Crystal structure of restriction endonuclease BglI bound to its interrupted DNA recognition sequence

EMBO Journal

Volumn 17, Issue 18, 1998, Pages 5466-5476

  Newman, Matthew ^a,c   Lunnen, Keith ^b   Wilson, Geoffrey ^b   Greci, John ^b   Schildkraut, Ira ^b   Phillips, Simon E V ^c  

^a IMPERIAL CANCER RESEARCH FUND   (United Kingdom)

^b NEW ENGLAND BIOLABS   (United States)

^c UNIVERSITY OF LEEDS   (United Kingdom)

Author keywords

BglI; Crystal structure; Protein DNA complex; Restriction endonuclease

Indexed keywords

RESTRICTION ENDONUCLEASE;

ARTICLE; CRYSTAL STRUCTURE; DIMERIZATION; DNA CLEAVAGE; DNA PROTEIN COMPLEX; DNA SEQUENCE; ENZYME SUBUNIT; HYDROLYSIS; NONHUMAN; PRIORITY JOURNAL; PROTEIN DNA BINDING;

BACILLUS; BINDING SITES; CALCIUM; CRYSTALLOGRAPHY, X-RAY; DEOXYRIBONUCLEASES, TYPE II SITE-SPECIFIC; DIMERIZATION; DNA; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; OLIGODEOXYRIBONUCLEOTIDES; PROTEIN STRUCTURE, SECONDARY;

EID: 0032530311     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1093/emboj/17.18.5466     Document Type: Article

References (55)

1. Abrahams, J.P. and Leslie, A.G.W. (1996) Methods used in the structure determination of the bovine mitochondrial F1 ATPase. Acta Crystallogr., D52, 30-42.
2. Aggarwal, A.K. (1995) Structure and function of restriction endonucleases. Curr. Biol., 5, 11-19.
3. Athanasiadis, A., Vlassi, M., Kotsifaki, D., Tucker, P.A., Wilson, K.S. and Kokkinidis, M. (1994) Crystal structure of PvuII endonuclease reveals extensive structural homologies to EcoRV. Struct. Biol., 1, 469-475.
4. Baker, E.N. and Hubbard, R.E. (1984) Hydrogen bonding in globular proteins. Prog. Biophys. Mol. Biol., 44, 97-179.
5. Beamer, L.J. and Pabo, C.O. (1992) Refined 1.8 Å crystal structure of the λ repressor-operator complex. J. Mol. Biol., 227, 177-196.
6. Beese, L.S. and Steitz, T.A. (1991) Structural bases for the 3′-5′ exonuclease activity of Escherichia coli DNA polymerase I: a two metal ion mechanism. EMBO J., 10, 25-33.
7. Bickle, T.A. and Ineichen, K. (1980) The DNA sequence recognized by BglI. Gene, 9, 205-212.
8. Bozic, D., Grazulis, S., Siksnys, V. and Huber, R. (1996) Crystal structure of Citrobacter freundii restriction endonuclease Cfr10I at 2.15 Å resolution. J. Mol. Biol., 255, 176-186.
9. Brünger, A.T. (1992) Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature, 355, 472-475.
10. Brünger, A.T., Kuriyan, J. and Karplus, M. (1987) Crystallographic R-factor refinement by molecular dynamics. Science, 235, 458-460.
11. Cheng, X., Balendiran, K., Schildkraut, I. and Anderson, J.E. (1994) Structure of PvuII endonuclease with cognate DNA. EMBO J., 13, 3927-3935.
12. Collaborative Computational Project Number 4. (1994) The CCP4 Suite - Programs for Protein Crystallography. Acta Crystallogr., D50, 760-763.
13. Connolly, B.A., Eckstein, F. and Pingoud, A. (1984) The stereochemical course of the restriction endonuclease EcoRI-catalysed reaction. J. Biol. Chem., 259, 10760-10763.
14. De la Fortelle, E. and Bricogne, G. (1997) Maximum-likelihood heavy-atom parameters refinement in the MIR and MAD methods. Methods Enzymol., 276, 472-494.
15. Engh, R.A. and Huber, R. (1991) Accurate bond and angle parameters for X-ray protein-structure refinement. Acta Crystallogr., A47, 392-400.
16. 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.
17. Goodsell, D.S., Kopka, M.L., Cascio, D. and Dickerson, R.E. (1993) Crystal structure of CATGGCCATG and its implications for A-tract bending models. Proc. Natl Acad. Sci. USA, 90, 2930-2934.
18. Grasby, J.A. and Connolly, B.A. (1992) Stereochemical outcome of the hydrolysis reaction catalysed by the EcoRV restriction endonuclease. Biochemistry, 31, 7855-7861.
19. Groll, D.H., Jeltsch, A., Selent, U. and Pingoud, A. (1997) Does the restriction endonuclease EcoRV employ a two-metal-ion mechanism for DNA cleavage? Biochemistry, 36, 11389-11401.
20. Harrison, C.J., Bohm, A.A. and Nelson, H.C.M. (1994) Crystal structure of the DNA binding domain of the heat shock transcription factor Science, 263, 224-227.
21. Hartmann, B. and Lavery, R. (1996) DNA structural forms. Quart. Rev. Biophys., 29, 309-368.
22. Janin, J., Miller, S. and Chothia, C. (1988) Surface, subunit interfaces and interior of oligomeric proteins. J. Mol. Biol., 204, 155-164.
23. Jeltsch, A., Alves, J., Wolfes, H., Maass, G. and Pingoud, A. (1993) Substrate-assisted catalysis in the cleavage of DNA by the EcoRI and EroRV restriction enzymes. Proc. Natl Acad. Sci. USA, 90, 8499-8503.
24. Jones, T.A., Zou, J.Y., Cowan, S.W. and Kjeldgaard, M. (1991) Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr., A47, 110-119.
25. Kabsch, W. and Sander, C. (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.
26. 10→α bulge. Biochemistry, 32, 2509-2513.
27. 2+ binding to the active site of EcoRV endonuclease: a crystallographic study of complexes with substrate and product DNA at 2 Å resolution. Biochemistry, 34, 683-696.
28. Kraulis, P.J. (1991) MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr., 24, 946-950.
29. Laskowski, R.A., MacArthur, M.W., Moss, D.S. and Thornton, J.M. (1993) PROCHECK: a program to check stereochemical quality of protein structures. J. Appl. Crystallogr., 26, 283-291.
30. Lautenberger, J.A., White, C.T., Haighwood, N.L., Edgell, M.H. and Hutchison, C.A. (1980) The recognition site of type II restriction enzyme BglI is interrupted. Gene, 9, 213-231.
31. Lavery, R. and Sklenar, H. (1988) The definition of generalised helicoidal parameters and of axis curvature for irregular nucleic acids. J. Biomol. Struct. Dynamics, 6, 63-91.
32. Lavery, R. and Sklenar, H. (1989) Defining the structure of irregular nucleic acids: conventions and principles. J. Biomol. Struct. Dynamics, 6, 655-667.
33. Lee, B.K. and Richards, F.M. (1971) The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol., 55, 379-400.
34. Lee, Y.H. and Chirikjian, J.G. (1979) Sequence-specific endonuclease BglI. J. Biol. Chem., 254, 6838-6843.
35. Lunnen, K.D. et al. (1988) Cloning type-II restriction and modification genes. Gene, 74, 25-32.
36. McClarin, J.A., Frederick, C.A., Wang, B.-C., Greene, P., Boyer, H.W., Grable, J. and Rosenberg, J.M. (1986) Structure of the DNA-EcoRI endonuclease recognition complex at 3 Å resolution. Science, 234, 1526-1541.
37. Merritt, E.A. and Murphy, M.E.P. (1994) Raster 3D version 2.0: A program for photorealistic molecular graphics. Acta Crystallogr., D50, 869-873.
38. Mueller, C.W., Rey, F.A., Sodeoka, M., Verdine, G.L. and Harrison, S.C. (1995) Structure of the NF-κB p50 homodimer bound to DNA. Nature, 373, 311-317.
39. Nastri, H.G., Evans, P.D., Walker, I.H. and Riggs, P.D. (1997) Catalytic and DNA binding properties of PvuII restriction endonuclease mutants. J. Biol. Chem., 272, 25761-25767.
40. Newman, M., Strzelecka, T., Dorner, L.F., Schildkraut, I. and Aggarwal, A.K. (1995) Restriction endonuclease BamHI partially folds and unfolds on DNA binding: crystal structure of BamHI-DNA complex at 2.2 Å resolution. Science, 269, 656-663.
41. Otwinowski, Z. and Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol., 276, 307-326.
42. Pabo, C.O. and Sauer, R.T. (1992) Transcription factors - structural families and principles of DNA recognition. Annu. Rev. Biochem., 61, 1053-1095.
43. Parkinson, G., Vojtechovsky, J., Clowney, L., Brünger, A.T. and Berman, H.M. (1996) New parameters for the refinement of nucleic acid containing structures. Acta Crystallogr., D52, 57-64.
44. Pingoud, A. and Jeltsch, A. (1997) Recognition and cleavage of DNA by type-II restriction endonucleases. Eur. J. Biochem., 246, 1-22.
45. Raumann, B.E., Rould, M.A., Pabo, C.O. and Sauer, R.T. (1994) DNA recognition by β-sheets in the Arc repressor-operator crystal structure. Nature, 367, 754-757.
46. Roberts, R.J. and Halford, S.E. (1993) Type II restriction endonucleases. In Linn, S.M., Lloyd, R.S. and Roberts, R.J. (eds), Nucleuses, Second Edition. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp. 35-88.
47. Saenger, W. (1984) Principles of Nucleic Acid Structure. Springer, New York.
48. Selent, U. et al. (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.
49. Somers, W.S. and Phillips, S.E.V. (1992) Crystal structure of the met repressor-operator complex at 2.8 Å resolution reveals DNA recognition by β-strands. Nature, 359, 387-393.
50. Van Heuverswyn, H. and Fiers, W. (1980) Recognition sequence for the restriction endonuclease BglI from Bacillus globigii. Gene, 9, 195-203.
51. Vipond, I.B. and Halford, S.E. (1995) Specific DNA recognition by EcoRV restriction endonuclease induced by calcium ions. Biochemistry, 34, 1113-1119.
52. Vipond, I.B., Baldwin, G.S. and Halford, S.E. (1995) Divalent metal ions at the active sites of the EcoRV and EcoRI restriction endonucleases. Biochemistry, 34, 697-704.
53. Wah, D.A., Hirsch, J.A., Dorner, L.F., Schildkraut, I. and Aggarwal, A.K. (1997) Structure of the multimodular endonuclease FokI bound to DNA. Nature, 388, 97-100.
54. Wilson, G.A. and Young, F.E. (1976) Restriction and modification in the Bacillus subtilis genuspecies. In Schlessinger, D. (ed.), Microbiology. American Society for Microbiology, Washington DC, pp. 350-357.
55. Winkler, F.K. et al. (1993) The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments. EMBO J., 12, 1781-1795.