type iii site specific deoxyribonucleases

Summary

Summary: Enzyme systems composed of two subunits and requiring ATP and magnesium for endonucleolytic activity; they do not function as ATPases. They exist as complexes with modification methylases of similar specificity listed under EC 2.1.1.72 or EC 2.1.1.73. The systems recognize specific short DNA sequences and cleave a short distance, about 24 to 27 bases, away from the recognition sequence to give specific double-stranded fragments with terminal 5'-phosphates. Enzymes from different microorganisms with the same specificity are called isoschizomers. EC 3.1.21.5.

Top Publications

  1. De Backer O, Colson C. Identification of the recognition sequence for the M.StyLTI methyltransferase of Salmonella typhimurium LT7: an asymmetric site typical of type-III enzymes. Gene. 1991;97:103-7 pubmed
    ..Thus, M.StyLTI recognises and methylates the DNA in a manner very similar to that of the three known type-III MTases, M.EcoPI, M.EcoP15, and M.HinfIII. This strongly suggests that StyLTI constitutes a fourth type-III R-M system. ..
  2. Kunz A, Mackeldanz P, Mucke M, Meisel A, Reuter M, Schroeder C, et al. Mutual activation of two restriction endonucleases: interaction of EcoP1 and EcoP15. Biol Chem. 1998;379:617-20 pubmed
    ..We conclude that two different type III enzymes can functionally cooperate in the cleavage of DNA. ..
  3. Ahmad I, Krishnamurthy V, Rao D. DNA recognition by the EcoP15I and EcoPI modification methyltransferases. Gene. 1995;157:143-7 pubmed
    ..Furthermore, we show that although c2 EcoPI mutant MTases are defective in AdoMet binding, they are still able to bind DNA in a sequence-specific manner. ..
  4. Sears A, Peakman L, Wilson G, Szczelkun M. Characterization of the Type III restriction endonuclease PstII from Providencia stuartii. Nucleic Acids Res. 2005;33:4775-87 pubmed
    ..We also demonstrate that PstII and EcoP15I cannot interact and cleave a DNA substrate suggesting that Type III enzymes must make specific protein-protein contacts to activate endonuclease activity...
  5. Ramanathan S, van Aelst K, Sears A, Peakman L, Diffin F, Szczelkun M, et al. Type III restriction enzymes communicate in 1D without looping between their target sites. Proc Natl Acad Sci U S A. 2009;106:1748-53 pubmed publisher
    ..Integrating our results with previous data, a simple communication scheme is concluded based on 1D diffusion along DNA. ..
  6. Meisel A, Bickle T, Kruger D, Schroeder C. Type III restriction enzymes need two inversely oriented recognition sites for DNA cleavage. Nature. 1992;355:467-9 pubmed
    ..This result may be of relevance to other manifestations of anisotropy in double-stranded DNA, such as genetic imprinting. ..
  7. Hegna I, Bratland H, Kolstø A. BceS1, a new addition to the type III restriction and modification family. FEMS Microbiol Lett. 2001;202:189-93 pubmed
    ..The R/M system was designated BceS1 as this endonuclease required ATP and Mg2+ as cofactors like other type III endonucleases. BceS1 is the first chromosomal type III R/M system characterized in a Gram-positive bacterium. ..
  8. Hümbelin M, Suri B, Rao D, Hornby D, Eberle H, Pripfl T, et al. Type III DNA restriction and modification systems EcoP1 and EcoP15. Nucleotide sequence of the EcoP1 operon, the EcoP15 mod gene and some EcoP1 mod mutants. J Mol Biol. 1988;200:23-9 pubmed
    ..Two alleles of the EcoP1 mod gene that are defective in modification but not in restriction were also sequenced. The mutations in both alleles lie within the non-conserved regions. ..
  9. Crampton N, Roes S, Dryden D, Rao D, Edwardson J, Henderson R. DNA looping and translocation provide an optimal cleavage mechanism for the type III restriction enzymes. EMBO J. 2007;26:3815-25 pubmed
    ..On the basis of these results, we present a model for restriction by type III restriction enzymes and highlight the similarities between this and other classes of restriction enzymes. ..

More Information

Publications62

  1. Sharrocks A, Hornby D. Transcriptional analysis of the restriction and modification genes of bacteriophage P1. Mol Microbiol. 1991;5:685-94 pubmed
    ..In addition a functional promoter is located on the antisense strand close to the res promoter region. The relationship between the transcription units of the res and mod genes is discussed. ..
  2. Saha S, Ahmad I, Reddy Y, Krishnamurthy V, Rao D. Functional analysis of conserved motifs in type III restriction-modification enzymes. Biol Chem. 1998;379:511-7 pubmed
    ..Taken collectively, these results form the basis for a detailed structure-function analysis of EcoP1I and EcoP15I restriction enzymes. ..
  3. Sears A, Szczelkun M. Subunit assembly modulates the activities of the Type III restriction-modification enzyme PstII in vitro. Nucleic Acids Res. 2005;33:4788-96 pubmed
    ..A potential role for disassembly in control of restriction activity in vivo is discussed. ..
  4. Raghavendra N, Rao D. Exogenous AdoMet and its analogue sinefungin differentially influence DNA cleavage by R.EcoP15I--usefulness in SAGE. Biochem Biophys Res Commun. 2005;334:803-11 pubmed
    ..The site of cleavage is comparable with that in the presence of AdoMet. The use of EcoP15I restriction in presence of sinefungin as an improved tool for serial analysis of gene expression is discussed. ..
  5. Janscak P, Sandmeier U, Szczelkun M, Bickle T. Subunit assembly and mode of DNA cleavage of the type III restriction endonucleases EcoP1I and EcoP15I. J Mol Biol. 2001;306:417-31 pubmed
  6. Saha S, Rao D. ATP hydrolysis is required for DNA cleavage by EcoPI restriction enzyme. J Mol Biol. 1995;247:559-67 pubmed
    ..The role of ATP in the cleavage mechanism of type III restriction enzymes is discussed. ..
  7. Su P, Im H, Hsieh H, Kang a S, Dunn N. LlaFI, a type III restriction and modification system in Lactococcus lactis. Appl Environ Microbiol. 1999;65:686-93 pubmed
    ..To our knowledge, this is the first type III R/M system that has been characterized not just in lactic acid bacteria but also in gram-positive bacteria. ..
  8. Bist P, Sistla S, Krishnamurthy V, Acharya A, Chandrakala B, Rao D. S-adenosyl-L-methionine is required for DNA cleavage by type III restriction enzymes. J Mol Biol. 2001;310:93-109 pubmed
    ..Taken together, these results suggest that AdoMet binding causes conformational changes in the restriction enzyme and is necessary to bring about DNA cleavage. ..
  9. Meisel A, Mackeldanz P, Bickle T, Kruger D, Schroeder C. Type III restriction endonucleases translocate DNA in a reaction driven by recognition site-specific ATP hydrolysis. EMBO J. 1995;14:2958-66 pubmed
    ..These results rule out DNA looping and strongly suggest that cleavage is triggered by the close proximity of two convergently tracking EcoP15I-DNA complexes. ..
  10. Dryden D, Murray N, Rao D. Nucleoside triphosphate-dependent restriction enzymes. Nucleic Acids Res. 2001;29:3728-41 pubmed
    ..The only well-documented GTP-dependent restriction enzyme, McrBC, requires methylated target sequences for the initiation of phosphodiester bond cleavage. ..
  11. Kruger D, Kupper D, Meisel A, Reuter M, Schroeder C. The significance of distance and orientation of restriction endonuclease recognition sites in viral DNA genomes. FEMS Microbiol Rev. 1995;17:177-84 pubmed
    ..In addition to podoviruses T3 and T7, strand bias of recognition sequences for different type III DNA modification-restriction enzymes is also observed in the inoviruses M13, IKE and PF3...
  12. Crampton N, Yokokawa M, Dryden D, Edwardson J, Rao D, Takeyasu K, et al. Fast-scan atomic force microscopy reveals that the type III restriction enzyme EcoP15I is capable of DNA translocation and looping. Proc Natl Acad Sci U S A. 2007;104:12755-60 pubmed
    ..On the basis of our results, we conclude that EcoP15I uses two distinct mechanisms to communicate between two recognition sites: diffusive DNA loop formation and ATPase-driven translocation of the intervening DNA contour. ..
  13. De Backer O, Colson C. Transfer of the genes for the StyLTI restriction-modification system of Salmonella typhimurium to strains lacking modification ability results in death of the recipient cells and degradation of their DNA. J Bacteriol. 1991;173:1328-30 pubmed
    ..This indicates that, in contrast to any other known restriction-modification systems, StyLTI cannot be established after horizontal transfer into a naive host. ..
  14. Möncke Buchner E, Rothenberg M, Reich S, Wagenführ K, Matsumura H, Terauchi R, et al. Functional characterization and modulation of the DNA cleavage efficiency of type III restriction endonuclease EcoP15I in its interaction with two sites in the DNA target. J Mol Biol. 2009;387:1309-19 pubmed publisher
    ..These results could also be exploited in the high-throughput, quantitative transcriptome analysis method SuperSAGE to optimize the crucial EcoP15I digestion step. ..
  15. Ahmad I, Rao D. Interaction of EcoP15I DNA methyltransferase with oligonucleotides containing the asymmetric sequence 5'-CAGCAG-3'. J Mol Biol. 1994;242:378-88 pubmed
    ..Taken together these results form the basis for a detailed structure-function analysis of EcoP15I DNA Mtase. ..
  16. Bourniquel A, Bickle T. Complex restriction enzymes: NTP-driven molecular motors. Biochimie. 2002;84:1047-59 pubmed
  17. Gorbalenya A, Koonin E. Endonuclease (R) subunits of type-I and type-III restriction-modification enzymes contain a helicase-like domain. FEBS Lett. 1991;291:277-81 pubmed
    ..17, 4713-4730]. A hypothesis is proposed that these enzymes may exert helicase activity possibly required for local unwinding of DNA in the cleavage sites. ..
  18. Ryan K, Lo R. Characterization of a CACAG pentanucleotide repeat in Pasteurella haemolytica and its possible role in modulation of a novel type III restriction-modification system. Nucleic Acids Res. 1999;27:1505-11 pubmed
    ..Restriction activity could also be detected in crude cytoplasmic extracts of Escherichia coli strains carrying the mod and res genes on recombinant plasmids. ..
  19. Reich S, Gössl I, Reuter M, Rabe J, Kruger D. Scanning force microscopy of DNA translocation by the Type III restriction enzyme EcoP15I. J Mol Biol. 2004;341:337-43 pubmed
    ..Moreover, our study revealed differences in the DNA-translocation processes mediated by Type I and Type III restriction enzymes. ..
  20. Bayliss C, Callaghan M, Moxon E. High allelic diversity in the methyltransferase gene of a phase variable type III restriction-modification system has implications for the fitness of Haemophilus influenzae. Nucleic Acids Res. 2006;34:4046-59 pubmed
  21. Redaschi N, Bickle T. Posttranscriptional regulation of EcoP1I and EcoP15I restriction activity. J Mol Biol. 1996;257:790-803 pubmed
    ..In addition, we have preliminary evidence from in vivo gene fusion studies that the res gene may code for more than one gene product...
  22. Hornby D, Muller M, Bickle T. High level expression of the EcoP1 modification methylase gene and characterisation of the gene product. Gene. 1987;54:239-45 pubmed
    ..Experiments with the methyl donor, S-adenosyl methionine, radioactively labelled in different positions indicate that a methyl group is transferred to the enzyme during the reaction in what is most likely a covalent bond. ..
  23. Rao D, Page M, Bickle T. Cloning, over-expression and the catalytic properties of the EcoP15 modification methylase from Escherichia coli. J Mol Biol. 1989;209:599-606 pubmed
    ..This suggestion is strengthened by the fact that a mutant of the closely related EcoP1 does not show such substrate inhibition. ..
  24. Raghavendra N, Rao D. Unidirectional translocation from recognition site and a necessary interaction with DNA end for cleavage by Type III restriction enzyme. Nucleic Acids Res. 2004;32:5703-11 pubmed
    ..This study demonstrates a new facet in the mode of action of these restriction enzymes. ..
  25. Dartois V, De Backer O, Colson C. Sequence of the Salmonella typhimurium StyLT1 restriction-modification genes: homologies with EcoP1 and EcoP15 type-III R-M systems and presence of helicase domains. Gene. 1993;127:105-10 pubmed
    ..In addition, the StyLT1 restriction endonuclease (ENase), like other type-I and type-III ENases, contains sequence motifs characteristic of superfamily-II helicases, which may be involved in DNA unwinding at the cleavage site. ..
  26. Peakman L, Szczelkun M. S-adenosyl homocysteine and DNA ends stimulate promiscuous nuclease activities in the Type III restriction endonuclease EcoPI. Nucleic Acids Res. 2009;37:3934-45 pubmed publisher
    ..We suggest a model for how DNA communication events initiating from non-specific sites, and in particular free DNA ends, could produce the observed cleavage patterns. ..
  27. Peakman L, Szczelkun M. DNA communications by Type III restriction endonucleases--confirmation of 1D translocation over 3D looping. Nucleic Acids Res. 2004;32:4166-74 pubmed
    ..No inhibition was observed, even under conditions where EcoPI translocation could also occur. ..
  28. Mucke M, Reich S, Möncke Buchner E, Reuter M, Kruger D. 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. 2001;312:687-98 pubmed
    ..We assume that the altered patterns are most likely due to a conformational change of the enzyme. Overall, our data further refine the tracking-collision model for type III restriction enzymes. ..
  29. Saha S, Rao D. Mutations in the Res subunit of the EcoPI restriction enzyme that affect ATP-dependent reactions. J Mol Biol. 1997;269:342-54 pubmed
    ..We suggest that these motifs play a role in the ATP-dependent translocation that has been proposed to occur in the type III restriction enzymes. ..
  30. Peakman L, Antognozzi M, Bickle T, Janscak P, Szczelkun M. S-adenosyl methionine prevents promiscuous DNA cleavage by the EcoP1I type III restriction enzyme. J Mol Biol. 2003;333:321-35 pubmed
    ..However, given the right conditions, AdoMet is not strictly required for DNA cleavage by a type III enzyme. ..
  31. Scott A, Waters R. The Saccharomyces cerevisiae RAD7 and RAD16 genes are required for inducible excision of endonuclease III sensitive-sites, yet are not needed for the repair of these lesions following a single UV dose. Mutat Res. 1997;383:39-48 pubmed
    ..In the latter case, the induction of RAD7 and RAD16 may increase the turnover of complexes stalled in nontranscribed DNA so as to increase the availability of NER proteins for the repair of CPDs and EIIISS in all regions of the genome. ..
  32. Möncke Buchner E, Reich S, Mucke M, Reuter M, Messer W, Wanker E, et al. Counting CAG repeats in the Huntington's disease gene by restriction endonuclease EcoP15I cleavage. Nucleic Acids Res. 2002;30:e83 pubmed
    ..Our results suggest that this high-resolution method can be used for the exact length determination of CAG repeats in HD genes as well as in genes affected in related CAG repeat disorders. ..
  33. Szczelkun M. How to proteins move along DNA? Lessons from type-I and type-III restriction endonucleases. Essays Biochem. 2000;35:131-43 pubmed
    ..The DNA-based motor proteins are mechanistically ill-defined. Further study using some of the techniques pioneered with classical motor proteins will be needed to reveal more detail. ..
  34. Lartigue C, Vashee S, Algire M, Chuang R, Benders G, Ma L, et al. Creating bacterial strains from genomes that have been cloned and engineered in yeast. Science. 2009;325:1693-6 pubmed publisher
    ..mycoides. These methods allow the construction of strains that could not be produced with genetic tools available for this bacterium...
  35. Winslow D, Anton E, Horlick R, Zagursky R, Tritch R, Scarnati H, et al. Construction of infectious molecular clones of HIV-1 containing defined mutations in the protease gene. Biochem Biophys Res Commun. 1994;205:1651-7 pubmed
    ..This method was successfully applied to constructing viruses containing various substitutions in protease. ..
  36. Bist P, Madhusoodanan U, Rao D. A mutation in the Mod subunit of EcoP15I restriction enzyme converts the DNA methyltransferase to a site-specific endonuclease. J Biol Chem. 2007;282:3520-30 pubmed
    ..DNA methyltransferase specifically binds to the recognition sequence 5'-CAGCAG-3' and cleaves DNA asymmetrically, 5'-CAGCAG(N)(10)-3', as indicated by the arrows, in presence of magnesium ions. ..
  37. De Backer O, Colson C. Two-step cloning and expression in Escherichia coli of the DNA restriction-modification system StyLTI of Salmonella typhimurium. J Bacteriol. 1991;173:1321-7 pubmed
    ..This suggests that expression of the StyLTI endonuclease activity requires at least one polypeptide involved in the methylation activity, as is the case for types I and III restriction-modification systems but not for type II systems. ..
  38. Williams R. Restriction endonucleases: classification, properties, and applications. Mol Biotechnol. 2003;23:225-43 pubmed
    ..An understanding of the enzymes and their properties can improve their productive application by maintaining critical digest parameters and enhancing or avoiding alternative activities. ..
  39. Zambon J, Sunday G, Smutko J. Molecular genetic analysis of Actinobacillus actinomycetemcomitans epidemiology. J Periodontol. 1990;61:75-80 pubmed
    ..abstract truncated at 250 words)..
  40. Sledziewska Gojska E, Torzewska D. Different repair of O6-methylguanine occurring in DNA modified by MMS in vivo or in vitro. Mutat Res. 1997;383:31-7 pubmed
    ..These mutations are avoided in adapted mutS- cells, when induced by MMS in vitro. This confirms that mismatch repair system of E. coli recognises mismatches formed in DNA by O6-methylguanine. ..
  41. Wagenführ K, Pieper S, Mackeldanz P, Linscheid M, Kruger D, Reuter M. Structural domains in the type III restriction endonuclease EcoP15I: characterization by limited proteolysis, mass spectrometry and insertional mutagenesis. J Mol Biol. 2007;366:93-102 pubmed
    ..All mutants tolerated the genetic manipulation and did not display loss of function or alteration of the DNA cleavage position. ..
  42. Corvaglia A, Francois P, Hernandez D, Perron K, Linder P, Schrenzel J. A type III-like restriction endonuclease functions as a major barrier to horizontal gene transfer in clinical Staphylococcus aureus strains. Proc Natl Acad Sci U S A. 2010;107:11954-8 pubmed publisher
    ..Inactivation of this restriction system dramatically increases the transformation efficiency of clinical S. aureus strains, opening the field of molecular genetic manipulation of these strains using DNA of exogenous origin. ..
  43. Gorodetsky A, Boal A, Barton J. Direct electrochemistry of endonuclease III in the presence and absence of DNA. J Am Chem Soc. 2006;128:12082-3 pubmed
  44. Glei M, Pool Zobel B. The main catechin of green tea, (-)-epigallocatechin-3-gallate (EGCG), reduces bleomycin-induced DNA damage in human leucocytes. Toxicol In Vitro. 2006;20:295-300 pubmed
    ..Together the findings support the hypotheses that EGCG acts protective in human cells. ..
  45. Ahmad I, Rao D. Photolabeling of the EcoP15 DNA methyltransferase with S-adenosyl-L-methionine. Gene. 1994;142:67-71 pubmed
    ..EcoP15. These results suggest that photolabeling is at the AdoMet-binding site and that the N-terminal half of M.EcoP15 may be involved in substrate binding. ..
  46. Handa N, Kobayashi I. Type III restriction is alleviated by bacteriophage (RecE) homologous recombination function but enhanced by bacterial (RecBCD) function. J Bacteriol. 2005;187:7362-73 pubmed
  47. Roberts R, Macelis D. REBASE-restriction enzymes and methylases. Nucleic Acids Res. 1999;27:312-3 pubmed
    ..Additionally, there is a search facility, help and NEWS pages, and a complete description of our various services. Specialized files are available that can be used directly by many software packages. ..
  48. Kruger D, Kupper D, Meisel A, Tierlich M, Reuter M, Schroeder C. Restriction endonucleases functionally interacting with two DNA sites. Gene. 1995;157:165 pubmed
    ..Nevertheless, the molecular mechanisms of the protein-DNA interaction are different between members of both classes of enzymes. ..
  49. Bailly V, Verly W. Importance of thiols in the repair mechanisms of DNA containing AP (apurinic or apyrimidinic) sites. Nucleic Acids Res. 1988;16:9489-96 pubmed
    ..In living cells, thiols might influence the pathways followed by the repair processes of AP site-containing DNA. ..
  50. Fox K, Dowideit S, Erwin A, Srikhanta Y, Smith A, Jennings M. Haemophilus influenzae phasevarions have evolved from type III DNA restriction systems into epigenetic regulators of gene expression. Nucleic Acids Res. 2007;35:5242-52 pubmed
    ..These data suggest that evolution of this type III R-M system into an epigenetic mechanism for controlling gene expression has, in some strains, resulted in loss of the DNA restriction function. ..
  51. Krishnamurthy V, Rao D. Interaction of EcoP1 modification methylase with S-adenosyl-L-methionine: a UV-crosslinking study. Biochem Mol Biol Int. 1994;32:623-32 pubmed
    ..These results suggest that photolabeling of EcoP1 DNA modification methylase occurs at the AdoMet binding site. ..
  52. Mitchell D, Jen J, Cleaver J. Relative induction of cyclobutane dimers and cytosine photohydrates in DNA irradiated in vitro and in vivo with ultraviolet-C and ultraviolet-B light. Photochem Photobiol. 1991;54:741-6 pubmed
    ..We found no evidence to support earlier inferences that intracellular conditions enhance the formation of cytosine photohydrates or other monobasic forms of DNA damage. ..
  53. Zhu F, Ji L, Luo B. [The role of urotensin II gene in the genetic susceptibility to type 2 diabetes in Chinese population]. Zhonghua Yi Xue Za Zhi. 2002;82:1473-5 pubmed
    ..86, P = 0.041 in the case group 1 and 4.03, P < 0.001 in the case control 2 after adjustment by sex, age and BMI. Urotensin II gene may contribute to the genetic susceptibility to type 2 diabetes in Han population. ..