메뉴 건너뛰기




Volumn 331, Issue 2, 2003, Pages 395-406

Structural and biochemical characterization of a new Mg2+ binding site near Tyr94 in the restriction endonuclease PvuII

Author keywords

Crystallography; DNA cleavage; Kinetics; Mechanism of catalysis; Metal ion binding

Indexed keywords

ASPARAGINE; DNA; ENDONUCLEASE; GLUTAMIC ACID; MAGNESIUM ION; PHENYLALANINE; PROTEIN SUBUNIT; TYROSINE;

EID: 0041347883     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(03)00692-2     Document Type: Article
Times cited : (14)

References (58)
  • 1
    • 0002598414 scopus 로고
    • Type II restriction enzymes
    • S.M. Linn, R.S. Lloyd, & R.J. Roberts. Cold Spring Harbor: Cold Spring Harbor Laboratory Press
    • Roberts R.J., Halford S.E. Type II restriction enzymes. Linn S.M., Lloyd R.S., Roberts R.J. Nucleases. 1993;35-88 Cold Spring Harbor Laboratory Press, Cold Spring Harbor.
    • (1993) Nucleases , pp. 35-88
    • Roberts, R.J.1    Halford, S.E.2
  • 2
    • 0030911133 scopus 로고    scopus 로고
    • Recognition and cleavage of DNA by type-II restriction endonucleases
    • Pingoud A., Jeltsch A. Recognition and cleavage of DNA by type-II restriction endonucleases. Eur. J. Biochem. 246:1997;1-22.
    • (1997) Eur. J. Biochem. , vol.246 , pp. 1-22
    • Pingoud, A.1    Jeltsch, A.2
  • 3
    • 0035883723 scopus 로고    scopus 로고
    • Structure and function of type II restriction endonucleases
    • Pingoud A., Jeltsch A. Structure and function of type II restriction endonucleases. Nucl. Acids Res. 29:2001;3705-3727.
    • (2001) Nucl. Acids Res. , vol.29 , pp. 3705-3727
    • Pingoud, A.1    Jeltsch, A.2
  • 4
    • 0025187081 scopus 로고
    • Refinement of EcoRI endonuclease crystal structure: A revised protein chain tracing
    • Kim Y., Grable J.C., Love R., Greene P.J., Rosenberg J.M. Refinement of EcoRI endonuclease crystal structure: a revised protein chain tracing. Science. 249:1990;1307-1309.
    • (1990) Science , vol.249 , pp. 1307-1309
    • Kim, Y.1    Grable, J.C.2    Love, R.3    Greene, P.J.4    Rosenberg, J.M.5
  • 5
    • 0027159254 scopus 로고
    • The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments
    • Winkler F.K., Banner D.W., Oefner C., Tsernoglou D., Brown R.S., Heathman S.P., et al. The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments. EMBO J. 12:1993;1781-1795.
    • (1993) EMBO J. , vol.12 , pp. 1781-1795
    • Winkler, F.K.1    Banner, D.W.2    Oefner, C.3    Tsernoglou, D.4    Brown, R.S.5    Heathman, S.P.6
  • 7
    • 0033818703 scopus 로고    scopus 로고
    • Structure of the tetrameric restriction endonuclease NgoMIV in complex with cleaved DNA
    • Deibert M., Grazulis S., Sasnauskas G., Siksnys V., Huber R. Structure of the tetrameric restriction endonuclease NgoMIV in complex with cleaved DNA. Nature Struct. Biol. 7:2000;792-799.
    • (2000) Nature Struct. Biol. , vol.7 , pp. 792-799
    • Deibert, M.1    Grazulis, S.2    Sasnauskas, G.3    Siksnys, V.4    Huber, R.5
  • 8
    • 0035902832 scopus 로고    scopus 로고
    • DNA cleavage reactions by type II restriction enzymes that require two copies of their recognition sites
    • Embleton M.L., Siksnys V., Halford S.E. DNA cleavage reactions by type II restriction enzymes that require two copies of their recognition sites. J. Mol. Biol. 311:2001;503-514.
    • (2001) J. Mol. Biol. , vol.311 , pp. 503-514
    • Embleton, M.L.1    Siksnys, V.2    Halford, S.E.3
  • 9
    • 0032848682 scopus 로고    scopus 로고
    • Type II restriction endonucleases: Structural, functional and evolutionary relationships
    • Kovall R.A., Matthews B.W. Type II restriction endonucleases: structural, functional and evolutionary relationships. Curr. Opin. Chem. Biol. 3:1999;578-583.
    • (1999) Curr. Opin. Chem. Biol. , vol.3 , pp. 578-583
    • Kovall, R.A.1    Matthews, B.W.2
  • 10
    • 0000001528 scopus 로고    scopus 로고
    • Metal activation of enzymes in nucleic acid biochemstry
    • Cowan J.A. Metal activation of enzymes in nucleic acid biochemstry. Chem. Rev. 98:1998;1067-1087.
    • (1998) Chem. Rev. , vol.98 , pp. 1067-1087
    • Cowan, J.A.1
  • 11
    • 85031135877 scopus 로고    scopus 로고
    • 2+ ions reveals two divalent metals bound in the active site
    • 2+ ions reveals two divalent metals bound in the active site. J. Biol. Chem. 9:2000;10.
    • (2000) J. Biol. Chem. , vol.9 , pp. 10
    • Goedken, E.R.1    Marqusee, S.2
  • 13
    • 0030886344 scopus 로고    scopus 로고
    • Does the restriction endonuclease EcoRV employ a two-metal-ion mechanism for DNA cleavage?
    • Groll D.H., Jeltsch A., Selent U., Pingoud A. Does the restriction endonuclease EcoRV employ a two-metal-ion mechanism for DNA cleavage? Biochemistry. 36:1997;11389-11401.
    • (1997) Biochemistry , vol.36 , pp. 11389-11401
    • Groll, D.H.1    Jeltsch, A.2    Selent, U.3    Pingoud, A.4
  • 14
    • 0035793706 scopus 로고    scopus 로고
    • Catalytic efficiency and sequence selectivity of a restriction endonuclease modulated by a distal manganese ion binding site
    • Sam M.D., Horton N.C., Nissan T.A., Perona J.J. Catalytic efficiency and sequence selectivity of a restriction endonuclease modulated by a distal manganese ion binding site. J. Mol. Biol. 306:2001;851-861.
    • (2001) J. Mol. Biol. , vol.306 , pp. 851-861
    • Sam, M.D.1    Horton, N.C.2    Nissan, T.A.3    Perona, J.J.4
  • 16
    • 0026633116 scopus 로고
    • Sequence and characterization of pvuIIR, the PvuII endonuclease gene, and of pvuIIC, its regulatory gene
    • Tao T., Blumenthal R.M. Sequence and characterization of pvuIIR, the PvuII endonuclease gene, and of pvuIIC, its regulatory gene. J. Bacteriol. 174:1992;3395-3398.
    • (1992) J. Bacteriol. , vol.174 , pp. 3395-3398
    • Tao, T.1    Blumenthal, R.M.2
  • 21
    • 0032545161 scopus 로고    scopus 로고
    • Asp34 of PvuII endonuclease is directly involved in DNA minor groove recognition and indirectly involved in catalysis
    • Horton J.R., Nastri H.G., Riggs P.D., Cheng X. Asp34 of PvuII endonuclease is directly involved in DNA minor groove recognition and indirectly involved in catalysis. J. Mol. Biol. 284:1998;1491-1504.
    • (1998) J. Mol. Biol. , vol.284 , pp. 1491-1504
    • Horton, J.R.1    Nastri, H.G.2    Riggs, P.D.3    Cheng, X.4
  • 22
    • 0031971246 scopus 로고    scopus 로고
    • How is modification of the DNA substrate recognized by the PvuII restriction endonuclease?
    • Horton J.R., Bonventre J., Cheng X. How is modification of the DNA substrate recognized by the PvuII restriction endonuclease? Biol. Chem. 379:1998;451-458.
    • (1998) Biol. Chem. , vol.379 , pp. 451-458
    • Horton, J.R.1    Bonventre, J.2    Cheng, X.3
  • 23
    • 0028932881 scopus 로고
    • Structure and function of restriction endonucleases
    • Aggarwal A.K. Structure and function of restriction endonucleases. Curr. Opin. Struct. Biol. 5:1995;11-19.
    • (1995) Curr. Opin. Struct. Biol. , vol.5 , pp. 11-19
    • Aggarwal, A.K.1
  • 24
    • 0034725527 scopus 로고    scopus 로고
    • PvuII endonuclease contains two calcium ions in active sites
    • Horton J.R., Cheng X. PvuII endonuclease contains two calcium ions in active sites. J. Mol. Biol. 300:2000;1049-1056.
    • (2000) J. Mol. Biol. , vol.300 , pp. 1049-1056
    • Horton, J.R.1    Cheng, X.2
  • 25
    • 0026351174 scopus 로고
    • Purification, crystallization and preliminary X-ray diffraction studies of the PvuII endonuclease
    • Athanasiadis A., Kokkinidis M. Purification, crystallization and preliminary X-ray diffraction studies of the PvuII endonuclease. J. Mol. Biol. 222:1991;451-453.
    • (1991) J. Mol. Biol. , vol.222 , pp. 451-453
    • Athanasiadis, A.1    Kokkinidis, M.2
  • 26
    • 0029038784 scopus 로고
    • Crystal structure of the PvuII restriction endonuclease
    • Cheng X., Balendiran K., Schildkraut I., Anderson J.E. Crystal structure of the PvuII restriction endonuclease. Gene. 157:1995;139-140.
    • (1995) Gene , vol.157 , pp. 139-140
    • Cheng, X.1    Balendiran, K.2    Schildkraut, I.3    Anderson, J.E.4
  • 27
    • 0028988416 scopus 로고
    • 2+ binding to the active site of EcoRV endonuclease: A crystallographic study of complexes with substrate and product DNA at 2 angstrom resolution
    • 2+ binding to the active site of EcoRV endonuclease: a crystallographic study of complexes with substrate and product DNA at 2 angstrom resolution. Biochemistry. 34:1995;683-696.
    • (1995) Biochemistry , vol.34 , pp. 683-696
    • Kostrewa, D.1    Winkler, F.K.2
  • 28
    • 0032506110 scopus 로고    scopus 로고
    • Metal ion-mediated substrate-assisted catalysis in type II restriction endonucleases
    • Horton N.C., Newberry K.J., Perona J.J. Metal ion-mediated substrate-assisted catalysis in type II restriction endonucleases. Proc. Natl Acad. Sci. USA. 95:1998;13489-13494.
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 13489-13494
    • Horton, N.C.1    Newberry, K.J.2    Perona, J.J.3
  • 29
    • 0031717755 scopus 로고    scopus 로고
    • The role of metals in catalysis by the restriction endonuclease BamHI
    • Viadiu H., Aggarwal A.K. The role of metals in catalysis by the restriction endonuclease BamHI. Nature Struct. Biol. 5:1998;910-916.
    • (1998) Nature Struct. Biol. , vol.5 , pp. 910-916
    • Viadiu, H.1    Aggarwal, A.K.2
  • 30
    • 0024833293 scopus 로고
    • Recognition of DNA by type II restriction enzymes
    • Bennett S.P., Halford S.E. Recognition of DNA by type II restriction enzymes. Curr. Top. Cell. Regul. 30:1989;57-104.
    • (1989) Curr. Top. Cell. Regul. , vol.30 , pp. 57-104
    • Bennett, S.P.1    Halford, S.E.2
  • 31
    • 0027164447 scopus 로고
    • Effect of site-specific methylation on restriction endonucleases and DNA modification methyltransferases
    • Nelson M., Raschke E., McClelland M. Effect of site-specific methylation on restriction endonucleases and DNA modification methyltransferases. Nucl. Acids Res. 21:1993;3139-3154.
    • (1993) Nucl. Acids Res. , vol.21 , pp. 3139-3154
    • Nelson, M.1    Raschke, E.2    McClelland, M.3
  • 32
    • 0027229635 scopus 로고
    • Restriction endonuclease cleavage of 5-methyl-deoxycytosine hemimethylated DNA at high enzyme-to-substrate ratios
    • Nelson P.S., Papas T.S., Schweinfest C.W. Restriction endonuclease cleavage of 5-methyl-deoxycytosine hemimethylated DNA at high enzyme-to-substrate ratios. Nucl. Acids Res. 21:1993;681-686.
    • (1993) Nucl. Acids Res. , vol.21 , pp. 681-686
    • Nelson, P.S.1    Papas, T.S.2    Schweinfest, C.W.3
  • 34
    • 0028944994 scopus 로고
    • Heterogeneity in molecular recognition by restriction endonucleases: Osmotic and hydrostatic pressure effects on BamHI, PvuII, and EcoRV specificity
    • Robinson C.R., Sligar S.G. Heterogeneity in molecular recognition by restriction endonucleases: osmotic and hydrostatic pressure effects on BamHI, PvuII, and EcoRV specificity. Proc. Natl Acad. Sci. USA. 92:1995;3444-3448.
    • (1995) Proc. Natl Acad. Sci. USA , vol.92 , pp. 3444-3448
    • Robinson, C.R.1    Sligar, S.G.2
  • 35
    • 0029053988 scopus 로고
    • Evidence for substrate-assisted catalysis in the DNA cleavage of several restriction endonucleases
    • Jeltsch A., Pleckaityte M., Selent U., Wolfes H., Siksnys V., Pingoud A. Evidence for substrate-assisted catalysis in the DNA cleavage of several restriction endonucleases. Gene. 157:1995;157-162.
    • (1995) Gene , vol.157 , pp. 157-162
    • Jeltsch, A.1    Pleckaityte, M.2    Selent, U.3    Wolfes, H.4    Siksnys, V.5    Pingoud, A.6
  • 36
    • 0030867835 scopus 로고    scopus 로고
    • Catalytic DNA binding properties of PvuII restriction endonuclease mutants
    • Nastri H.G., Evans P.D., Walker I.H., Riggs P.D. Catalytic DNA binding properties of PvuII restriction endonuclease mutants. J. Biol. Chem. 272:1997;25761-25767.
    • (1997) J. Biol. Chem. , vol.272 , pp. 25761-25767
    • Nastri, H.G.1    Evans, P.D.2    Walker, I.H.3    Riggs, P.D.4
  • 37
    • 0033556694 scopus 로고    scopus 로고
    • Substrate recognition by the PvuII endonuclease: Binding and cleavage of CAG5mCTG sites
    • Rice M.R., Koons M.D., Blumenthal R.M. Substrate recognition by the PvuII endonuclease: binding and cleavage of CAG5mCTG sites. Nucl. Acids Res. 27:1999;1032-1038.
    • (1999) Nucl. Acids Res. , vol.27 , pp. 1032-1038
    • Rice, M.R.1    Koons, M.D.2    Blumenthal, R.M.3
  • 39
    • 0032733278 scopus 로고    scopus 로고
    • Quantitative evaluation of metal ion binding to PvuII restriction endonuclease
    • Jose T.J., Conlan L.H., Dupureur C.M. Quantitative evaluation of metal ion binding to PvuII restriction endonuclease. J. Biol. Inorg. Chem. 4:1999;814-823.
    • (1999) J. Biol. Inorg. Chem. , vol.4 , pp. 814-823
    • Jose, T.J.1    Conlan, L.H.2    Dupureur, C.M.3
  • 40
    • 0033118838 scopus 로고    scopus 로고
    • Effects of divalent metal ions on the activity and conformation of native and 3-fluorotyrosine-PvuII endonucleases
    • Dupureur C.M., Hallman L.M. Effects of divalent metal ions on the activity and conformation of native and 3-fluorotyrosine-PvuII endonucleases. Eur. J. Biochem. 261:1999;261-268.
    • (1999) Eur. J. Biochem. , vol.261 , pp. 261-268
    • Dupureur, C.M.1    Hallman, L.M.2
  • 41
    • 0034609520 scopus 로고    scopus 로고
    • A catalytically deficient active site variant of PvuII endonuclease binds Mg(II) ions
    • Dupureur C.M., Conlan L.H. A catalytically deficient active site variant of PvuII endonuclease binds Mg(II) ions. Biochemistry. 39:2000;10921-10927.
    • (2000) Biochemistry , vol.39 , pp. 10921-10927
    • Dupureur, C.M.1    Conlan, L.H.2
  • 42
    • 0035895362 scopus 로고    scopus 로고
    • The PD...(D/E)XK motif in restriction enzymes: A link between function and conformation
    • Dupureur C.M., Dominguez M.A. The PD...(D/E)XK motif in restriction enzymes: a link between function and conformation. Biochemistry. 40:2001;387-394.
    • (2001) Biochemistry , vol.40 , pp. 387-394
    • Dupureur, C.M.1    Dominguez, M.A.2
  • 43
    • 0027464412 scopus 로고
    • Mutational analysis of the function of Gln115 in the EcoRI restriction endonuclease, a critical amino acid for recognition of the inner thymidine residue in the sequence GAATTC and for coupling specific DNA binding to catalysis
    • Jeltsch A., Alves J., Oelgeschlager T., Wolfes H., Maass G., Pingoud A. Mutational analysis of the function of Gln115 in the EcoRI restriction endonuclease, a critical amino acid for recognition of the inner thymidine residue in the sequence GAATTC and for coupling specific DNA binding to catalysis. J. Mol. Biol. 229:1993;221-234.
    • (1993) J. Mol. Biol. , vol.229 , pp. 221-234
    • Jeltsch, A.1    Alves, J.2    Oelgeschlager, T.3    Wolfes, H.4    Maass, G.5    Pingoud, A.6
  • 44
    • 0029975922 scopus 로고    scopus 로고
    • Probing the indirect readout of the restriction enzyme EcoRV
    • Wenz C., Jeltsch A., Pingoud A. Probing the indirect readout of the restriction enzyme EcoRV. J. Biol. Chem. 271:1996;5565-5573.
    • (1996) J. Biol. Chem. , vol.271 , pp. 5565-5573
    • Wenz, C.1    Jeltsch, A.2    Pingoud, A.3
  • 45
    • 0032554644 scopus 로고    scopus 로고
    • Intra- versus intersubunit communication in the homodimeric restriction enzyme EcoRV: Thr37 and Lys38 involved in indirect readout are only important for the catalytic activity of their own subunit
    • Stahl F., Wende W., Wenz C., Jeltsch A., Pingoud A. Intra- versus intersubunit communication in the homodimeric restriction enzyme EcoRV: Thr37 and Lys38 involved in indirect readout are only important for the catalytic activity of their own subunit. Biochemistry. 37:1998;5682-5688.
    • (1998) Biochemistry , vol.37 , pp. 5682-5688
    • Stahl, F.1    Wende, W.2    Wenz, C.3    Jeltsch, A.4    Pingoud, A.5
  • 46
    • 0031960447 scopus 로고    scopus 로고
    • The mechanism of DNA cleavage by the type II restriction enzyme EcoRV: Asp36 is not directly involved in DNA cleavage but serves to couple indirect readout to catalysis
    • Stahl F., Wende W., Jeltsch A., Pingoud A. The mechanism of DNA cleavage by the type II restriction enzyme EcoRV: Asp36 is not directly involved in DNA cleavage but serves to couple indirect readout to catalysis. Biol. Chem. 379:1998;467-473.
    • (1998) Biol. Chem. , vol.379 , pp. 467-473
    • Stahl, F.1    Wende, W.2    Jeltsch, A.3    Pingoud, A.4
  • 47
    • 0030985132 scopus 로고    scopus 로고
    • Rapid-reaction analysis of plasmid DNA cleavage by the EcoRV restriction endonuclease
    • Erskine S.G., Baldwin G.S., Halford S.E. Rapid-reaction analysis of plasmid DNA cleavage by the EcoRV restriction endonuclease. Biochemistry. 36:1997;7567-7576.
    • (1997) Biochemistry , vol.36 , pp. 7567-7576
    • Erskine, S.G.1    Baldwin, G.S.2    Halford, S.E.3
  • 48
    • 0020585395 scopus 로고
    • Single turnovers of the EcoRI restriction endonuclease
    • Halford S.E., Johnson N.P. Single turnovers of the EcoRI restriction endonuclease. Biochem. J. 211:1983;405-415.
    • (1983) Biochem. J. , vol.211 , pp. 405-415
    • Halford, S.E.1    Johnson, N.P.2
  • 49
    • 0024974062 scopus 로고
    • Fluorescence stopped-flow kinetics of the cleavage of synthetic oligodeoxynucleotides by the EcoRI restriction endonuclease
    • Alves J., Urbanke C., Fliess A., Maass G., Pingoud A. Fluorescence stopped-flow kinetics of the cleavage of synthetic oligodeoxynucleotides by the EcoRI restriction endonuclease. Biochemistry. 28:1989;7879-7888.
    • (1989) Biochemistry , vol.28 , pp. 7879-7888
    • Alves, J.1    Urbanke, C.2    Fliess, A.3    Maass, G.4    Pingoud, A.5
  • 50
    • 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. 276:1997;307-326.
    • (1997) Methods Enzymol. , vol.276 , pp. 307-326
    • Otwinowski, Z.1    Minor, W.2
  • 51
    • 84889120137 scopus 로고
    • Improved methods for binding 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 binding 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
  • 54
    • 0027169515 scopus 로고
    • Main-chain bond lengths and bond angles in protein structures
    • Laskowski R.A., Moss D.S., Thornton J.M. Main-chain bond lengths and bond angles in protein structures. J. Mol. Biol. 231:1993;1049-1067.
    • (1993) J. Mol. Biol. , vol.231 , pp. 1049-1067
    • Laskowski, R.A.1    Moss, D.S.2    Thornton, J.M.3
  • 55
    • 0030815133 scopus 로고    scopus 로고
    • Raster3D: Photorealistic molecular graphics
    • Merrit E.A., Bacon D.J. Raster3D: photorealistic molecular graphics. Methods Enzymol. 277:1997;505-524.
    • (1997) Methods Enzymol. , vol.277 , pp. 505-524
    • Merrit, E.A.1    Bacon, D.J.2
  • 56
    • 0024520745 scopus 로고
    • Site-directed mutagenesis by overlap extension using the polymerase chain reaction
    • Ho S.N., Hunt H.D., Horton R.M., Pullen J.K., Pease L.R. Site-directed mutagenesis by overlap extension using the polymerase chain reaction. Gene. 77:1989;51-59.
    • (1989) Gene , vol.77 , pp. 51-59
    • Ho, S.N.1    Hunt, H.D.2    Horton, R.M.3    Pullen, J.K.4    Pease, L.R.5
  • 57
    • 0031582086 scopus 로고    scopus 로고
    • Single-chain repressors containing engineered DNA-binding domains of the phage 434 repressor recognize symmetric or asymmetric DNA operators
    • Simoncsits A., Chen J., Percipalle P., Wang S., Toro I., Pongor S. Single-chain repressors containing engineered DNA-binding domains of the phage 434 repressor recognize symmetric or asymmetric DNA operators. J. Mol. Biol. 267:1997;118-131.
    • (1997) J. Mol. Biol. , vol.267 , pp. 118-131
    • Simoncsits, A.1    Chen, J.2    Percipalle, P.3    Wang, S.4    Toro, I.5    Pongor, S.6
  • 58
    • 0020418554 scopus 로고
    • Versatile low-copy-number plasmid vectors for cloning in Escherichia coli
    • Stoker N.G., Fairweather N.F., Spratt B.G. Versatile low-copy-number plasmid vectors for cloning in Escherichia coli. Gene. 18:1982;335-341.
    • (1982) Gene , vol.18 , pp. 335-341
    • Stoker, N.G.1    Fairweather, N.F.2    Spratt, B.G.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.