Type IIE and IIF restriction endonucleases interacting with two recognition sites in DNA

Molekulyarnaya Biologiya

Volumn 38, Issue 5, 2004, Pages 886-900

  Kirsanova, O V ^a,b   Baskunov, V B ^a   Gromova, E S ^a  

^a MOSCOW STATE UNIVERSITY   (Russian Federation)

^b ENGELHARDT INSTITUTE OF MOLECULAR BIOLOGY   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

POLYPEPTIDE; RESTRICTION ENDONUCLEASE; RESTRICTION ENDONUCLEASE IIE; RESTRICTION ENDONUCLEASE IIF; UNCLASSIFIED DRUG; DNA; TYPE II SITE SPECIFIC DEOXYRIBONUCLEASE;

AMINO ACID SEQUENCE; CATALYSIS; CRYSTAL STRUCTURE; DNA SEQUENCE; GENETIC ENGINEERING; HYDROLYSIS; MOLECULAR BIOLOGY; REVIEW; BINDING SITE; CHEMISTRY; METABOLISM; NUCLEOTIDE SEQUENCE; PHYSIOLOGY; PROTEIN SECONDARY STRUCTURE;

BASE SEQUENCE; BINDING SITES; CATALYSIS; DEOXYRIBONUCLEASES, TYPE II SITE-SPECIFIC; DNA; PROTEIN STRUCTURE, SECONDARY;

EID: 16644399511     PISSN: 00268984     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review

References (64)

1. Pingoud A., Jeltsch A. 2001. Structure and function of type II restriction endonucleases. Nucleic Acids Res. 29, 3705-3727.
2. Roberts R.J., Halford S.E. 1993. Type II restriction endonucleases. in Nucleuses. Cold Spring Harbor; N.Y.: Cold Spring Harbor Laboratory Press, 35-88.
3. Heitman J. 1993. On the origins, structures and functions of restriction-modification enzymes. in Genetic Engineering. N.Y.: Plenum Press, 15, 57-108.
4. Pingoud A., Jeltsch A. 1997. Recognition and cleavage by type-II restriction endonucleases. Eur. J. Biochem. 246, 1-22.
5. Halford S.E. 2001. Hopping, jumping and looping by restriction enzymes. Biochem. Soc. Transactions 29, 363-373.
6. Kovall R.A., Matthews B.W. 1999. Type II restriction endonucleases: structural, functional and evolutionary relationships. Current Opin. Chem. Biol. 3, 578-583.
7. Roberts R.J., Belfort M., Bestor T. et al. 2003. A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes. Nucleic Acids Res. 31, 1805-1812.
8. Bath A.J., Halford S.E., Scott D.J. 2004. Analysis of Type II restriction endonucleases that interact with two recognition sites, in Restriction endonucleases. Ed. Pingoud A. Berlin: Springer-Verlag, 297-317.
9. Kruger D.H., Barcak G.J., Reuter M., Smith H.O. 1988. EcoRII can be activated to cleave refractory DNA recognition sites. Nucleic Acids Res. 16, 3997-4008.
10. Conrad M., Topal M.D. 1989. DNA and spermidine provide a switch mechanism to regulate the activity of restriction enzyme NaeI. Proc. Natl. Acad. Sci. USA. 86, 9707-9711.
11. Wentzell L.M., Halford S.E. 1998. DNA looping by the SfiI restriction endonuclease. J. Mol. Biol. 281, 433-444.
12. Bozic D., Grazulis S., Siksnys V., Huber R. 1996. Crystal structure of Citrobacter freundii restriction endonuclease Cfr10I at 2.15 Å resolution. J. Mol. Biol. 255, 176-186.
13. Deibert M., Grazulis S., Sasnauskas G., Siksnys V. et al. 2000. Structure of the tetrameric restriction endonuclease NgoMIV in complex with cleaved DNA. Nature Struct. Biol. 7, 792-799.
14. Grazulis S., Deibert M., Rimseliene R. et al. 2002. Crystal structure of the Bse634I restriction endonuclease: comparison of two enzymes recognizing the same DNA sequence. Nucleic Acids Res. 30, 876-885.
15. Bath A.J., Milsom S.E., Gormley N.A., Halford S.E. 2002. Many type IIS restriction endonucleases interact with two recognition sites before cleaving DNA. J. Biol. Chem. 277, 4024-4033.
16. Kong H., Smith C.L. 1998. Does BcgI, a unique restriction endonuclease, require two sites for cleavage? Biol. Chem. 379, 605-609.
17. Mucke M., Kruger D.H., Reuter M. 2003. Diversity of type II restriction endonucleases that require two DNA recognition sites. Nucleic Acids Res. 31, 6079-6084.
18. Oller A.R., Broek W.V., Conrad M., Topal M.D. 1991. Ability of DNA and spermidine to affect the activity of restriction endonucleases from several bacterial species. Biochemistry 30, 2543-2549.
19. Reuter M., Kupper D., Pein C.D. et al. 1993. Use of specific oligonucleotide duplexes to stimulate cleavage of refractory DNA sites by restriction endonucleases. Anal. Biochem. 209, 232-237.
20. Pein C.D., Reuter M., Cech D., Krüger D.H. 1989. Oligonucleotide duplexes containing CC(A/T)GG stimulate cleavage of refractory DNA by restriction endonuclease EcoRII. FEBS Lett. 245, 141-144.
21. Krüger D.H., Kupper D., Meisel A. et al. 1995. The significance of orientation of restriction endonuclease recognition sites in viral DNA genomes. FEMS Microbiol. Rev. 17, 177-184.
22. Ban C., Yang W. 1998. Structural basis for MutH activation in E. coli mismatch repair and relationship of MutH to restriction endonucleases. EMBO J. 17, 1526-1534.
23. Tsutakawa S.E., Jingami H., Morikawa K. 1999. Recognition of a TG mismatch: the crystal structure of very short patch repair endonuclease in complex with a DNA duplex. Cell. 99, 615-623.
24. Hickman A.B., Li Y., Mathew S.V. et al. 2000. Unexpected structural diversity in DNA recombination: the restriction endonuclease connection. Mol. Cell. 5, 1025-1034.
25. Mücke M., Grelle G., Behlke J. et al. 2002. EcoRII: a restriction enzyme evolving recombination functions? EMBO J. 21, 5262-5268.
26. Wah D.A., Bitinaite J., Schildkraut I., Agarwal A.K. 1998. Structure of FokI has implications for DNA cleavage. Proc. Natl. Acad. Sci. USA. 95, 10564-10569.
27. Huai Q., Colandene J.D., Chen Y. et al. 2000. Crystal structure of NaeI-an evolutionary bridge between DNA endonuclease and topoisomerase. EMBO J. 19, 3110-3118.
28. Huai Q., Colandene J.D., Topai M.D., Ke H. 2001. Structure of Naei-DNA complex reveals dual-mode DNA recognition and complete dimer rearrangement. Nature Struct. Biol. 8, 665-669.
29. Zhou X.E., Wang Y., Reuter M. et al. 2004. Crystal structure of type IIE restriction endonuclease EcoRII reveals an autoinhibition mechanism by a novel effector-binding fold. J. Mol. Biol. 335, 307-319.
30. Halford S.E., Gowers D.M., Sessions R. 2000. Two are better than one. Nature Struct. Biol. 7, 705-707.
31. Wentzell L.M., Nobbs T.J., Halford S.E. 1995. The SfiI restriction endonuclease makes a four-strand DNA break at two copies of its recognition sequence. J. Mol. Biol. 248, 581-595.
32. Siksnys V., Skirgaila R., Sasnauskas G. et al. 1999. The Cfr10I restriction enzyme is functional as a tetramer. J. Mol. Biol. 291, 1105-1118.
33. Watson M.A., Gowers A.M., Halford S.E. 2000. Alternative geometries of DNA looping: an analysis using the SfiI endonuclease. J. Mol. Biol. 298, 461-475.
34. Jo K., Topal M.D. 1995. DNA topoisomerase and recombinase activities in NaeI restriction endonuclease. Science. 267, 1817-1820.
35. Petrauskene O.V., Karpova E.A., Gromova E.S., Guschlbauer W. 1994. Two subunits of EcoRII restriction endonuclease interact with two DNA recognition sites. Biochem. Biophys. Res. Commun. 198, 885-890.
36. Reuter M., Kupper D., Meisel A. et al. 1998. Cooperative binding properties of restriction endonuclease EcoRII with DNA recognition sites. J. Biol. Chem. 273, 8294-8300.
37. Yolov A.A., Gromova E.S., Romanova E.A. et al. 1984. Interaction of EcoRII restriction and modification enzymes with synthetic DNA fragments. EcoRII endonuclease cleavage of substrates with repeated natural and modified recognition sites. FEBS Lett. 167, 147-150.
38. Szczelkun M., Halford S.E. 1996. Recombination by resolvase to analyse DNA communications by the SfiI restriction endonuclease. EMBO J. 15, 1460-1469.
39. Milsom S.E., Halford S.E., Embleton M.L., Szczelkun M. 2001. Analysis of DNA looping interaction by type II of restriction enzymes that require two copies of their recognition sites. J. Mol. Biol. 311, 515-527.
40. Pingoud V., Kubareva E., Stengel G. et al. 2002. Evolutionary relationship between different subgroups of restriction endonucleases. J. Biol. Chem. 277, 14306-14314.
41. Tamulaitis G., Solonin A.S., Siksnys V. 2002. Alternative arrangements of catalytic residues at the sites of restriction enzymes. FEBS Lett. 518, 17-22.
42. Reuter M., Schneider-Mergener J., Kupper D. et al. 1999. Regions of endonuclease EcoRII involved in DNA target recognition identified by membrane-bound peptide repertoires. J. Biol. Chem. 274, 5213-5221.
43. Mücke M., Pingoud V., Grelle G. et al. 2002. Asymmetric photocross-linking pattern of restriction endonuclease EcoRII to the DNA recognition sequence. J. Biol. Chem. 277, 14288-14293.
44. Embleton M.L., Siksnys V., Haiford S.E. 2001. DNA cleavage reactions by type II restriction enzymes that require two copies of their recognition sites. J. Mol. Biol. 311, 503-514.
45. Petrauskene O.V., Kubareva E.A., Gromova E.S. et al. 1992. Mechanism of the interaction of EcoRII restriction endonuclease with two recognition sites. Eur. J. Biochem. 208, 617-622.
46. Gabbara S., Bhagwat A.S. 1992. Interaction of EcoRII endonuclease with DNA substrates containing single recognition sites. J. Biol. Chem. 267, 18623-18630.
47. Mücke M., Lurz R., Mackeldanz P. et al. 2000. Imaging DNA loops induced by restriction endonuclease EcoRII. A single amino acids substitution uncouples target recognition from cooperative interaction and cleavage. J. Biol. Chem. 275, 30631-30637.
48. Topal M.D., Thresher R.J., Conrad M., Griffith J. 1991. NaeI endonuclease binding to pBR322 DNA induces looping. Biochemistry. 30, 2006-2010.
49. Baxter B.K., Topal M.D. 1993. Formation of cleavasome: enhancer DNA-2 stabilizes an active conformation of NaeI dimer. Biochemistry. 32, 8291-8298.
50. Petrauskene O.V., Babkina O.V., Tashlitsky V.N. et al. 1998. EcoRII endonuclease has two identical DNA-binding sites and cleaves one of two co-ordinated recognition sites in one catalytic event. FEBS Lett. 425, 29-34.
51. Yolov A.A., Gromova E.S., Kubareva E.A. et al. 1985. Interaction of EcoRII restriction and modification enzymes with synthetic DNA fragment. V. Study of single-strand cleavages. Nucleic Acids Res. 13, 8969-8981.
52. Yang C.C., Topal M.D. 1992. Nonidentical DNA-binding sites of endonuclease NaeI recognize different families of sequences flanking the recognition site. Biochemistry. 31, 9657-9664.
53. Nobbs T.J., Haiford S.E. 1995. DNA cleavage at two recognition sites by the SfiI restriction endonuclease: salt dependence of cis and trans interaction between distant DNA sites. J. Mol. Biol. 252, 399-411.
54. Connoly B.A., Eckstein F., Pingoud A. 1984. The stereochemical course of the restriction endonuclease EcoRI-catalyzed reaction. J. Biol. Chem. 259, 10760-10763.
55. Grasby J.A., Connoly B.A. 1992. Stereochemical outcome of the hydrolysis reaction catalysed by the EcoRV restriction endonuclease. Biochemistry. 31, 7855-7861.
56. Galburt E.A., Stoddard B.L. 2002. Catalytic mechanisms of restriction and homing endonucleases. Biochemistry. 41, 13851-13860.
57. Mizuuchi K., Nobbs T.J., Halford S.E. et al. 1999. A new method or determining the stereochemistry of DNA cleavage reactions: application to the SfiI and HpaII restriction endonucleases and to the MuA transposase. Biochemistry. 38, 4640-4648.
58. Topal M.D., Conrad M. 1993. Changing endonuclease EcoRII Tyr308 to Phe abolishes cleavage but not recognition: possible homology with the Int-family of recombinases. Nucleic Acids Res. 21, 2599-2603.