Roles of metal ions in nucleases

Current Opinion in Chemical Biology

Volumn 12, Issue 2, 2008, Pages 250-255

  Dupureur, Cynthia M ^a  

^a UNIVERSITY OF MISSOURI ST LOUIS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

METAL ION; NUCLEASE;

BIODIVERSITY; CHEMICAL STRUCTURE; HYDROLYSIS; MATHEMATICAL COMPUTING; NUCLEIC ACID ANALYSIS; REVIEW;

BINDING SITES; DEOXYRIBONUCLEASES; METALLOPROTEINS; METALS; MODELS, BIOLOGICAL; RIBONUCLEASES;

EID: 43049110531     PISSN: 13675931     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cbpa.2008.01.012     Document Type: Review

References (41)

1. Mishra N. Nucleases - Molecular Biology and Applications (2002), Wiley & Sons, Hoboken
2. Dupureur CM: An integrated look at metallonuclease mechanism. Curr Chem Biol 2008, 2, in press. Full-length discussion that examines various approaches to the one-metal ion nuclease mechanism versus two-metal ion nuclease mechanism in both protein and nucleic acid catalysts.
3. Sigel R.K.O. Group II intron ribozymes and metal ions - a delicate relationship. Eur J Inorg Chem 2005 (2005) 2281-2292
4. a's in mechanism.
5. Conlan L.H., and Dupureur C.M. Dissecting the metal ion dependence of DNA binding by PvuII endonuclease. Biochemistry 41 (2002) 1335-1342
6. Bowen L.M., and Dupureur C.M. Investigation of restriction enzyme cofactor requirements: a relationship between metal ion properties and sequence specificity. Biochemistry 42 (2003) 12643-12653
7. Cowan J.A. Metal activation of enzymes in nucleic acid biochemistry. Chem Rev 98 (1998) 1067-1088
8. Williams N., Takasaki B., Wall M., and Chin J. Structure and nuclease activity of simple dinuclear metal complexes: quantitative dissection of the role of metal ions. Acc Chem Res 32 (1999) 485-493
9. Horton J.R., Blumenthal R., and Cheng X. 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 vol 14 (2004), Springer Verlag 361-392
10. Chevalier B.S., Monnat R.J., and Stoddard B.L. The homing endonuclease I-CreI uses three metals, one of which is shared between the two active sites. Nat Struct Biol 8 (2001) 312-316
11. Mannino S.J., Jenkins C.L., and Raines R.T. Chemical mechanism of DNA cleavage by the homing endonuclease I-PpoI. Biochemistry 38 (1999) 16178-16186
12. Galburt E.A., and Stoddard B.L. Catalytic mechanisms of restriction and homing endonucleases. Biochemistry 41 (2002) 13851-13860
13. Ghosh M., Meiss G., Pingoud A., London R.E., and Pedersen L.C. Structural insights into the mechanism of nuclease A, a ββα metal nuclease from Anabaena. J Biol Chem 280 (2005) 27990-27997
14. Walker D.C., Georgiou T., Pommer A.J., Walker D., Moore G.R., Kleanthous C., and James R. Mutagenic scan of the H-N-H motif of colicin E9: implications for the mechanistic enzymology of colicins, homing enzymes and apoptotic endonucleases. Nucleic Acids Res 30 (2002) 3225-3234
15. Pommer A.J., Kuhlmann U.C., Cooper A., Hemmings A.M., Moore G.R., James R., and Kleanthous C. Homing in on the role of transition metals in the HNH motif of colicin endonucleases. J Biol Chem 274 (1999) 27153-27160
16. Ku W.Y., Liu Y.W., Hsu Y.C., Liao C.C., Liang P.H., Yuan H.S., and Chak K.F. 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 (2002) 1670-1678
17. Mate M.J., and Kleanthous C. Structure-based analysis of the metal-dependent mechanism of H-N-H endonucleases. J Biol Chem 279 (2004) 34763-34769
18. Keeble A.H., Hemmings A.M., James R., Moore G.R., and Kleanthous C. Multistep binding of transition metals to the H-N-H endonuclease toxin colicin E9. Biochemistry 41 (2002) 10234-10244
19. Pommer A.J., Cal S., Keeble A.H., Walker D., Evans S.J., Kuhlmann U.C., Cooper A., Connolly B.A., Hemmings A.M., Moore G.R., et al. Mechanism and cleavage specificity of the H-N-H endonuclease colicin E9. J Mol Biol 314 (2001) 735-749
20. 2+. Protein Sci 15 (2006) 269-280. Highlights diverse active site configurations in the nuclease domain of colicin E7.
21. Cheng Y., and Patel D.J. Crystallographic structure of the nuclease domain of 3′hExo, a DEDDh family member, bound to rAMP. J Mol Biol 343 (2004) 305-312
22. Steitz T.A., and Steitz J.A. A general two-metal ion mechanism for catalytic RNA. Proc Natl Acad Sci U S A 90 (1993) 6498-6502
23. Fothergill M., Goodman M.F., Petruska J., and Warshel A. Structure-energy analysis of the role of metal ions in phosphodiester bond hydrolysis by DNA polymerase I. J Am Chem Soc 117 (1995) 11619-11627
24. Boero M., Tateno M., Terakura K., and Oshiyama A. Double-metal-ion/single-metal-ion mechanisms of the cleavage reaction of ribozymes: first-principles molecular dynamics simulations of a fully hydrated model system. J Chem Theory Comput 1 (2005) 925-934
25. Leclerc F., and Karplus M. Two-metal ion mechanism for hammerhead-ribozyme catalysis. J Phys Chem B 110 (2006) 3395-3409. Important use of computational approaches (DFT) to evaluate the importance of metal ions in models of the hammerhead ribozyme.
26. Bastock J.A., Webb M., and Grasby J.A. The pH-dependence of the Escherichia coli RNase HII-catalysed reaction suggests that an active site carboxylate group participates directly in catalysis. J Mol Biol 368 (2007) 421-433
27. as in RNA: on the structural origins and functional roles of protonated nucleotides. J Mol Biol 366 (2007) 1475-1496
28. a values using QM and QM/MM methods. J Phys Chem A 109 (2005) 6634-6643
29. a values. Proteins 61 (2005) 704-721
30. Horton N.C., Newberry K.J., and Perona J.J. Metal ion-mediated substrate-assisted catalysis in type II restriction endonucleases. Proc Natl Acad Sci U S A 95 (1998) 13489-13494
31. Shan S., Kravchuk A.V., Piccirilli J.A., and Herschlag D. Defining the catalytic metal ion interactions in the Tetrahymena ribozyme reaction. Biochemistry 40 (2001) 5161-5171
32. Horton N.C., and Perona J.J. DNA cleavage by EcoRV endonuclease: two metal ions in three metal ion binding sites. Biochemistry 43 (2004) 6841-6857
33. Stahley M.R., and Strobel S.A. Structural evidence for a two-metal-ion mechanism of group I intron splicing. Science 309 (2005) 1587-1590
34. Nowotny M., Gaidamakov S.A., Crouch R.J., and Yang W. Crystal structures of RNase H bound to an RNA/DNA hybrid: substrate specificity and metal-dependent catalysis. Cell 121 (2005) 1005-1016
35. 2+-ion catalysis and substrate specificity. Mol Cell 22 (2006) 5-13. With an emphasis on work with RNase H from Bacillus halodurans, this is a detailed discussion of the two-metal ion mechanism among metallonucleases in general. It includes proposals for mechanisms of specificity and metal ion movement.
36. Harding M.M. The geometry of metal-ligand interactions relevant to proteins. Acta Crystallogr D Biol Crystallogr 55 (1999) 1432-1443
37. 2+ binding sites required for activation of the mutant proteins of E. coli RNase HI at Glu48 and/or Asp134 by X-ray crystallography. J Mol Biol 345 (2005) 1171-1183. In addition to presenting single-metal ion crystal structure of RNase H from E. coli, the authors use temperature factors in a number of metallonuclease systems to argue for a 'metal ion fluctuation model' or metal ion movement.
38. Ivanov I., Tainer J.A., and McCammon J.A. Unraveling the three-metal-ion catalytic mechanism of the DNA repair enzyme endonuclease IV. Proc Natl Acad Sci U S A 104 (2007) 1465-1470
39. Galburt E.A., Chevalier B., Tang W., Jurica M.S., Flick K.E., Monnat Jr. R.J., and Stoddard B.L. A novel endonuclease mechanism directly visualized for I-PpoI. Nat Struct Biol 6 (1999) 1096-1099
40. Mones L., Simon I., and Fuxreiter M. Metal-binding sites at the active site of restriction endonuclease BamHI can conform to a one-ion mechanism. Biol Chem 388 (2007) 73-78
41. Mones L., Kulhanek P., Florian J., Simon I., and Fuxreiter M. Probing the Two-Metal Ion Mechanism in the Restriction Endonuclease BamHI. Biochemistry 46 (2007) 14514-14523