Understanding the immutability of restriction enzymes: Crystal structure of Bg/II and its DNA substrate at 1.5 Å resolution

Nature Structural Biology

Volumn 7, Issue 2, 2000, Pages 134-140

  Lukacs, Christine M ^a   Kucera, Rebecca ^b   Schildkraut, Ira ^b   Aggarwal, Aneel K ^a  

^a MOUNT SINAI SCHOOL OF MEDICINE   (United States)

^b NEW ENGLAND BIOLABS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

RESTRICTION ENDONUCLEASE; TYPE II SITE SPECIFIC DEOXYRIBONUCLEASE;

ARTICLE; BASE PAIRING; CONTROLLED STUDY; CRYSTAL STRUCTURE; DNA BINDING; DNA CONFORMATION; ENZYME ACTIVE SITE; ENZYME CONFORMATION; ENZYME SPECIFICITY; ENZYME STRUCTURE; ENZYME SUBSTRATE; MOLECULAR RECOGNITION; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN DOMAIN; PROTEIN FOLDING; STRUCTURE ANALYSIS;

BACTERIAL PROTEINS; BINDING SITES; CATALYTIC DOMAIN; CRYSTALLOGRAPHY, X-RAY; DEOXYRIBONUCLEASE BAMHI; DEOXYRIBONUCLEASES, TYPE II SITE-SPECIFIC; DNA; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; PROTEIN CONFORMATION; PROTEIN FOLDING;

EID: 0033981010     PISSN: 10728368     EISSN: None     Source Type: Journal    
DOI: 10.1038/72405     Document Type: Article

References (41)

1. Roberts, R.J. & Halford, S.E. Type II restriction endonucleases. in Nucleases (eds. Linn, S.M., Lloyd, R.S. & Roberts, R.J.) 35-88 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York; 1993).
2. Aggarwal, A.K. Structure and function of restriction endonucleases. Curr. Opin. Struct. Biol. 5, 11-19 (1995).
3. Pingoud, A. & Jeltsch, A. Recognition and cleavage of DNA by type-II restriction endonucleases. Eur. J. Biochem. 246, 1-22 (1997).
4. Newman, M., Strzelecka, T., Dorner, L.F., Schildkraut, I. & Aggarwal, A.K. Structure of restriction endonuclease BamHI and its relationship to EcoRI. Nature 368, 660-664 (1994).
5. Newman, M., Strzelecka, T., Dorner, L.F., Schildkraut, I. & Aggarwal, A.K. Structure of restriction endonuclease BamHI phased at 1.95Å resolution by MAD analysis. Structure 2, 439-452 (1994).
6. Kim, Y.C., Grable, J.C., Love, R., Greene, P.J. & Rosenberg, J.M. Refinement of EcoRI endonuclease crystal structure: a revised protein chain tracing. Science 249, 1307-1309 (1990).
7. Winkler, F.K. et al. The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments. EMBO J. 12, 1781-1795 (1993).
8. Cheng, X., Balendiran, K., Schildkraut, I. & Anderson, J.E. Structure of Pvull endonuclease with cognate DNA. EMBO J. 13, 3927-3935 (1994).
9. Athanasiadis, A. et al. Crystal structure of Pvull endonuclease reveals extensive structural homologies to EcoRV. Nature Struct. Biol. 1, 469-475 (1994).
10. Alves, J. et al. Changing the hydrogen-bonding potential in the DNA binding site of EcoRI by site-directed mutagenesis drastically reduces the enzymatic activity, not, however, the preference of this restriction endonuclease for cleavage within the site -GAATTC-. Biochemistry 28(1989).
11. Heitman, J. & Model, P. Substrate recognition by the EcoRI endonuclease. Proteins 7, 185-197 (1990).
12. Osuna, J., Flores, H. & Soberon, X. Combinatorial mutagenesis of three major groove-contacting residues of EcoRI: single and double amino acid replacements retaining methyltransferase-sensitive activities. Gene 106, 7-12 (1991).
13. Xu, S. & Schildkraut, I. Isolation of BamHI variants with reduced cleavage activities. J. Biol. Chem. 266, 4425-4429 (1991).
14. Wenz, C. et al. Protein engineering of the restriction endonuclease EcoRV: replacement of an amino acid residue in the DNA binding site leads to an altered selectivity towards unmodified and modified substrates. Biochem. Biophys. Acta 1219, 73-80 (1994).
15. Dorner, L.F., Bitinaite, J., Whitaker, R.D. & Schildraut, I. Genetic analysis of the base-specific contacts of BamHI restriction endonuclease. J. Mol. Biol. 285, 1515-1523 (1999).
16. Newman, M., Strzelecka, T., Dorner, L.F., Schildkraut, I. & Aggarwal, A.K. Structure of BamHI endonuclease bound to DNA: partial folding and unfolding on DNA binding. Science 269, 656-663 (1995).
17. Viadiu, H. & Aggarwal, A.K. The role of metals in catalysis by the restriction endonuclease BamHI. Nature Struct. Biol. 5, 910-916 (1998).
18. Anton, B.P. et al. Cloning and characterization of the Bg/II restriction-modification system reveals a possible evolutionary footprint. Gene 187, 19-27 (1997).
19. Schneider, B., Neidle, S. & Berman, H.M. Conformations of the sugar-phosphate backbone in helical DNA crystal structures. Biopolymers 42, 113-124 (1997).
20. Beamer, L.J. & Pabo, C.O. Refined 1.8 Angstrom crystal structure of the λ-repressor operator complex. J. Mol. Biol. 227, 177-196 (1992).
21. Dorner, L.F. & Schildkraut, I. Direct selection of binding proficient/catalytic deficient variants of BamHI endonuclease. Nucleic Acids Res. 22, 1068-1074 (1994).
22. Reber, E.J. & Pabo, C.O. Zinc finger phage: affinity selection of fingers with new DNA-binding specificities. Science 263, 671-673 (1994).
23. Choo, Y. & Klug, A. Toward a code for the interactions of zinc fingers with DNA: selection of randomized fingers displayed on phage. Proc. Natl. Acad. Sci. 91, 11163-11167 (1994).
24. Wharton, R.P. & Ptashne, M. Changing the binding specificity of a repressor by redesigning an alpha-helix. Nature 316, 601-605 (1985).
25. Selent, U. et al. 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).
26. Vipond, I.B., Baldwin, G.S. & Halford, S.E. Divalent metal ions at the active sites of EcoRV and EcoRI restriction endonucleases. Biochemistry 34, 697-704 (1995).
27. Jeltsch, A., Alves, J., Wolfes, H., Maass, G. & Pingoud, A. Substrate-assisted catalysis in the cleavage of DNA by the EcoRI and EcoRV restriction enzymes. Proc. Natl. Acad. Sci. USA 90, 8499-8503 (1993).
28. Horton, N.C., Newberry, K.J. & Perona, J.J. Metal ion-mediated substrate-assisted catalysis in type II restriction endonucleases. Biochemistry 95, 13489-13494 (1998).
29. Jurica, M.S., Monnat, J., R.J. & Stoddard, B.L. DNA recognition and cleavage by the LAGLIDADG homing endonuclease I-Crel. Mol. Cell 2, 469-476 (1998).
30. Hendrickson, W.A. Determination of macromolecular structures from anomalous diffraction of synchrotron radiation. Science 254, 51-58 (1991).
31. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326 (1997).
32. Furey, W. & Swaminathan, S. PHASES-95: a program package for the processing and analysis of diffraction data from macromolecules. Methods Enzymol. 277, 590-629 (1997).
33. Tong, L. PATSOL - v1.2. (1993).
34. de La Fortelle, E. & Bricogne, G. Maximum-likelihood heavy-atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods. Methods Enzymol. 276, 472-494 (1997).
35. Collaborative Computational Project Number 4. CCP4 Suite: programs for protein crystallography, Acta Crystallogr. D 50, 760-763 (1994).
36. Jones, A.T., Zou, J.Y., Cowan, S.W. & Kjeldgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110-119 (1991).
37. Adams, P.D., Pannu, N.S., Read, R.J. & Brunger, A.T. Cross-validated manximum likelihood enhances crystallographic simulated annealing refinement. Proc. Natl. Acad. Sci. USA 94, 5018-5023 (1997).
38. Kraulis, P.J. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24, 946-950 (1991).
39. Merritt, E.A. & Bacon, D.J. Raster3D photorealistic molecular graphics. Methods Enzymol 277, 505-524 (1997).
40. Nicholls, A., Sharp, K. & Honig, B. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins Struct. Funct. Genet. 11, 281-296 (1991).
41. Laverly, R. & Sklenar, H. The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. J. Biomol. Struct. Dyn. 6, 63-91 (1988).