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Volumn 373, Issue 5, 2007, Pages 1169-1183

A Switch in the Mechanism of Communication between the Two DNA-Binding Sites in the SfiI Restriction Endonuclease

Author keywords

allostery; cooperativity; DNA protein interaction; protein protein interaction; restriction enzyme

Indexed keywords

DNA; MUTANT PROTEIN; RESTRICTION ENDONUCLEASE; SFII RESTRICTION ENDONUCLEASE; UNCLASSIFIED DRUG;

EID: 35148841533     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2007.08.030     Document Type: Article
Times cited : (17)

References (53)
  • 3
    • 0002598414 scopus 로고
    • Type II restriction enzymes
    • Linn S.M., Lloyd R.S., and Roberts R.J. (Eds), Cold Spring Harbor Laboratory Press, Cold Spring Harbor
    • Roberts R.J., and Halford S.E. Type II restriction enzymes. In: Linn S.M., Lloyd R.S., and Roberts R.J. (Eds). Nucleases (1993), Cold Spring Harbor Laboratory Press, Cold Spring Harbor 35-88
    • (1993) Nucleases , pp. 35-88
    • Roberts, R.J.1    Halford, S.E.2
  • 4
    • 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
  • 5
    • 0036440653 scopus 로고    scopus 로고
    • Type II restriction endonucleases
    • Perona J.J. Type II restriction endonucleases. Methods 28 (2002) 353-364
    • (2002) Methods , vol.28 , pp. 353-364
    • Perona, J.J.1
  • 6
    • 0033527546 scopus 로고    scopus 로고
    • The kinetic mechanism of EcoRI endonuclease
    • Wright D.J., Jack W.E., and Modrich P. The kinetic mechanism of EcoRI endonuclease. J. Biol. Chem. 274 (1999) 31896-31902
    • (1999) J. Biol. Chem. , vol.274 , pp. 31896-31902
    • Wright, D.J.1    Jack, W.E.2    Modrich, P.3
  • 7
    • 0034629080 scopus 로고    scopus 로고
    • Reactions of BglI and other Type II restriction endonucleases with discontinuous recognition sites
    • Gormley N.A., Bath A.J., and Halford S.E. Reactions of BglI and other Type II restriction endonucleases with discontinuous recognition sites. J. Biol. Chem. 275 (2000) 6928-6936
    • (2000) J. Biol. Chem. , vol.275 , pp. 6928-6936
    • Gormley, N.A.1    Bath, A.J.2    Halford, S.E.3
  • 8
    • 0030985132 scopus 로고    scopus 로고
    • Rapid-reaction analysis of plasmid DNA cleavage by the EcoRV restriction endonuclease
    • Erskine S.G., Baldwin G.S., and 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
  • 9
    • 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
  • 10
    • 0028934112 scopus 로고
    • Specific DNA recognition by EcoRV restriction endonuclease induced by calcium ions
    • Vipond I.B., and Halford S.E. Specific DNA recognition by EcoRV restriction endonuclease induced by calcium ions. Biochemistry 34 (1995) 1113-1119
    • (1995) Biochemistry , vol.34 , pp. 1113-1119
    • Vipond, I.B.1    Halford, S.E.2
  • 11
    • 0033614808 scopus 로고    scopus 로고
    • Divalent metal dependence of site-specific DNA binding by EcoRV endonuclease
    • Martin A.M., Horton N.C., Luseti S., Reich N.O., and Perona J.J. Divalent metal dependence of site-specific DNA binding by EcoRV endonuclease. Biochemistry 38 (1999) 8430-8439
    • (1999) Biochemistry , vol.38 , pp. 8430-8439
    • Martin, A.M.1    Horton, N.C.2    Luseti, S.3    Reich, N.O.4    Perona, J.J.5
  • 12
    • 0035957061 scopus 로고    scopus 로고
    • Binding and recognition of GATATC target sequences by the EcoRV restriction endonuclease: a study using fluorescent oligonucleotides and fluorescence polarization
    • Reid S.L., Parry D., Liu H.-H., and Connolly B.A. Binding and recognition of GATATC target sequences by the EcoRV restriction endonuclease: a study using fluorescent oligonucleotides and fluorescence polarization. Biochemistry 40 (2001) 2484-2494
    • (2001) Biochemistry , vol.40 , pp. 2484-2494
    • Reid, S.L.1    Parry, D.2    Liu, H.-H.3    Connolly, B.A.4
  • 13
    • 0029048413 scopus 로고
    • Structure of BamHI endonuclease bound to DNA: partial folding and unfolding on DNA binding
    • Newman M., Strzelecka T., Dorner L.F., Schildkraut I., and Aggarwal A.K. Structure of BamHI endonuclease bound to DNA: partial folding and unfolding on DNA binding. Science 269 (1995) 656-663
    • (1995) Science , vol.269 , pp. 656-663
    • Newman, M.1    Strzelecka, T.2    Dorner, L.F.3    Schildkraut, I.4    Aggarwal, A.K.5
  • 15
    • 17844400537 scopus 로고    scopus 로고
    • How restriction enzymes became the workhorses of molecular biology
    • Roberts R.J. How restriction enzymes became the workhorses of molecular biology. Proc. Natl. Acad. Sci. USA 102 (2005) 5905-5908
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 5905-5908
    • Roberts, R.J.1
  • 16
    • 0034877122 scopus 로고    scopus 로고
    • Hopping, jumping and looping by restriction enzymes
    • Halford S.E. Hopping, jumping and looping by restriction enzymes. Biochem. Soc. Trans. 29 (2001) 363-373
    • (2001) Biochem. Soc. Trans. , vol.29 , pp. 363-373
    • Halford, S.E.1
  • 17
    • 0344011130 scopus 로고    scopus 로고
    • Diversity of Type II restriction endonucleases that require two DNA recognition sites
    • Mucke M., Kruger D.H., and Reuter M. Diversity of Type II restriction endonucleases that require two DNA recognition sites. Nucleic Acids Res. 31 (2003) 6079-6084
    • (2003) Nucleic Acids Res. , vol.31 , pp. 6079-6084
    • Mucke, M.1    Kruger, D.H.2    Reuter, M.3
  • 18
    • 0037040271 scopus 로고    scopus 로고
    • Many type IIs restriction endonucleases interact with two recognition sites before cleaving DNA
    • Bath A.J., Milsom S.E., Gormley N.A., and Halford S.E. Many type IIs restriction endonucleases interact with two recognition sites before cleaving DNA. J. Biol. Chem. 277 (2002) 4024-4033
    • (2002) J. Biol. Chem. , vol.277 , pp. 4024-4033
    • Bath, A.J.1    Milsom, S.E.2    Gormley, N.A.3    Halford, S.E.4
  • 19
    • 3042785825 scopus 로고    scopus 로고
    • One recognition sequence, seven restriction enzymes, five reaction mechanisms
    • Gowers D.M., Bellamy S.R.W., and Halford S.E. One recognition sequence, seven restriction enzymes, five reaction mechanisms. Nucleic Acids Res. 32 (2004) 3469-3479
    • (2004) Nucleic Acids Res. , vol.32 , pp. 3469-3479
    • Gowers, D.M.1    Bellamy, S.R.W.2    Halford, S.E.3
  • 20
    • 33847162746 scopus 로고    scopus 로고
    • Restriction endonucleases that bridge and excise two recognition sites from DNA
    • Marshall J.M., Gowers D.M., and Halford S.E. Restriction endonucleases that bridge and excise two recognition sites from DNA. J. Mol. Biol. 387 (2007) 419-431
    • (2007) J. Mol. Biol. , vol.387 , pp. 419-431
    • Marshall, J.M.1    Gowers, D.M.2    Halford, S.E.3
  • 21
    • 0037389511 scopus 로고    scopus 로고
    • A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes
    • Roberts R.J., Belfort M., Bestor T., Bhagwat A.S., Bickle T.A., Bitinaite J., et al. A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes. Nucleic Acids Res. 31 (2003) 1805-1812
    • (2003) Nucleic Acids Res. , vol.31 , pp. 1805-1812
    • Roberts, R.J.1    Belfort, M.2    Bestor, T.3    Bhagwat, A.S.4    Bickle, T.A.5    Bitinaite, J.6
  • 22
    • 33646119884 scopus 로고    scopus 로고
    • Simultaneous binding of three recognition sites is necessary for a concerted plasmid DNA cleavage by EcoRII restriction endonuclease
    • Tamulaitis G., Sasnauskas G., Mucke M., and Siksnys V. Simultaneous binding of three recognition sites is necessary for a concerted plasmid DNA cleavage by EcoRII restriction endonuclease. J. Mol. Biol. 358 (2006) 406-419
    • (2006) J. Mol. Biol. , vol.358 , pp. 406-419
    • Tamulaitis, G.1    Sasnauskas, G.2    Mucke, M.3    Siksnys, V.4
  • 23
    • 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., and 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
  • 24
    • 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., and Huber R. Structure of the tetrameric restriction endonuclease NgoMIV in complex with cleaved DNA. Nat. Struct. Biol. 7 (2000) 792-799
    • (2000) Nat. Struct. Biol. , vol.7 , pp. 792-799
    • Deibert, M.1    Grazulis, S.2    Sasnauskas, G.3    Siksnys, V.4    Huber, R.5
  • 25
    • 28644435380 scopus 로고    scopus 로고
    • A view of consecutive binding events from structures of tetrameric endonuclease SfiI bound to DNA
    • Vanamee E.S., Viadiu H., Kucera R., Dorner L., Picone S., Schildkraut I., and Aggarwal A.K. A view of consecutive binding events from structures of tetrameric endonuclease SfiI bound to DNA. EMBO J. 24 (2005) 4198-4208
    • (2005) EMBO J. , vol.24 , pp. 4198-4208
    • Vanamee, E.S.1    Viadiu, H.2    Kucera, R.3    Dorner, L.4    Picone, S.5    Schildkraut, I.6    Aggarwal, A.K.7
  • 26
    • 0028988946 scopus 로고
    • The SfiI restriction endonuclease makes a four-strand DNA break at two copies of its recognition sequence
    • Wentzell L.M., Nobbs T.J., and Halford S.E. The SfiI restriction endonuclease makes a four-strand DNA break at two copies of its recognition sequence. J. Mol. Biol. 248 (1995) 581-595
    • (1995) J. Mol. Biol. , vol.248 , pp. 581-595
    • Wentzell, L.M.1    Nobbs, T.J.2    Halford, S.E.3
  • 27
    • 0029091376 scopus 로고
    • DNA cleavage at two recognition sites by the SfiI restriction endonuclease: salt dependence of cis and trans interactions between distant DNA sites
    • Nobbs T.J., and Halford S.E. DNA cleavage at two recognition sites by the SfiI restriction endonuclease: salt dependence of cis and trans interactions between distant DNA sites. J. Mol. Biol. 252 (1995) 399-411
    • (1995) J. Mol. Biol. , vol.252 , pp. 399-411
    • Nobbs, T.J.1    Halford, S.E.2
  • 29
    • 0037040190 scopus 로고    scopus 로고
    • The type IIs restriction endonuclease BspMI is a tetramer that acts concertedly at two copies of an asymmetric DNA sequence
    • Gormley N.A., Hillberg A.L., and Halford S.E. The type IIs restriction endonuclease BspMI is a tetramer that acts concertedly at two copies of an asymmetric DNA sequence. J. Biol. Chem. 277 (2002) 4034-4041
    • (2002) J. Biol. Chem. , vol.277 , pp. 4034-4041
    • Gormley, N.A.1    Hillberg, A.L.2    Halford, S.E.3
  • 30
    • 20444368444 scopus 로고    scopus 로고
    • Long-range communications between DNA sites by the dimeric restriction endonuclease SgrAl
    • Wood K.M., Daniels L.E., and Halford S.E. Long-range communications between DNA sites by the dimeric restriction endonuclease SgrAl. J. Mol. Biol. 350 (2005) 240-253
    • (2005) J. Mol. Biol. , vol.350 , pp. 240-253
    • Wood, K.M.1    Daniels, L.E.2    Halford, S.E.3
  • 31
    • 0021760476 scopus 로고
    • A type II restriction endonuclease with an eight nucleotide specificity from Streptomyces fimbriatus
    • Qiang B.-Q., and Schildkraut I. A type II restriction endonuclease with an eight nucleotide specificity from Streptomyces fimbriatus. Nucleic Acids Res. 12 (1984) 4507-4515
    • (1984) Nucleic Acids Res. , vol.12 , pp. 4507-4515
    • Qiang, B.-Q.1    Schildkraut, I.2
  • 33
    • 0029978713 scopus 로고    scopus 로고
    • Recombination by resolvase to analyse DNA communications by the SfiI restriction endonuclease
    • Szczelkun M.D., and Halford S.E. Recombination by resolvase to analyse DNA communications by the SfiI restriction endonuclease. EMBO J. 15 (1996) 1460-1469
    • (1996) EMBO J. , vol.15 , pp. 1460-1469
    • Szczelkun, M.D.1    Halford, S.E.2
  • 34
    • 0032555293 scopus 로고    scopus 로고
    • DNA looping by the SfiI restriction endonuclease
    • Wentzell L.M., and Halford S.E. DNA looping by the SfiI restriction endonuclease. J. Mol. Biol. 281 (1998) 433-444
    • (1998) J. Mol. Biol. , vol.281 , pp. 433-444
    • Wentzell, L.M.1    Halford, S.E.2
  • 35
    • 0035902776 scopus 로고    scopus 로고
    • Analysis of DNA looping interactions by type II restriction enzymes that require two copies of their recognition sites
    • Milsom S.E., Halford S.E., Embleton M.L., and Szczelkun M.D. Analysis of DNA looping interactions by type II restriction enzymes that require two copies of their recognition sites. J. Mol. Biol. 311 (2001) 515-527
    • (2001) J. Mol. Biol. , vol.311 , pp. 515-527
    • Milsom, S.E.1    Halford, S.E.2    Embleton, M.L.3    Szczelkun, M.D.4
  • 36
    • 0032983155 scopus 로고    scopus 로고
    • Specificity from the synapsis of DNA elements by the SfiI endonuclease
    • Embleton M.L., Williams S.A., Watson M.A., and Halford S.E. Specificity from the synapsis of DNA elements by the SfiI endonuclease. J. Mol. Biol. 289 (1999) 785-797
    • (1999) J. Mol. Biol. , vol.289 , pp. 785-797
    • Embleton, M.L.1    Williams, S.A.2    Watson, M.A.3    Halford, S.E.4
  • 37
    • 0034607553 scopus 로고    scopus 로고
    • Alternative geometries of DNA looping: an analysis using the Sfi I endonuclease
    • Watson M.A., Gowers D.M., and Halford S.E. Alternative geometries of DNA looping: an analysis using the Sfi I endonuclease. J. Mol. Biol. 298 (2000) 461-475
    • (2000) J. Mol. Biol. , vol.298 , pp. 461-475
    • Watson, M.A.1    Gowers, D.M.2    Halford, S.E.3
  • 38
    • 0036302286 scopus 로고    scopus 로고
    • Communications between catalytic sites in the protein-DNA synapse by the SfiI endonuclease
    • Williams S.A., and Halford S.E. Communications between catalytic sites in the protein-DNA synapse by the SfiI endonuclease. J. Mol. Biol. 318 (2002) 387-394
    • (2002) J. Mol. Biol. , vol.318 , pp. 387-394
    • Williams, S.A.1    Halford, S.E.2
  • 40
    • 0037082418 scopus 로고    scopus 로고
    • Crystal structure of the Bse634I restriction endonuclease: comparison of two enzymes recognizing the same DNA sequence
    • Grazulis S., Deibert M., Rimseliene R., Skirgaila R., Sasnauskas G., Lagunavicius A., et al. Crystal structure of the Bse634I restriction endonuclease: comparison of two enzymes recognizing the same DNA sequence. Nucleic Acids Res. 30 (2002) 876-885
    • (2002) Nucleic Acids Res. , vol.30 , pp. 876-885
    • Grazulis, S.1    Deibert, M.2    Rimseliene, R.3    Skirgaila, R.4    Sasnauskas, G.5    Lagunavicius, A.6
  • 41
    • 16244422033 scopus 로고    scopus 로고
    • Conversion of the tetrameric restriction endonuclease Bse634I into a dimer: oligomeric structure-stability-function correlations
    • Zaremba M., Sasnauskas G., Urbanke C., and Siksnys V. Conversion of the tetrameric restriction endonuclease Bse634I into a dimer: oligomeric structure-stability-function correlations. J. Mol. Biol. 348 (2005) 459-478
    • (2005) J. Mol. Biol. , vol.348 , pp. 459-478
    • Zaremba, M.1    Sasnauskas, G.2    Urbanke, C.3    Siksnys, V.4
  • 42
    • 33749579918 scopus 로고    scopus 로고
    • Allosteric communication network in the tetrameric restriction endonuclease Bse634I
    • Zaremba M., Sasnauskas G., Urbanke C., and Siksnys V. Allosteric communication network in the tetrameric restriction endonuclease Bse634I. J. Mol. Biol. 363 (2006) 800-812
    • (2006) J. Mol. Biol. , vol.363 , pp. 800-812
    • Zaremba, M.1    Sasnauskas, G.2    Urbanke, C.3    Siksnys, V.4
  • 43
    • 0033579567 scopus 로고    scopus 로고
    • Reactions of type II restriction endonucleases with 8-base pair recognition sites
    • Bilcock D.T., Daniels L.E., Bath A.J., and Halford S.E. Reactions of type II restriction endonucleases with 8-base pair recognition sites. J. Biol. Chem. 274 (1999) 36379-36386
    • (1999) J. Biol. Chem. , vol.274 , pp. 36379-36386
    • Bilcock, D.T.1    Daniels, L.E.2    Bath, A.J.3    Halford, S.E.4
  • 44
    • 0037470637 scopus 로고    scopus 로고
    • Subunit assembly for DNA cleavage by restriction endonuclease SgrAI
    • Daniels L.E., Wood K.M., Scott D.J., and Halford S.E. Subunit assembly for DNA cleavage by restriction endonuclease SgrAI. J. Mol. Biol. 327 (2003) 579-591
    • (2003) J. Mol. Biol. , vol.327 , pp. 579-591
    • Daniels, L.E.1    Wood, K.M.2    Scott, D.J.3    Halford, S.E.4
  • 45
    • 33645275997 scopus 로고    scopus 로고
    • Loops in DNA: an overview of experimental and theoretical approaches
    • Allemand J.F., Cocco S., Douarche N., and Lia G. Loops in DNA: an overview of experimental and theoretical approaches. Eur. Phys. J. E 19 (2006) 293-302
    • (2006) Eur. Phys. J. E , vol.19 , pp. 293-302
    • Allemand, J.F.1    Cocco, S.2    Douarche, N.3    Lia, G.4
  • 46
    • 0032530311 scopus 로고    scopus 로고
    • Crystal structure of restriction endonuclease BglI bound to its interrupted DNA recognition sequence
    • Newman M., Lunnen K., Wilson G., Greci J., Schildkraut I., and Phillips S.E.V. Crystal structure of restriction endonuclease BglI bound to its interrupted DNA recognition sequence. EMBO J. 17 (1998) 5466-5476
    • (1998) EMBO J. , vol.17 , pp. 5466-5476
    • Newman, M.1    Lunnen, K.2    Wilson, G.3    Greci, J.4    Schildkraut, I.5    Phillips, S.E.V.6
  • 47
    • 21544433515 scopus 로고    scopus 로고
    • A homology model of restriction endonuclease SfiI in complex with DNA
    • Chmiel A.A., Bujnicki J.M., and Skowronek K.J. A homology model of restriction endonuclease SfiI in complex with DNA. BMC Struct. Biol. 5 (2005) 2
    • (2005) BMC Struct. Biol. , vol.5 , pp. 2
    • Chmiel, A.A.1    Bujnicki, J.M.2    Skowronek, K.J.3
  • 48
    • 0026319199 scopus 로고
    • Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons
    • Nicholls A., Sharp K.A., and Honig B. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins: Struct. Funct. Genet. 11 (1991) 281-296
    • (1991) Proteins: Struct. Funct. Genet. , vol.11 , pp. 281-296
    • Nicholls, A.1    Sharp, K.A.2    Honig, B.3
  • 51
    • 78651189765 scopus 로고
    • On the nature of allosteric transitions: a plausible model
    • Monod J., Wyman J., and Changeux J.P. On the nature of allosteric transitions: a plausible model. J. Mol Biol. 12 (1965) 88-118
    • (1965) J. Mol Biol. , vol.12 , pp. 88-118
    • Monod, J.1    Wyman, J.2    Changeux, J.P.3
  • 52
    • 0013863816 scopus 로고
    • Comparison of experimental binding data and theoretical models in proteins containing subunits
    • Koshland Jr. D.E., Nemethy G., and Filmer D. Comparison of experimental binding data and theoretical models in proteins containing subunits. Biochemistry 5 (1966) 365-385
    • (1966) Biochemistry , vol.5 , pp. 365-385
    • Koshland Jr., D.E.1    Nemethy, G.2    Filmer, D.3
  • 53
    • 23844514076 scopus 로고    scopus 로고
    • Structure of a synaptic γδ resolvase tetramer covalently linked to two cleaved DNAs
    • Li W., Kamtekar S., Xiong Y., Sarkis G.J., Grindley N.D.F., and Steitz T.A. Structure of a synaptic γδ resolvase tetramer covalently linked to two cleaved DNAs. Science 309 (2005) 1210-1215
    • (2005) Science , vol.309 , pp. 1210-1215
    • Li, W.1    Kamtekar, S.2    Xiong, Y.3    Sarkis, G.J.4    Grindley, N.D.F.5    Steitz, T.A.6


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