A view of consecutive binding events from structures of tetrameric endonuclease SfiI bound to DNA

EMBO Journal

Volumn 24, Issue 23, 2005, Pages 4198-4208

  Vanamee, Éva Scheuring ^a   Viadiu, Hector ^a,c   Kucera, Rebecca ^b   Dorner, Lydia ^b   Picone, Stephen ^b   Schildkraut, Ira ^b,d   Aggarwal, Aneel K ^a  

^a MOUNT SINAI SCHOOL OF MEDICINE   (United States)

^b NEW ENGLAND BIOLABS   (United States)

^c HARVARD MEDICAL SCHOOL   (United States)

^d CerroSci LLC   (United States)

Author keywords

Protein DNA complex; Specific DNA cleavage; Type IIF restriction endonuclease

Indexed keywords

DIMER; ENDONUCLEASE; RESTRICTION ENDONUCLEASE; TETRAMER;

ARTICLE; BINDING SITE; COMPLEX FORMATION; DNA BINDING; DNA CLEAVAGE; DNA SEQUENCE; DNA STRUCTURE; ENZYME ACTIVITY; ENZYME STRUCTURE; GENE TARGETING; NONHUMAN; PRIORITY JOURNAL;

CATALYTIC DOMAIN; CRYSTALLOGRAPHY, X-RAY; DEOXYRIBONUCLEASES, TYPE II SITE-SPECIFIC; DIMERIZATION; DNA; NUCLEIC ACID CONFORMATION; PROTEIN BINDING; PROTEIN STRUCTURE, QUATERNARY; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; STREPTOMYCES;

EID: 28644435380     PISSN: 02614189     EISSN: 14602075     Source Type: Journal    
DOI: 10.1038/sj.emboj.7600880     Document Type: Article

References (67)

1. Aggarwal AK (1995) Structure and function of restriction endonucleases. Curr Opin Struct Biol 5: 11-19
2. Aggarwal AK, Rodgers DW, Drottar M, Ptashne M, Harrison SC (1988) Recognition of a DNA operator by the repressor of phage 434: a view at high resolution. Science 242: 899-907
3. Alves J, Ruter T, Geiger R, Fliess A, Maass G, Pingoud A (1989) 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: 2678-2684
4. Alves J, Vennekohl P (2004) Protein engineering of restriction enzymes. In Restriction Endonucleases, Pingoud A (ed), Vol 14, pp 393-411. Berlin, Heidelberg: Springer-Verlag
5. Bath AJ, Milsom SE, Gormley NA, Halford SE (2002) Many type IIs restriction endonucleases interact with two recognition sites before cleaving DNA. J Biol Chem 277: 4024-4033
6. Bilcock DT, Daniels LE, Bath AJ, Halford SE (1999) Reactions of type II restriction endonucleases with 8-base pair recognition sites. J Biol Chem 274: 36379-36386
7. Bilcock DT, Halford SE (1999) DNA restriction dependent on two recognition sites: activities of the SfiI restriction-modification system in Escherichia coli. Mol Microbiol 31: 1243-1254
8. Bozic D, Grazulis S, Siksnys V, Huber R (1996) Crystal structure of Citrobacter freundii restriction endonuclease Cfr10I at 2.15 A resolution. J Mol Biol 255: 176-186
9. Brunger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS, Read RJ, Rice LM, Simonson T, Warren GL (1998) Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr D 54 (Part 5): 905-921
10. Cheng X, Balendiran K, Schildkraut I, Anderson JE (1994) Structure of PvuII endonuclease with cognate DNA. EMBO J 13: 3927-3935
11. Chmiel AA, Bujnicki JM, Skowronek KJ (2005) A homology model of restriction endonuclease SfiI in complex with DNA. BMC Struct Biol 5: 2
12. Deibert M, Grazulis S, Janulaitis A, Siksnys V Huber R (1999) Crystal structure of MunI restriction endonuclease in complex with cognate DNA at 1.7 A resolution. EMBO J 18: 5805-5816
13. Deibert M, Grazulis S, Sasnauskas G, Siksnys V, Huber R (2000) Structure of the tetrameric restriction endonuclease NgoMIV in complex with cleaved DNA. Nat Struct Biol 7: 792-799
14. DeLano WL (2003) The PyMOL Molecular Graphics System. San Carlos, CA, USA: DeLano Scientific LLC http://www.pymol.org
15. Dorner LF, Bitinaite J, Whitaker RD, Schildkraut I (1999) Genetic analysis of the base-specific contacts of BamHI restriction endonuclease. J Mol Biol 285: 1515-1523
16. Embleton ML, Siksnys V, Halford SE (2001) DNA cleavage reactions by type II restriction enzymes that require two copies of their recognition sites. J Mol Biol 311: 503-514
17. Embleton ML, Vologodskii AV, Halford SE (2004) Dynamics of DNA loop capture by the SfiI restriction endonuclease on supercoiled and relaxed DNA. J Mol Biol 339: 53-66
18. Embleton ML, Williams SA, Watson MA, Halford SE (1999) Specificity from the synapsis of DNA elements by the Sfi I endonuclease. J Mol Biol 289: 785-797
19. Flores H, Osuna J, Heitman J, Soberon X (1995) Saturation mutagenesis of His114 of EcoRI reveals relaxed-specificity mutants. Gene 157: 295-301
20. Gormley NA, Hillberg AL, Halford SE (2002) The type IIs restriction endonuclease BspMI is a tetramer that acts concertedly at two copies of an asymmetric DNA sequence. J Biol Chem 277: 4034-4041
21. Grabowski G, Jeltsch A, Wolfes H, Maass G, Alves J (1995) Site-directed mutagenesis in the catalytic center of the restriction endonuclease EcoRI. Gene 157: 113-118
22. Grazulis S, Deibert M, Rimseliene R, Skirgaila R, Sasnauskas G, Lagunavicius A, Repin V, Urbanke C, Huber R, Siksnys V (2002) Crystal structure of the Bse634I restriction endonuclease: comparison of two enzymes recognizing the same DNA sequence. Nucleic Acids Res 30: 876-885
23. Heitman J, Model P (1990) Substrate recognition by the EcoRI endonuclease. Proteins 7: 185-197
24. Hickman AB, Li Y, Mathew SV, May EW, Craig NL, Dyda F (2000) Unexpected structural diversity in DNA recombination: the restriction endonuclease connection. Mol Cell 5: 1025-1034
25. Holm L, Sander C (1993) Protein structure comparison by alignment of distance matrices. J Mol Biol 233: 123-138
26. Ivanenko T, Heitman J, Kiss A (1998) Mutational analysis of the function of Met137 and Ile197, two amino acids implicated in sequence-specific DNA recognition by the EcoRI endonuclease. Biol Chem 379: 459-465
27. Jo K, Topal MD (1995) DNA topoisomerase and recombinase activities in Nae I restriction endonuclease. Science 267: 1817-1820
28. Jones TA, Zou JY, Cowan SW, Kjeldgaard (1991) Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr A 47 (Part 2): 110-119
29. Jordan SR, Pabo CO (1988) Structure of the lambda complex at 2.5 A resolution: details of the repressor-operator interactions. Science 242: 893-899
30. Kim YC, Grable JC, Love R, Greene PJ, Rosenberg JM (1990) Refinement of Eco RI endonuclease crystal structure: a revised protein chain tracing. Science 249: 1307-1309
31. Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr 26: 283-291
32. Lavery R, Sklenar H (1988) The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. J Biomol Struct Dyn 6: 63-91
33. Lee B, Richards FM (1971) The interpretation of protein structures: estimation of static accessibility. J Mol Biol 55: 379-400
34. Lu XJ, Olson WK (2003) 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res 31: 5108-5121
35. Lukacs CM, Kucera R, Schildkraut I, Aggarwal AK (2000) Understanding the immutability of restriction enzymes: crystal structure of BglII and its DNA substrate at 1.5 A resolution. Nat Struct Biol 7: 134-140
36. Newman M, Lunnen K, Wilson G, Greci J, Schildkraut I, Phillips SE (1998) Crystal structure of restriction endonuclease BglI bound to its interrupted DNA recognition sequence. EMBO J 17: 5466-5476
37. Newman M, Strzelecka T, Dorner LF, Schildkraut I, Aggarwal AK (1994) Structure of restriction endonuclease BamHI and its relationship to EcoRI. Nature 368: 660-664
38. Newman M, Strzelecka T, Dorner LF, Schildkraut I, Aggarwal AK (1995) Structure of Bam HI endonuclease bound to DNA: partial folding and unfolding on DNA binding. Science 269: 656-663
39. Nobbs TJ, Halford SE (1995) DNA cleavage at two recognition sites by the SfiI restriction endonuclease: salt dependence of cis and trans interactions between distant DNA sites. J Mol Biol 252: 399-411
40. Nobbs TJ, Szczelkun MD, Wentzell LM, Halford SE (1998a) DNA excision by the Sfi I restriction endonuclease. J Mol Biol 281: 419-432
41. Nobbs TJ, Williams SA, Connolly BA, Halford SE (1998b) Phosphorothioate substrates for the SfiI restriction endonuclease. Biol Chem 379: 599-604
42. Osuna J, Flores H, Soberon X (1991) Combinatorial mutagenesis of three major groove-contacting residues of EcoRI: single and double amino acid replacements retaining methyltransferase-sensitive activities. Gene 106: 7-12
43. Otwinowski Z, Schevitz RW, Zhang RG, Lawson CL, Joachimiak A, Marmorstein RQ, Luisi BF, Sigler PB (1988) Crystal structure of trp repressor/operator complex at atomic resolution. Nature 335: 321-329
44. Pingoud A, Fuxreiter M, Pingoud V, Wende W (2005) Type II restriction endonucleases: structure and mechanism. Cell Mol Life Sci 62: 685-707
45. Qiang BQ, Schildkraut I (1984) A type II restriction endonuclease with an eight nucleotide specificity from Streptomyces fimbriatus. Nucleic Acids Res 12: 4507-4516
46. Reuter M, Kupper D, Meisel A, Schroeder C, Kruger DH (1998) Cooperative binding properties of restriction endonuclease EcoRII with DNA recognition sites. J Biol Chem 273: 8294-8300
47. Roberts RJ, Halford SE (1993) Type II restriction endonucleases. In Nucleuses, Roberts RJ (ed) Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press
48. Roberts RJ, Vincze T, Posfai J, Macelis D (2005) REBASE-restriction enzymes and DNA methyltransferases. Nucleic Acids Res 33 (database issue): D230-D232
49. Szczelkun MD, Halford SE (1996) Recombination by resolvase to analyse DNA communications by the SfiI restriction endonuclease. EMBO J 15: 1460-1469
50. Topal MD, 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
51. Townson SA, Samuelson JC, Xu SY, Aggarwal AK (2005) Implications for switching restriction enzyme specificities from the structure of BstYI bound to a BglII DNA sequence. Structure (Cambridge) 13: 791-801
52. Townson SA, Samuelson JC, Vanamee ES, Edwards TA, Escalante CR, Xu SY, Aggarwal AK (2004) Crystal structure of BstYI at 1.85A resolution: a thermophilic restriction endonuclease with overlapping specificities to BamHI and BglII. J Mol Biol 338: 725-733
53. Travers AA (1991) DNA bending and kinking - sequence dependence and function. Curr Opin Struct Biol 1: 114-122
54. Vanamee ES, Aggarwal AK (2004) Metal-dependent type II restriction endonucleases. In Handbook of Metalloproteins, Cygler M (ed), Vol 3, pp 742-756. Chichester, UK: John Wiley and Sons, Ltd
55. Vanamee ES, Santagata S, Aggarwal AK (2001) FokI requires two specific DNA sites for cleavage. J Mol Biol 309: 69-78
56. Viadiu H, Aggarwal AK (1998) The role of metals in catalysis by the restriction endonuclease BamHI. Nat Struct Biol 5: 910-916
57. Viadiu H, Vanamee ES, Jacobson EM, Schildkraut I, Aggarwal AK (2003) Crystallization of restriction endonuclease SfiI in complex with DNA. Acta Crystallogr D 59: 1493-1495
58. Vologodskii A, Cozzarelli NR (1996) Effect of supercoiling on the juxtaposition and relative orientation of DNA sites. Biophys J 70: 2548-2556
59. Watson MA, Gowers DM, Halford SE (2000) Alternative geometries of DNA looping: an analysis using the SfiI endonuclease. J Mol Biol 298: 461-475
60. Wentzell LM, Halford SE (1998) DNA looping by the Sfi I restriction endonuclease. J Mol Biol 281: 433-444
61. Wentzell LM, Nobbs TJ, Halford SE (1995) The SfiI restriction endonuclease makes a four-strand DNA break at two copies of its recognition sequence. J Mol Biol 248: 581-595
62. Wentzell LM, Oram M, Halford SE (1994) Purification and characterisation of the SfiI restriction endonuclease. Biochem Soc Trans 22: 302S
63. Williams SA, Halford SE (2001) SfiI endonuclease activity is strongly influenced by the non-specific sequence in the middle of its recognition site. Nucleic Acids Res 29: 1476-1483
64. Williams SA, Halford SE (2002) Communications between catalytic sites in the protein-DNA synapse by the SfiI endonuclease. J Mol Biol 318: 387-394
65. Winkler FK, Banner DW, Oefner C, Tsernoglou D, Brown RS, Heathman SP, Bryan RK, Martin PD, Petratos K, Wilson KS (1993) The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments. EMBO J 12: 1781-1795
66. Xu QS, Kucera RB, Roberts RJ, Guo HC (2004) An asymmetric complex of restriction endonuclease MspI on its palindromic DNA recognition site. Structure (Cambridge) 12: 1741-1747
67. Yang Z, Horton JR, Maunus R, Wilson GG, Roberts RJ, Cheng X (2005) Structure of HinP1I endonuclease reveals a striking similarity to the monomeric restriction enzyme MspI. Nucleic Acids Res 33: 1892-1901