메뉴 건너뛰기




Volumn 37, Issue 16, 2009, Pages 5443-5453

Differences between Ca2+ and Mg2+ in DNA binding and release by the SfiI restriction endonuclease: Implications for DNA looping

Author keywords

[No Author keywords available]

Indexed keywords

CALCIUM ION; DNA; EDETIC ACID; MAGNESIUM ION; PROTEIN SFIL; RESTRICTION ENDONUCLEASE; UNCLASSIFIED DRUG; CALCIUM; DIVALENT CATION; DNA BINDING PROTEIN; ENDODEOXYRIBONUCLEASE SFII; MAGNESIUM; TYPE II SITE SPECIFIC DEOXYRIBONUCLEASE;

EID: 70349258664     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp569     Document Type: Article
Times cited : (18)

References (50)
  • 1
    • 0032005866 scopus 로고    scopus 로고
    • Structural and functional insights provided by crystal structures of DNA polymerases and their substrate complexes
    • Brautigam,C.A. and Steitz,T.A. (1998) Structural and functional insights provided by crystal structures of DNA polymerases and their substrate complexes. Curr. Opin. Struct. Biol., 8, 54-63.
    • (1998) Curr. Opin. Struct. Biol. , vol.8 , pp. 54-63
    • Brautigam, C.A.1    Steitz, T.A.2
  • 2
    • 0037180394 scopus 로고    scopus 로고
    • Catalytic mechanisms of restriction and homing endonucleases
    • Galburt,E.A. and Stoddard,B.L. (2002) Catalytic mechanisms of restriction and homing endonucleases. Biochemistry, 41, 13851-13860.
    • (2002) Biochemistry , vol.41 , pp. 13851-13860
    • Galburt, E.A.1    Stoddard, B.L.2
  • 3
    • 33645962475 scopus 로고    scopus 로고
    • 2+-ion catalysis and substrate specificity
    • 2+-ion catalysis and substrate specificity. Mol. Cell, 22, 5-13.
    • (2006) Mol. Cell , vol.22 , pp. 5-13
    • Yang, W.1    Lee, J.2    Nowotny, M.3
  • 4
    • 0037470599 scopus 로고    scopus 로고
    • The metal-independent Type IIS restriction enzyme BfiI is a dimer that binds two DNA sites but has only one catalytic centre
    • Lagunavicius,A., Sasnauskas,G., Halford,S.E. and Siksnys,V. (2003) The metal-independent Type IIS restriction enzyme BfiI is a dimer that binds two DNA sites but has only one catalytic centre. J. Mol. Biol., 326, 1051-1064.
    • (2003) J. Mol. Biol. , vol.326 , pp. 1051-1064
    • Lagunavicius, A.1    Sasnauskas, G.2    Halford, S.E.3    Siksnys, V.4
  • 5
  • 7
    • 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. (1993) Type II restriction enzymes. In Linn,S.M., Lloyd,R.S. and Roberts,R.J. (eds), Nucleases. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, pp. 35-88.
    • (1993) Nucleases , pp. 35-88
    • Roberts, R.J.1    Halford, S.E.2
  • 8
    • 0028932881 scopus 로고
    • Structure and function of restriction endonucleases
    • Aggarwal,A.K. (1995) Structure and function of restriction endonucleases. Curr. Opin. Struct. Biol., 5, 11-19.
    • (1995) Curr. Opin. Struct. Biol. , vol.5 , pp. 11-19
    • Aggarwal, A.K.1
  • 9
    • 0036440653 scopus 로고    scopus 로고
    • Type II restriction endonucleases
    • Perona,J.J. (2002) Type II restriction endonucleases. Methods, 28, 353-364.
    • (2002) Methods , vol.28 , pp. 353-364
    • Perona, J.J.1
  • 11
    • 0019186907 scopus 로고
    • The EcoRI restriction endonuclease with bacteriophage lambda DNA. Equilibrium binding studies
    • Halford,S.E. and Johnson,N.P. (1980) The EcoRI restriction endonuclease with bacteriophage lambda DNA. Equilibrium binding studies. Biochem. J., 191, 593-604.
    • (1980) Biochem. J. , vol.191 , pp. 593-604
    • Halford, S.E.1    Johnson, N.P.2
  • 12
    • 0021112461 scopus 로고
    • Thermodynamic parameters governing interaction of EcoRI endonuclease with specific and nonspecific DNA sequences
    • Terry,B.J., Jack,W.E., Rubin,R.A. and Modrich,P. (1983) Thermodynamic parameters governing interaction of EcoRI endonuclease with specific and nonspecific DNA sequences. J. Biol. Chem., 258, 9820-9825.
    • (1983) J. Biol. Chem. , vol.258 , pp. 9820-9825
    • Terry, B.J.1    Jack, W.E.2    Rubin, R.A.3    Modrich, P.4
  • 14
    • 0025889005 scopus 로고
    • EcoRV restriction endonuclease binds all DNA sequences with equal affinity
    • Taylor,J.D., Badcoe,I.G., Clarke,A.R. and Halford,S.E. (1991) EcoRV restriction endonuclease binds all DNA sequences with equal affinity. Biochemistry, 30, 8743-8753.
    • (1991) Biochemistry , vol.30 , pp. 8743-8753
    • Taylor, J.D.1    Badcoe, I.G.2    Clarke, A.R.3    Halford, S.E.4
  • 15
    • 0026722915 scopus 로고
    • Characterization of steady state, single-turnover, and binding kinetics of the TaqI restriction endonuclease
    • Zebala,J., Choi,J. and Barany,F. (1992) Characterization of steady state, single-turnover, and binding kinetics of the TaqI restriction endonuclease. J. Biol. Chem., 267, 8097-8105.
    • (1992) J. Biol. Chem. , vol.267 , pp. 8097-8105
    • Zebala, J.1    Choi, J.2    Barany, F.3
  • 16
    • 0030886218 scopus 로고    scopus 로고
    • Site-directed mutagenesis of putative active site residues of MunI restriction endonuclease: replacement of catalytically essential carboxylate residues triggers DNA binding specificity
    • Lagunavicius,A. and Siksnys,V. (1997) Site-directed mutagenesis of putative active site residues of MunI restriction endonuclease: replacement of catalytically essential carboxylate residues triggers DNA binding specificity. Biochemistry, 36, 11086-11092.
    • (1997) Biochemistry , vol.36 , pp. 11086-11092
    • Lagunavicius, A.1    Siksnys, V.2
  • 17
    • 0032488670 scopus 로고    scopus 로고
    • Reactions of the EcoRV restriction endonuclease with fluorescent oligodeoxynucleotides: identical equilibrium constants for binding to specific and non-specific DNA
    • Erskine,S.G. and Halford,S.E. (1998) Reactions of the EcoRV restriction endonuclease with fluorescent oligodeoxynucleotides: identical equilibrium constants for binding to specific and non-specific DNA. J. Mol. Biol., 275, 759-772.
    • (1998) J. Mol. Biol. , vol.275 , pp. 759-772
    • Erskine, S.G.1    Halford, S.E.2
  • 18
    • 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. (1999) Specificity from the synapsis of DNA elements by the SfiI endonuclease. J. Mol. Biol., 289, 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
  • 19
    • 0035946911 scopus 로고    scopus 로고
    • FokI requires two specific DNA sites for cleavage
    • Vanamee,E.S., Santagata,S. and Aggarwal,A.K. (2001) FokI requires two specific DNA sites for cleavage. J. Mol. Biol., 309, 69-78.
    • (2001) J. Mol. Biol. , vol.309 , pp. 69-78
    • Vanamee, E.S.1    Santagata, S.2    Aggarwal, A.K.3
  • 20
    • 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. (2003) Subunit assembly for DNA cleavage by restriction endonuclease SgrAI. J. Mol. Biol., 327, 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
  • 21
    • 0028934112 scopus 로고
    • Specific DNA recognition by EcoRV restriction endonuclease induced by calcium ions
    • Vipond,I.B. and Halford,S.E. (1995) Specific DNA recognition by EcoRV restriction endonuclease induced by calcium ions. Biochemistry, 34, 1113-1119.
    • (1995) Biochemistry , vol.34 , pp. 1113-1119
    • Vipond, I.B.1    Halford, S.E.2
  • 22
    • 0030885532 scopus 로고    scopus 로고
    • DNA binding specificity of MunI restriction endonuclease is controlled by pH and calcium ions: Involvement of active site carboxylate residues
    • Lagunavicius,A., Grazulis,S., Balciunaite,E., Vainius,D. and Siksnys,V. (1997) DNA binding specificity of MunI restriction endonuclease is controlled by pH and calcium ions: Involvement of active site carboxylate residues. Biochemistry, 36, 11093-11099.
    • (1997) Biochemistry , vol.36 , pp. 11093-11099
    • Lagunavicius, A.1    Grazulis, S.2    Balciunaite, E.3    Vainius, D.4    Siksnys, V.5
  • 23
    • 0033594928 scopus 로고    scopus 로고
    • Binding kinetics and footprinting of TaqI endonuclease: Effects of metal cofactors on sequence-specific interactions
    • Cao,W. (1999) Binding kinetics and footprinting of TaqI endonuclease: Effects of metal cofactors on sequence-specific interactions. Biochemistry, 38, 8080-8087.
    • (1999) Biochemistry , vol.38 , pp. 8080-8087
    • Cao, W.1
  • 24
    • 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. (1999) Divalent metal dependence of site-specific DNA binding by EcoRV endonuclease. Biochemistry, 38, 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
  • 25
    • 14244252109 scopus 로고    scopus 로고
    • Restriction endonucleases: Structure of the conserved catalytic core and the role of metal ions in DNA cleavage
    • Pingoud,A. (ed.), Springer-Verlag, Berlin
    • Horton,J.R., Blumenthal,R.M. and Cheng,X. (2004) Restriction endonucleases: Structure of the conserved catalytic core and the role of metal ions in DNA cleavage. In Pingoud,A. (ed.), Nucleic Acids and Molecular Biology, Restriction Endonucleases. Vol. 14, Springer-Verlag, Berlin, pp. 361-392.
    • (2004) Nucleic Acids and Molecular Biology, Restriction Endonucleases , vol.14 , pp. 361-392
    • Horton, J.R.1    Blumenthal, R.M.2    Cheng, X.3
  • 26
    • 0024379261 scopus 로고
    • Glu-111 is required for activation of the DNA cleavage center of EcoRI endonuclease
    • King,K., Benkovic,S.J. and Modrich,P. (1989) Glu-111 is required for activation of the DNA cleavage center of EcoRI endonuclease. J. Biol. Chem., 264, 11807-11815.
    • (1989) J. Biol. Chem. , vol.264 , pp. 11807-11815
    • King, K.1    Benkovic, S.J.2    Modrich, P.3
  • 27
    • 0026696177 scopus 로고
    • A site-directed mutagenesis study to identify amino acid residues involved in the catalytic function of the restriction endonuclease EcoRV
    • Selent,U., Ruter,T., Kohler,E., Liedtke,M., Thielking,V., Alves,J., Oelgeschlager,T., Wolfes,H., Peters,F. and Pingoud,A. (1992) A site-directed mutagenesis study to identify amino acid residues involved in the catalytic function of the restriction endonuclease EcoRV. Biochemistry, 31, 4808-4815.
    • (1992) Biochemistry , vol.31 , pp. 4808-4815
    • Selent, U.1    Ruter, T.2    Kohler, E.3    Liedtke, M.4    Thielking, V.5    Alves, J.6    Oelgeschlager, T.7    Wolfes, H.8    Peters, F.9    Pingoud, A.10
  • 28
    • 0031591392 scopus 로고    scopus 로고
    • Specific binding by EcoRV endonuclease to its DNA recognition site GATATC
    • Engler,L.E., Welch,K.K. and Jen-Jacobson,L. (1997) Specific binding by EcoRV endonuclease to its DNA recognition site GATATC. J. Mol. Biol., 269, 82-101.
    • (1997) J. Mol. Biol. , vol.269 , pp. 82-101
    • Engler, L.E.1    Welch, K.K.2    Jen-Jacobson, L.3
  • 30
    • 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. (2003) Diversity of type II restriction endonucleases that require two DNA recognition sites. Nucleic Acids Res., 31, 6079-6084.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 6079-6084
    • Mucke, M.1    Kruger, D.H.2    Reuter, M.3
  • 32
    • 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. (2004) One recognition sequence, seven restriction enzymes, five reaction mechanisms. Nucleic Acids Res., 32, 3469-3479.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 3469-3479
    • Gowers, D.M.1    Bellamy, S.R.W.2    Halford, S.E.3
  • 33
    • 16644399511 scopus 로고    scopus 로고
    • Type IIE and IIF restriction endonucleases interacting with two recognition sites on DNA
    • Kirsanova,O.V., Baskunov,V.B. and Gromova,E.S. (2004) Type IIE and IIF restriction endonucleases interacting with two recognition sites on DNA. Mol. Biol. (Mosk), 38, 886-900.
    • (2004) Mol. Biol. (Mosk) , vol.38 , pp. 886-900
    • Kirsanova, O.V.1    Baskunov, V.B.2    Gromova, E.S.3
  • 34
    • 33746824311 scopus 로고    scopus 로고
    • Tension-dependent DNA cleavage by restriction endonucleases: Two-site enzymes are "switched off " at low force
    • Gemmen,G.J., Millin,R. and Smith,D.E. (2006) Tension-dependent DNA cleavage by restriction endonucleases: Two-site enzymes are "switched off " at low force. Proc. Natl Acad. Sci. USA, 103, 11555-11560.
    • (2006) Proc. Natl Acad. Sci. USA , vol.103 , pp. 11555-11560
    • Gemmen, G.J.1    Millin, R.2    Smith, D.E.3
  • 35
    • 31544452261 scopus 로고    scopus 로고
    • Real-time observation of DNA looping dynamics of Type IIE restriction enzymes NaeI and NarI
    • van den Broek,B., Vanzi,F., Normanno,D., Pavone,F.S. and Wuite,G.J.L. (2006) Real-time observation of DNA looping dynamics of Type IIE restriction enzymes NaeI and NarI. Nucleic Acids Res., 34, 167-174.
    • (2006) Nucleic Acids Res. , vol.34 , pp. 167-174
    • van den Broek, B.1    Vanzi, F.2    Normanno, D.3    Pavone, F.S.4    Wuite, G.J.L.5
  • 36
    • 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. (2001) DNA cleavage reactions by type II restriction enzymes that require two copies of their recognition sites. J. Mol. Biol., 311, 503-514.
    • (2001) J. Mol. Biol. , vol.311 , pp. 503-514
    • Embleton, M.L.1    Siksnys, V.2    Halford, S.E.3
  • 37
    • 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. (1995) The SfiI restriction endonuclease makes a four-strand DNA break at two copies of its recognition sequence. J. Mol. Biol., 248, 581-595.
    • (1995) J. Mol. Biol. , vol.248 , pp. 581-595
    • Wentzell, L.M.1    Nobbs, T.J.2    Halford, S.E.3
  • 38
    • 14244262078 scopus 로고    scopus 로고
    • Structure and function of the tetrameric restriction enzymes
    • Pingoud,A. (ed.), Springer-Verlag, Berlin
    • Siksnys,V., Grazulis,S. and Huber,R. (2004) Structure and function of the tetrameric restriction enzymes. In Pingoud,A. (ed.), Nucleic Acids and Molecular Biology, Restriction Endonucleases. Vol. 14, Springer-Verlag, Berlin, pp. 237-259.
    • (2004) Nucleic Acids and Molecular Biology, Restriction Endonucleases , vol.14 , pp. 237-259
    • Siksnys, V.1    Grazulis, S.2    Huber, R.3
  • 39
    • 35148841533 scopus 로고    scopus 로고
    • A switch in the mechanism of communication between the two DNA-binding sites in the SfiI restriction endonuclease
    • Bellamy,S.R.W., Milsom,S.E., Kovacheva,Y.S., Sessions,R.B. and Halford,S.E. (2007) A switch in the mechanism of communication between the two DNA-binding sites in the SfiI restriction endonuclease. J. Mol. Biol., 373, 1169-1183.
    • (2007) J. Mol. Biol. , vol.373 , pp. 1169-1183
    • Bellamy, S.R.W.1    Milsom, S.E.2    Kovacheva, Y.S.3    Sessions, R.B.4    Halford, S.E.5
  • 41
    • 0032555293 scopus 로고    scopus 로고
    • DNA looping by the SfiI restriction endonuclease
    • Wentzell,L.M. and Halford,S.E. (1998) DNA looping by the SfiI restriction endonuclease. J. Mol. Biol., 281, 433-444.
    • (1998) J. Mol. Biol. , vol.281 , pp. 433-444
    • Wentzell, L.M.1    Halford, S.E.2
  • 42
    • 0021760476 scopus 로고
    • A type II restriction endonuclease with an eight nucleotide specificity from Streptomyces fimbriatus
    • Qiang,B.-Q. and Schildkraut,I. (1984) A type II restriction endonuclease with an eight nucleotide specificity from Streptomyces fimbriatus. Nucleic Acids Res., 12, 4507-4515.
    • (1984) Nucleic Acids Res. , vol.12 , pp. 4507-4515
    • Qiang, B.-Q.1    Schildkraut, I.2
  • 43
    • 0029978713 scopus 로고    scopus 로고
    • Recombination by resolvase to analyse DNA communications by the SfiI restriction endonuclease
    • Szczelkun,M.D. and Halford,S.E. (1996) Recombination by resolvase to analyse DNA communications by the SfiI restriction endonuclease. EMBO J., 15, 1460-1469.
    • (1996) EMBO J. , vol.15 , pp. 1460-1469
    • Szczelkun, M.D.1    Halford, S.E.2
  • 44
    • 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. (2001) Analysis of DNA looping interactions by type II restriction enzymes that require two copies of their recognition sites. J. Mol. Biol., 311, 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
  • 45
    • 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. (2005) A view of consecutive binding events from structures of tetrameric endonuclease SfiI bound to DNA. EMBO J., 24, 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
  • 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. (1998) Crystal structure of restriction endonuclease BglI bound to its interrupted DNA recognition sequence. EMBO J., 17, 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. (2005) A homology model of restriction endonuclease SfiI in complex with DNA. BMC Struct. Biol., 5,2.
    • (2005) BMC Struct. Biol. , vol.5 , pp. 2
    • Chmiel, A.A.1    Bujnicki, J.M.2    Skowronek, K.J.3
  • 49
    • 0031576347 scopus 로고    scopus 로고
    • Conformational transitions and structural deformability of EcoRV endonuclease revealed by crystallographic analysis
    • Perona,J.J. and Martin,A.M. (1997) Conformational transitions and structural deformability of EcoRV endonuclease revealed by crystallographic analysis. J. Mol. Biol., 273, 207-225.
    • (1997) J. Mol. Biol. , vol.273 , pp. 207-225
    • Perona, J.J.1    Martin, A.M.2
  • 50
    • 5144224923 scopus 로고    scopus 로고
    • 2+ binding in the active site of HincII: implications for the catalytic mechanism
    • 2+ binding in the active site of HincII: implications for the catalytic mechanism. Biochemistry, 43, 13256 13270.
    • (2004) Biochemistry , vol.43 , pp. 13256-13270
    • Etzkorn, C.1    Horton, N.C.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.