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Volumn 51, Issue 44, 2012, Pages 8939-8949

Ca2+ binding to the ExDxD motif regulates the DNA Cleavage specificity of a promiscuous endonuclease

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVE SITE; ACTIVE SITE RESIDUES; BINDING MOTIF; DNA CLEAVAGE; ENDONUCLEASES; GENERAL BASE; MUTANT ENZYMES; PROMISCUOUS ACTIVITY; RESTRICTION ENDONUCLEASES; SEQUENCE RECOGNITION; SITE-SPECIFIC; SPATIAL ORGANIZATION;

EID: 84868531803     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi301151y     Document Type: Article
Times cited : (7)

References (50)
  • 1
    • 77956332252 scopus 로고    scopus 로고
    • One is enough: Insights into the two-metal ion nuclease mechanism from global analysis and computational studies
    • Dupureur, C. M. (2010) One is enough: Insights into the two-metal ion nuclease mechanism from global analysis and computational studies Metallomics 2, 609-620
    • (2010) Metallomics , vol.2 , pp. 609-620
    • Dupureur, C.M.1
  • 2
    • 43049110531 scopus 로고    scopus 로고
    • Roles of metal ions in nucleases
    • Dupureur, C. M. (2008) Roles of metal ions in nucleases Curr. Opin. Chem. Biol. 12, 250-255
    • (2008) Curr. Opin. Chem. Biol. , vol.12 , pp. 250-255
    • Dupureur, C.M.1
  • 3
    • 17044403057 scopus 로고    scopus 로고
    • Type II restriction endonucleases: Structure and mechanism
    • Pingoud, A., Fuxreiter, M., Pingoud, V., and Wende, W. (2005) Type II restriction endonucleases: Structure and mechanism Cell. Mol. Life Sci. 62, 685-707
    • (2005) Cell. Mol. Life Sci. , vol.62 , pp. 685-707
    • Pingoud, A.1    Fuxreiter, M.2    Pingoud, V.3    Wende, W.4
  • 4
    • 0242286660 scopus 로고    scopus 로고
    • Investigation of restriction enzyme cofactor requirements: A relationship between metal ion properties and sequence specificity
    • Bowen, L. M. and Dupureur, C. M. (2003) Investigation of restriction enzyme cofactor requirements: A relationship between metal ion properties and sequence specificity Biochemistry 42, 12643-12653
    • (2003) Biochemistry , vol.42 , pp. 12643-12653
    • Bowen, L.M.1    Dupureur, C.M.2
  • 5
    • 0036316773 scopus 로고    scopus 로고
    • Magnesium chemistry and biochemistry
    • Maguire, M. E. and Cowan, J. A. (2002) Magnesium chemistry and biochemistry BioMetals 15, 203-210
    • (2002) BioMetals , vol.15 , pp. 203-210
    • Maguire, M.E.1    Cowan, J.A.2
  • 6
    • 0000001528 scopus 로고    scopus 로고
    • Metal Activation of Enzymes in Nucleic Acid Biochemistry
    • Cowan, J. A. (1998) Metal Activation of Enzymes in Nucleic Acid Biochemistry Chem. Rev. 98, 1067-1088
    • (1998) Chem. Rev. , vol.98 , pp. 1067-1088
    • Cowan, J.A.1
  • 7
    • 0028985732 scopus 로고
    • Stringent and relaxed specificities of TaqI endonuclease: Interactions with metal cofactors and DNA sequences
    • Cao, W., Mayer, A. N., and Barany, F. (1995) Stringent and relaxed specificities of TaqI endonuclease: Interactions with metal cofactors and DNA sequences Biochemistry 34, 2276-2283
    • (1995) Biochemistry , vol.34 , pp. 2276-2283
    • Cao, W.1    Mayer, A.N.2    Barany, F.3
  • 8
    • 0038136893 scopus 로고    scopus 로고
    • Why do divalent metal ions either promote or inhibit enzymatic reactions? the case of BamHI restriction endonuclease from combined quantum-classical simulations
    • Mordasini, T., Curioni, A., and Andreoni, W. (2003) Why do divalent metal ions either promote or inhibit enzymatic reactions? The case of BamHI restriction endonuclease from combined quantum-classical simulations J. Biol. Chem. 278, 4381-4384
    • (2003) J. Biol. Chem. , vol.278 , pp. 4381-4384
    • Mordasini, T.1    Curioni, A.2    Andreoni, W.3
  • 9
    • 33646004109 scopus 로고    scopus 로고
    • Stepwise analyses of metal ions in RNase H catalysis from substrate destabilization to product release
    • Nowotny, M. and Yang, W. (2006) Stepwise analyses of metal ions in RNase H catalysis from substrate destabilization to product release EMBO J. 25, 1924-1933
    • (2006) EMBO J. , vol.25 , pp. 1924-1933
    • Nowotny, M.1    Yang, W.2
  • 11
    • 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
  • 13
    • 67649888360 scopus 로고    scopus 로고
    • Crystal structure of the ββα-Me type II restriction endonuclease Hpy99I with target DNA
    • Sokolowska, M., Czapinska, H., and Bochtler, M. (2009) Crystal structure of the ββα-Me type II restriction endonuclease Hpy99I with target DNA Nucleic Acids Res. 37, 3799-3810
    • (2009) Nucleic Acids Res. , vol.37 , pp. 3799-3810
    • Sokolowska, M.1    Czapinska, H.2    Bochtler, M.3
  • 14
    • 0037072261 scopus 로고    scopus 로고
    • Multistep binding of transition metals to the H-N-H endonuclease toxin colicin E9
    • Keeble, A. H., Hemmings, A. M., James, R., Moore, G. R., and Kleanthous, C. (2002) Multistep binding of transition metals to the H-N-H endonuclease toxin colicin E9 Biochemistry 41, 10234-10244
    • (2002) Biochemistry , vol.41 , pp. 10234-10244
    • Keeble, A.H.1    Hemmings, A.M.2    James, R.3    Moore, G.R.4    Kleanthous, C.5
  • 16
    • 0036529553 scopus 로고    scopus 로고
    • The zinc ion in the HNH motif of the endonuclease domain of colicin E7 is not required for DNA binding but is essential for DNA hydrolysis
    • Ku, W. Y., Liu, Y. W., Hsu, Y. C., Liao, C. C., Liang, P. H., Yuan, H. S., and Chak, K. F. (2002) The zinc ion in the HNH motif of the endonuclease domain of colicin E7 is not required for DNA binding but is essential for DNA hydrolysis Nucleic Acids Res. 30, 1670-1678
    • (2002) Nucleic Acids Res. , vol.30 , pp. 1670-1678
    • Ku, W.Y.1    Liu, Y.W.2    Hsu, Y.C.3    Liao, C.C.4    Liang, P.H.5    Yuan, H.S.6    Chak, K.F.7
  • 17
    • 0034668391 scopus 로고    scopus 로고
    • Biochemical characterization of I-CmoeI reveals that this H-N-H homing endonuclease shares functional similarities with H-N-H colicins
    • Drouin, M., Lucas, P., Otis, C., Lemieux, C., and Turmel, M. (2000) Biochemical characterization of I-CmoeI reveals that this H-N-H homing endonuclease shares functional similarities with H-N-H colicins Nucleic Acids Res. 28, 4566-4572
    • (2000) Nucleic Acids Res. , vol.28 , pp. 4566-4572
    • Drouin, M.1    Lucas, P.2    Otis, C.3    Lemieux, C.4    Turmel, M.5
  • 18
    • 77949345175 scopus 로고    scopus 로고
    • Cofactor requirement of HpyAV restriction endonuclease
    • Chan, S. H., Opitz, L., Higgins, L., O'Loane, D., and Xu, S. Y. (2010) Cofactor requirement of HpyAV restriction endonuclease PLoS One 5, e9071
    • (2010) PLoS One , vol.5 , pp. 9071
    • Chan, S.H.1    Opitz, L.2    Higgins, L.3    O'Loane, D.4    Xu, S.Y.5
  • 19
    • 80053615743 scopus 로고    scopus 로고
    • Endonuclease Active Site Plasticity Allows DNA Cleavage with Diverse Alkaline Earth and Transition Metal Ions
    • Vasu, K., Saravanan, M., and Nagaraja, V. (2011) Endonuclease Active Site Plasticity Allows DNA Cleavage with Diverse Alkaline Earth and Transition Metal Ions ACS Chem. Biol. 6, 934-942
    • (2011) ACS Chem. Biol. , vol.6 , pp. 934-942
    • Vasu, K.1    Saravanan, M.2    Nagaraja, V.3
  • 20
    • 9644259059 scopus 로고    scopus 로고
    • 2+-mediated site-specific DNA cleavage and suppression of promiscuous activity of KpnI restriction endonuclease
    • 2+-mediated site-specific DNA cleavage and suppression of promiscuous activity of KpnI restriction endonuclease J. Biol. Chem. 279, 49736-49740
    • (2004) J. Biol. Chem. , vol.279 , pp. 49736-49740
    • Chandrashekaran, S.1    Saravanan, M.2    Radha, D.R.3    Nagaraja, V.4
  • 21
    • 0032883428 scopus 로고    scopus 로고
    • Characterization of DNA binding activities of over-expressed KpnI restriction endonuclease and modification methylase
    • Chandrashekaran, S., Babu, P., and Nagaraja, V. (1999) Characterization of DNA binding activities of over-expressed KpnI restriction endonuclease and modification methylase J. Biosci. 24, 269-277
    • (1999) J. Biosci. , vol.24 , pp. 269-277
    • Chandrashekaran, S.1    Babu, P.2    Nagaraja, V.3
  • 22
    • 0032052278 scopus 로고    scopus 로고
    • An improved PCR-mutagenesis strategy for two-site mutagenesis or sequence swapping between related genes
    • Kirsch, R. D. and Joly, E. (1998) An improved PCR-mutagenesis strategy for two-site mutagenesis or sequence swapping between related genes Nucleic Acids Res. 26, 1848-1850
    • (1998) Nucleic Acids Res. , vol.26 , pp. 1848-1850
    • Kirsch, R.D.1    Joly, E.2
  • 24
    • 0037423270 scopus 로고    scopus 로고
    • Characterization of the metal ion binding properties of the hepatitis C virus RNA polymerase
    • Bougie, I., Charpentier, S., and Bisaillon, M. (2003) Characterization of the metal ion binding properties of the hepatitis C virus RNA polymerase J. Biol. Chem. 278, 3868-3875
    • (2003) J. Biol. Chem. , vol.278 , pp. 3868-3875
    • Bougie, I.1    Charpentier, S.2    Bisaillon, M.3
  • 25
    • 77957023154 scopus 로고    scopus 로고
    • Generation of a manganese specific restriction endonuclease with nicking activity
    • Vasu, K., Saravanan, M., Rajendra, B. V., and Nagaraja, V. (2010) Generation of a manganese specific restriction endonuclease with nicking activity Biochemistry 49, 8425-8433
    • (2010) Biochemistry , vol.49 , pp. 8425-8433
    • Vasu, K.1    Saravanan, M.2    Rajendra, B.V.3    Nagaraja, V.4
  • 26
    • 5144226338 scopus 로고    scopus 로고
    • The DxDxDG motif for calcium binding: Multiple structural contexts and implications for evolution
    • Rigden, D. J. and Galperin, M. Y. (2004) The DxDxDG motif for calcium binding: Multiple structural contexts and implications for evolution J. Mol. Biol. 343, 971-984
    • (2004) J. Mol. Biol. , vol.343 , pp. 971-984
    • Rigden, D.J.1    Galperin, M.Y.2
  • 27
    • 0037432703 scopus 로고    scopus 로고
    • An extracellular calcium-binding domain in bacteria with a distant relationship to EF-hands
    • Rigden, D. J., Jedrzejas, M. J., and Galperin, M. Y. (2003) An extracellular calcium-binding domain in bacteria with a distant relationship to EF-hands FEMS Microbiol. Lett. 221, 103-110
    • (2003) FEMS Microbiol. Lett. , vol.221 , pp. 103-110
    • Rigden, D.J.1    Jedrzejas, M.J.2    Galperin, M.Y.3
  • 29
    • 11344267268 scopus 로고    scopus 로고
    • Type II restriction endonuclease R.KpnI is a member of the HNH nuclease superfamily
    • Saravanan, M., Bujnicki, J. M., Cymerman, I. A., Rao, D. N., and Nagaraja, V. (2004) Type II restriction endonuclease R.KpnI is a member of the HNH nuclease superfamily Nucleic Acids Res. 32, 6129-6135
    • (2004) Nucleic Acids Res. , vol.32 , pp. 6129-6135
    • Saravanan, M.1    Bujnicki, J.M.2    Cymerman, I.A.3    Rao, D.N.4    Nagaraja, V.5
  • 31
    • 33646594153 scopus 로고    scopus 로고
    • Calcium is a cofactor of polymerization but inhibits pyrophosphorolysis by the Sulfolobus solfataricus DNA polymerase Dpo4
    • Irimia, A., Zang, H., Loukachevitch, L. V., Eoff, R. L., Guengerich, F. P., and Egli, M. (2006) Calcium is a cofactor of polymerization but inhibits pyrophosphorolysis by the Sulfolobus solfataricus DNA polymerase Dpo4 Biochemistry 45, 5949-5956
    • (2006) Biochemistry , vol.45 , pp. 5949-5956
    • Irimia, A.1    Zang, H.2    Loukachevitch, L.V.3    Eoff, R.L.4    Guengerich, F.P.5    Egli, M.6
  • 32
    • 0041707971 scopus 로고    scopus 로고
    • A combined experimental and theoretical study of divalent metal ion selectivity and function in proteins: Application to E. coli ribonuclease H1
    • Babu, C. S., Dudev, T., Casareno, R., Cowan, J. A., and Lim, C. (2003) A combined experimental and theoretical study of divalent metal ion selectivity and function in proteins: Application to E. coli ribonuclease H1 J. Am. Chem. Soc. 125, 9318-9328
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 9318-9328
    • Babu, C.S.1    Dudev, T.2    Casareno, R.3    Cowan, J.A.4    Lim, C.5
  • 33
    • 0031717755 scopus 로고    scopus 로고
    • The role of metals in catalysis by the restriction endonuclease BamHI
    • Viadiu, H. and Aggarwal, A. K. (1998) The role of metals in catalysis by the restriction endonuclease BamHI Nat. Struct. Biol. 5, 910-916
    • (1998) Nat. Struct. Biol. , vol.5 , pp. 910-916
    • Viadiu, H.1    Aggarwal, A.K.2
  • 34
    • 0034725527 scopus 로고    scopus 로고
    • PvuII endonuclease contains two calcium ions in active sites
    • Horton, J. R. and Cheng, X. (2000) PvuII endonuclease contains two calcium ions in active sites J. Mol. Biol. 300, 1049-1056
    • (2000) J. Mol. Biol. , vol.300 , pp. 1049-1056
    • Horton, J.R.1    Cheng, X.2
  • 35
    • 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
  • 37
    • 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
  • 38
    • 44449085373 scopus 로고    scopus 로고
    • The Fidelity Index provides a systematic quantitation of star activity of DNA restriction endonucleases
    • Wei, H., Therrien, C., Blanchard, A., Guan, S., and Zhu, Z. (2008) The Fidelity Index provides a systematic quantitation of star activity of DNA restriction endonucleases Nucleic Acids Res. 36, e50
    • (2008) Nucleic Acids Res. , vol.36 , pp. 50
    • Wei, H.1    Therrien, C.2    Blanchard, A.3    Guan, S.4    Zhu, Z.5
  • 39
    • 27344446537 scopus 로고    scopus 로고
    • Non-cognate enzyme-DNA complex: Structural and kinetic analysis of EcoRV endonuclease bound to the EcoRI recognition site GAATT
    • Hiller, D. A., Rodriguez, A. M., and Perona, J. J. (2005) Non-cognate enzyme-DNA complex: Structural and kinetic analysis of EcoRV endonuclease bound to the EcoRI recognition site GAATT J. Mol. Biol. 354, 121-136
    • (2005) J. Mol. Biol. , vol.354 , pp. 121-136
    • Hiller, D.A.1    Rodriguez, A.M.2    Perona, J.J.3
  • 40
    • 0037192151 scopus 로고    scopus 로고
    • Dissecting the metal ion dependence of DNA binding by PvuII endonuclease
    • Conlan, L. H. and Dupureur, C. M. (2002) Dissecting the metal ion dependence of DNA binding by PvuII endonuclease Biochemistry 41, 1335-1342
    • (2002) Biochemistry , vol.41 , pp. 1335-1342
    • Conlan, L.H.1    Dupureur, C.M.2
  • 41
    • 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. (2001) Binding and recognition of GATATC target sequences by the EcoRV restriction endonuclease: A study using fluorescent oligonucleotides and fluorescence polarization Biochemistry 40, 2484-2494
    • (2001) Biochemistry , vol.40 , pp. 2484-2494
    • Reid, S.L.1    Parry, D.2    Liu, H.H.3    Connolly, B.A.4
  • 42
    • 77955267122 scopus 로고    scopus 로고
    • Mechanism of DNA recognition by the restriction enzyme EcoRV
    • Zahran, M., Daidone, I., Smith, J. C., and Imhof, P. (2010) Mechanism of DNA recognition by the restriction enzyme EcoRV J. Mol. Biol. 401, 415-432
    • (2010) J. Mol. Biol. , vol.401 , pp. 415-432
    • Zahran, M.1    Daidone, I.2    Smith, J.C.3    Imhof, P.4
  • 43
    • 0025203657 scopus 로고
    • The energetic basis of specificity in the Eco RI endonuclease-DNA interaction
    • Lesser, D. R., Kurpiewski, M. R., and Jen-Jacobson, L. (1990) The energetic basis of specificity in the Eco RI endonuclease-DNA interaction Science 250, 776-786
    • (1990) Science , vol.250 , pp. 776-786
    • Lesser, D.R.1    Kurpiewski, M.R.2    Jen-Jacobson, L.3
  • 44
    • 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., and Perona, J. J. (2001) Catalytic efficiency and sequence selectivity of a restriction endonuclease modulated by a distal manganese ion binding site J. Mol. Biol. 306, 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
  • 45
    • 48749094277 scopus 로고    scopus 로고
    • Evolution of sequence specificity in a restriction endonuclease by a point mutation
    • Saravanan, M., Vasu, K., and Nagaraja, V. (2008) Evolution of sequence specificity in a restriction endonuclease by a point mutation Proc. Natl. Acad. Sci. U.S.A. 105, 10344-10347
    • (2008) Proc. Natl. Acad. Sci. U.S.A. , vol.105 , pp. 10344-10347
    • Saravanan, M.1    Vasu, K.2    Nagaraja, V.3
  • 46
    • 0034008773 scopus 로고    scopus 로고
    • The acidic triad conserved in type IA DNA topoisomerases is required for binding of Mg(II) and subsequent conformational change
    • Zhu, C. X. and Tse-Dinh, Y. C. (2000) The acidic triad conserved in type IA DNA topoisomerases is required for binding of Mg(II) and subsequent conformational change J. Biol. Chem. 275, 5318-5322
    • (2000) J. Biol. Chem. , vol.275 , pp. 5318-5322
    • Zhu, C.X.1    Tse-Dinh, Y.C.2
  • 47
    • 23044476578 scopus 로고    scopus 로고
    • Structural insights into the mechanism of nuclease A, a ββα metal nuclease from Anabaena
    • Ghosh, M., Meiss, G., Pingoud, A., London, R. E., and Pedersen, L. C. (2005) Structural insights into the mechanism of nuclease A, a ββα metal nuclease from Anabaena J. Biol. Chem. 280, 27990-27997
    • (2005) J. Biol. Chem. , vol.280 , pp. 27990-27997
    • Ghosh, M.1    Meiss, G.2    Pingoud, A.3    London, R.E.4    Pedersen, L.C.5
  • 48
    • 63449119852 scopus 로고    scopus 로고
    • Mutagenesis identifies the critical amino acid residues of human endonuclease G involved in catalysis, magnesium coordination, and substrate specificity
    • Wu, S. L., Li, C. C., Chen, J. C., Chen, Y. J., Lin, C. T., Ho, T. Y., and Hsiang, C. Y. (2009) Mutagenesis identifies the critical amino acid residues of human endonuclease G involved in catalysis, magnesium coordination, and substrate specificity J. Biomed. Sci. 16, 6
    • (2009) J. Biomed. Sci. , vol.16 , pp. 6
    • Wu, S.L.1    Li, C.C.2    Chen, J.C.3    Chen, Y.J.4    Lin, C.T.5    Ho, T.Y.6    Hsiang, C.Y.7
  • 49
    • 0035968001 scopus 로고    scopus 로고
    • Femtomolar sensitivity of metalloregulatory proteins controlling zinc homeostasis
    • Outten, C. E. and O'Halloran, T. V. (2001) Femtomolar sensitivity of metalloregulatory proteins controlling zinc homeostasis Science 292, 2488-2492
    • (2001) Science , vol.292 , pp. 2488-2492
    • Outten, C.E.1    O'Halloran, T.V.2
  • 50
    • 0037168427 scopus 로고    scopus 로고
    • 2+ is a native metal ion activator for bacteriophage λ protein phosphatase
    • 2+ is a native metal ion activator for bacteriophage λ protein phosphatase Biochemistry 41, 15404-15409
    • (2002) Biochemistry , vol.41 , pp. 15404-15409
    • Reiter, T.A.1    Reiter, N.J.2    Rusnak, F.3


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