1994) Acta Crystallogr. , vol.D50 , pp. 869-873
    • Merritt, E.A.1    Murphy, M.E.P.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.