Type III restriction enzymes cleave DNA by long-range interaction between sites in both head-to-head and tail-to-tail inverted repeat

Proceedings of the National Academy of Sciences of the United States of America

Volumn 107, Issue 20, 2010, Pages 9123-9128

  Van Aelst, Kara ^a   Tóth, Júlia ^a   Ramanathan, Subramanian P ^b   Schwarz, Friedrich W ^b   Seidel, Ralf ^b   Szczelkun, Mark D ^a  

^a UNIVERSITY OF BRISTOL   (United Kingdom)

^b DRESDEN UNIVERSITY OF TECHNOLOGY   (Germany)

Author keywords

Diffusion; Helicase; Motor; Switch

Indexed keywords

ADENOSINE TRIPHOSPHATE; DNA; HELICASE; RESTRICTION ENDONUCLEASE; TYPE III SITE SPECIFIC DEOXYRIBONUCLEASE;

ARTICLE; CONTROLLED STUDY; DNA CLEAVAGE; ENZYME ACTIVITY; ENZYME SUBSTRATE; HYDROLYSIS; MISMATCH REPAIR; PRIORITY JOURNAL; PROTEIN DOMAIN; RESTRICTION MAPPING;

BINDING SITES; DEOXYRIBONUCLEASES, TYPE III SITE-SPECIFIC; DNA, VIRAL; INVERTED REPEAT SEQUENCES; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; OLIGONUCLEOTIDES; SUBSTRATE SPECIFICITY;

BACTERIA (MICROORGANISMS);

EID: 77952722979     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1001637107     Document Type: Article

References (37)

1. Halford SE, Welsh AJ, Szczelkun MD (2004) Enzyme-mediated DNA looping. Annu Rev Biophys Biomol Struct 33:1-24.
2. Kadauke S, Blobel GA (2009) Chromatin loops in gene regulation. Biochim Biophys Acta 1789:17-25.
3. Mizuuchi K (1992) TRANSPOSITIONAL RECOMBINATION: Mechanistic insights from studies of Mu and other elements. Annu Rev Biochem 61:1011-1051.
4. Stark WM, Boocock MR, Sherratt DJ (1992) Catalysis by site-specific recombinases. Trends Genet 8:432-439.
5. Grindley ND, Whiteson KL, Rice PA (2006) Mechanisms of site-specific recombination. Annu Rev Biochem 75:567-605.
6. Krasnow MA, Cozzarelli NR (1983) Site-specific relaxation and recombination by the Tn 3 resolvase: recognition of the DNA path between oriented res sites. Cell 32:1313-1324.
7. Brown JL, He J, Sherratt DJ, Stark WM, Boocock MR (2002) Interactions of protein complexes on supercoiled DNA: the mechanism of selective synapsis by Tn3 resolvase. J Mol Biol 319:371-383. (Pubitemid 34729465)
8. Stark WM, Sherratt DJ, Boocock MR (1989) Site-specific recombination by Tn3 resolvase: topological changes in the forward and reverse reactions. Cell 58:779-790.
9. Moitoso de Vargas L, Kim S, Landy A (1989) DNA looping generated by DNA bending protein IHF and the two domains of lambda integrase. Science 244:1457-1461. (Pubitemid 19171678)
10. Wasserman SA, Dungan JM, Cozzarelli NR (1985) Discovery of a predicted DNA knot substantiates a model for site-specific recombination. Science 229:171-174.
11. Wasserman SA, Cozzarelli NR (1985) Determination of the stereostructure of the product of Tn3 resolvase by a general method. Proc Natl Acad Sci USA 82:1079-1083.
12. Benjamin HW, Cozzarelli NR (1990) Geometric arrangements of Tn3 resolvase sites. J Biol Chem 265:6441-6447.
13. Travers A (1974) RNA-polymerase promoter interactions: some general principles. Cell 3:97-104.
14. Platt T (1986) Transcription termination and the regulation of gene expression. Annu Rev Biochem 55:339-372. (Pubitemid 16070773)
15. Bourniquel AA, Bickle TA (2002) Complex restriction enzymes: NTP-driven molecular motors. Biochimie 84:1047-1059.
16. Smith RM, Josephsen J, Szczelkun MD (2009) The single polypeptide restriction-modification enzyme LlaGI is a self-contained molecular motor that translocates DNA loops. Nucleic Acids Res 37:7219-7230.
17. Smith RM, Diffin FM, Savery NJ, Josephsen J, Szczelkun MD (2009) DNA cleavage and methylation specificity of the single polypeptide Restriction Modification enzyme LlaGI. Nucleic Acids Res 37:7206-7218.
18. Seidel R, Bloom JGP, Dekker C, Szczelkun MD (2008) Motor step size and ATP coupling efficiency of the dsDNA translocase EcoR124I. EMBO J 27:1388-1398. (Pubitemid 351655181)
19. Iyer RR, Pluciennik A, Burdett V, Modrich PL (2006) DNA mismatch repair: functions and mechanisms. Chem Rev 106:302-323. (Pubitemid 43316559)
20. Szczelkun MD, Friedhoff P, Seidel R (2010) Maintaining a sense of direction during long-range communication on DNA. Biochem Soc Trans 38:404-409.
21. Meisel A, Bickle TA, Krüger DH, Schroeder C (1992) Type III restriction enzymes need two inversely oriented recognition sites for DNA cleavage. Nature 355:467-469.
22. Meisel A, Mackeldanz P, Bickle TA, Krüger DH, Schroeder C (1995) Type III restriction endonucleases translocate DNA in a reaction driven by recognition site-specific ATP hydrolysis. EMBO J 14:2958-2966.
23. Saha S, Rao DN (1995) ATP hydrolysis is required for DNA cleavage by EcoPI restriction enzyme. J Mol Biol 247:559-567.
24. Saha S, Rao DN (1997) Mutations in the Res subunit of the EcoPI restriction enzyme that affect ATP-dependent reactions. J Mol Biol 269:342-354. (Pubitemid 27267757)
25. Peakman LJ, Antognozzi M, Bickle TA, Janscak P, Szczelkun MD (2003) S-adenosyl methionine prevents promiscuous DNA cleavage by the EcoP1I type III restriction enzyme. J Mol Biol 333:321-335. (Pubitemid 37188575)
26. Peakman LJ, Szczelkun MD (2004) DNA communications by Type III restriction endonucleases-confirmation of one-dimensional translocation over three-dimensional looping. Nucleic Acids Res 32:4166-4174.
27. Sears A, Peakman LJ, Wilson GG, Szczelkun MD (2005) Characterization of the Type III restriction endonuclease PstII from Providencia stuartii. Nucleic Acids Res 33:4775-4787. (Pubitemid 41418878)
28. Raghavendra NK, Rao DN (2004) Unidirectional translocation from recognition site and a necessary interaction with DNA end for cleavage by Type III restriction enzyme. Nucleic Acids Res 32:5703-5711.
29. Crampton N, et al. (2007) DNA Looping and translocation provide an optimal cleavage mechanism for the type III restriction enzymes. EMBO J 26:3815-3825. (Pubitemid 47295874)
30. Ramanathan SP, et al. (2009) Type III restriction enzymes communicate in onedimensional without looping between their target sites. Proc Natl Acad Sci USA 106:1748-1753.
31. Mücke M, Reich S, Möncke-Buchner E, Reuter M, Krüger DH (2001) DNA cleavage by type III restriction-modification enzyme EcoP15I is independent of spacer distance between two head to head oriented recognition sites. J Mol Biol 312:687-698.
32. Kim K, Saleh OA (2009) A high-resolution magnetic tweezer for single-molecule measurements. Nucleic Acids Res e136.
33. Oram M, Marko JF, Halford SE (1997) Communications between distant sites on super-coiled DNA from non-exponential kinetics for DNA synapsis by resolvase. J Mol Biol 270:396-412. (Pubitemid 27326679)
34. Firman K, Szczelkun MD (2000) Measuring motion on DNA by the type I restriction endonuclease EcoR124I using triplex displacement. EMBO J 19:2094-2102. (Pubitemid 30237584)
35. Halford SE, Marko JF (2004) How do site-specific DNA-binding proteins find their targets?. Nucleic Acids Res 32:3040-3052.
36. O'Donnell M, Kuriyan J (2006) Clamp loaders and replication initiation. Curr Opin Struct Biol 16:35-41.
37. Ahmad I, Krishnamurthy V, Rao DN (1995) DNA recognition by the EcoP15I and EcoPI modification methyltransferases. Gene 157:143-147.