Role of magnesium ions in DNA recognition by the EcoRV restriction endonuclease

FEBS Letters

Volumn 585, Issue 17, 2011, Pages 2739-2743

  Zahran, Mai ^a   Berezniak, Tomasz ^a   Imhof, Petra ^a   Smith, Jeremy C ^b  

^a UNIVERSITY OF HEIDELBERG   (Germany)

^b OAK RIDGE NATIONAL LABORATORY   (United States)

Author keywords

Divalent metal ions; Mg 2+; Nuclease; Protein DNA interaction; Restriction enzyme

Indexed keywords

ECORV RESTRICTION ENDONUCLEASE; MAGNESIUM ION; TYPE II SITE SPECIFIC DEOXYRIBONUCLEASE; UNCLASSIFIED DRUG;

ARTICLE; BASE PAIRING; BINDING AFFINITY; CATALYSIS; CONTROLLED STUDY; DNA CLEAVAGE; DNA CONFORMATION; DNA PROTEIN COMPLEX; ENZYME ACTIVE SITE; ENZYME ACTIVITY; HYDROGEN BOND; METAL BINDING; MOLECULAR DYNAMICS; MOLECULAR RECOGNITION; MOLECULAR STABILITY; NUCLEOPHILICITY; NUCLEOTIDE BINDING SITE; PRIORITY JOURNAL;

CRYSTALLOGRAPHY, X-RAY; DEOXYRIBONUCLEASES, TYPE II SITE-SPECIFIC; DNA; HYDROGEN BONDING; MAGNESIUM; MOLECULAR DYNAMICS SIMULATION; PROTEIN BINDING;

EID: 80052198028     PISSN: 00145793     EISSN: 18733468     Source Type: Journal    
DOI: 10.1016/j.febslet.2011.07.036     Document Type: Article

References (31)

1. R.A. Kovall, and B.W. Matthews Type II restriction endonucleases: structural, functional and evolutionary relationships Curr. Opin. Chem. Biol. 3 1999 578 583 (Pubitemid 29447494)
2. F.K. Winkler, D.W. Banner, C. Oefner, D. Tsernoglou, R.S. Brown, S.P. Heathman, R.K. Bryan, P.D. Martin, K. Petratos, and K.S. Wilson The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments EMBO J. 12 1993 1781 1795 (Pubitemid 23157693)
3. R. Chandrasekaran, and S. Arnott The structure of B-DNA in oriented fibers J. Biomol. Struct. Dyn. 13 1996 1015 1027
4. C. Sissi, and M. Palumbo Effects of magnesium and related divalent metal ions in topoisomerase structure and function Nucleic Acids Res. 37 2009 702 711
5. L. Mones, P. Kulhnek, J. Florin, I. Simon, and M. Fuxreiter Probing the two-metal ion mechanism in the restriction endonuclease BamHI Biochemistry 46 2007 14514 14523 (Pubitemid 350276357)
6. 2+ confers DNA binding specificity to the EcoRV restriction endonuclease Biochemistry 31 1992 3727 3732
7. J.D. Taylor, I.G. Badcoe, A.R. Clarke, and S.E. Halford EcoRV restriction endonuclease binds all DNA sequences with equal affinity Biochemistry 30 1991 8743 8753
8. L.E. Engler, K.K. Welch, and L. Jen-Jacobson Specific binding by EcoRV endonuclease to its DNA recognition site GATATC J. Mol. Biol. 269 1997 82 101 (Pubitemid 27243623)
9. N.Y. Sidorova, S. Muradymov, and D.C. Rau Solution parameters modulating DNA binding specificity of the restriction endonuclease EcoRV FEBS J. 278 2011 2713 2727
10. A. Pingoud, M. Fuxreiter, V. Pingoud, and W. Wende Type II restriction endonucleases: structure and mechanism Cell. Mol. Life Sci. 62 2005 685 707
11. V. Pingoud, W. Wende, P. Friedhoff, M. Reuter, J. Alves, A. Jeltsch, L. Mones, M. Fuxreiter, and A. Pingoud On the divalent metal ion dependence of DNA cleavage by restriction endonucleases of the EcoRI family J. Mol. Biol. 393 2009 140 160
12. N.C. Horton, K.J. Newberry, and J.J. Perona Metal ion-mediated substrate-assisted catalysis in type II restriction endonucleases Proc. Natl. Acad. Sci. USA 95 1998 13489 13494 (Pubitemid 28522999)
13. G.S. Baldwin, R.B. Sessions, S.G. Erskine, and S.E. Halford DNA cleavage by the EcoRV restriction endonuclease: roles of divalent metal ions in specificity and catalysis J. Mol. Biol. 288 1999 87 103 (Pubitemid 29201506)
14. N.C. Horton, and J.J. Perona DNA cleavage by EcoRV endonuclease: two metal ions in three metal ion binding sites Biochemistry 43 2004 6841 6857 (Pubitemid 38720502)
15. D.H. Groll, A. Jeltsch, U. Selent, and A. Pingoud Does the restriction endonuclease EcoRV employ a two-metal-ion mechanism for DNA cleavage? Biochemistry 36 1997 11389 11401 (Pubitemid 27408621)
16. P. Imhof, S. Fischer, and J.C. Smith Catalytic mechanism of DNA backbone cleavage by the restriction enzyme EcoRV: a quantum mechanical/molecular mechanical analysis Biochemistry 48 2009 9061 9075
17. L. Mones, I. Simon, and M. Fuxreiter Metal-binding sites at the active site of restriction endonuclease BamHI can conform to a one-ion mechanism Biol. Chem. 388 2007 73 78 (Pubitemid 46090176)
18. A.D. Mackerell, and L. Nilsson Molecular dynamics simulations of nucleic acid-protein complexes Curr. Opin. Struct. Biol. 18 2008 194 199
19. M. Zahran, I. Daidone, J.C. Smith, and P. Imhof Mechanism of DNA recognition by the restriction enzyme EcoRV J. Mol. Biol. 401 2010 415 432
20. M. Guroult, D. Picot, J. Abi-Ghanem, B. Hartmann, and M. Baaden How cations can assist DNase I in DNA binding and hydrolysis PLoS Comput. Biol. 6 2010 e1001000
21. D.A. Hiller, A.M. Rodriguez, and J.J. Perona Non-cognate enzyme-DNA complex: structural and kinetic analysis of EcoRV endonuclease bound to the EcoRI recognition site GAATTC J. Mol. Biol. 354 2005 121 136 (Pubitemid 41527218)
22. R.E. Dickerson DNA bending: the prevalence of kinkiness and the virtues of normality Nucleic Acids Res. 26 1998 1906 1926 (Pubitemid 28291723)
23. M.A. El Hassan, and C.R. Calladine Propeller-twisting of base-pairs and the conformational mobility of dinucleotide steps in DNA J. Mol. Biol. 259 1996 95 103 (Pubitemid 26162624)
24. N.C. Horton, and J.J. Perona Crystallographic snapshots along a protein-induced DNA-bending pathway Proc. Natl. Acad. Sci. USA 97 2000 5729 5734 (Pubitemid 30367466)
25. 2+ J. Biol. Chem. 268 1993 8645 8650 (Pubitemid 23118648)
26. S. Selvaraj, H. Kono, and A. Sarai Specificity of protein-DNA recognition revealed by structure-based potentials: symmetric/asymmetric and cognate/non-cognate binding J. Mol. Biol. 322 2002 907 915 (Pubitemid 35266502)
27. N.C. Horton, C. Otey, S. Lusetti, M.D. Sam, J. Kohn, A.M. Martin, V. Ananthnarayan, and J.J. Perona Electrostatic contributions to site specific DNA cleavage by EcoRV endonuclease Biochemistry 41 2002 10754 10763 (Pubitemid 34971051)
28. K. Syson, C. Tomlinson, B.R. Chapados, J.R. Sayers, J.A. Tainer, N.H. Williams, and J.A. Grasby Three metal ions participate in the reaction catalyzed by T5 flap endonuclease J. Biol. Chem. 283 2008 28741 28746
29. T.C. Mueser, N.G. Nossal, and C.C. Hyde Structure of bacteriophage T4 RNase H, a 5′ to 3′ RNA-DNA and DNA-DNA exonuclease with sequence similarity to the RAD2 family of eukaryotic proteins Cell 85 1996 1101 1112 (Pubitemid 26231175)
30. C.M. Dupureur Roles of metal ions in nucleases Curr. Opin. Chem. Biol. 12 2008 250 255
31. C.M. Dupureur One is enough: insights into the two-metal ion nuclease mechanism from global analysis and computational studies Metallomics 2 2010 609 620