Structural and functional analysis of the engineered type I DNA methyltransferase EcoR124INT

Journal of Molecular Biology

Volumn 398, Issue 3, 2010, Pages 391-399

  Taylor, James E N ^a   Callow, Phil ^b   Swiderska, Anna ^a   Kneale, G Geoff ^a  

^a UNIVERSITY OF PORTSMOUTH   (United Kingdom)

^b INSTITUT LAUE LANGEVIN   (France)

Author keywords

DNA methylation; DNA methyltransferase; Restriction modification; Sedimentation velocity; Small angle neutron scattering

Indexed keywords

DNA METHYLTRANSFERASE 1; DNA METHYLTRANSFERASE ECOR124I NT; UNCLASSIFIED DRUG; BACTERIAL DNA; ESCHERICHIA COLI PROTEIN; METHYLTRANSFERASE; PROTEIN SUBUNIT; RECOMBINANT PROTEIN; RESTRICTION ENDONUCLEASE;

AMINO TERMINAL SEQUENCE; ARTICLE; CONTROLLED STUDY; DNA METHYLATION; DNA SEQUENCE; ENZYME ACTIVITY; ENZYME ENGINEERING; ENZYME STRUCTURE; METHANOCOCCUS JANNASCHII; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FUNCTION; ULTRACENTRIFUGATION; CHEMICAL STRUCTURE; CHEMISTRY; GENETICS; METABOLISM; PROTEIN BINDING; PROTEIN QUATERNARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; SMALL ANGLE SCATTERING;

DNA RESTRICTION-MODIFICATION ENZYMES; DNA, BACTERIAL; ESCHERICHIA COLI PROTEINS; METHYLTRANSFERASES; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN STRUCTURE, QUATERNARY; PROTEIN STRUCTURE, TERTIARY; PROTEIN SUBUNITS; RECOMBINANT PROTEINS; SCATTERING, SMALL ANGLE; ULTRACENTRIFUGATION;

EID: 77951626827     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2010.03.008     Document Type: Article

References (33)

1. Wilson G.G. Organization of restriction-modification systems. Nucleic Acids Res. 1991, 19:2539-2566.
2. Bickle T.A., Kruger D.H. Biology of DNA restriction. Microbiol. Rev. 1993, 57:434-450.
3. Rao D.N., Saha S., Krishnamurthy V. ATP-dependent restriction enzymes. Proc. Natl Acad. Sci. USA 2000, 64:1-63.
4. Kneale G.G. Symmetrical model for the domain-structure of type-I DNA methyltransferases. J. Mol. Biol. 1994, 243:1-5.
5. Janscak P., Bickle T.A. The DNA recognition subunit of the type I restriction-modification enzyme EcoAI tolerates circular permutions of its polypeptide chain. J. Mol. Biol. 1998, 284:937-948.
6. Calisto B.M., Pich O.Q., Pinol J., Fita I., Querol E., Carpena X. Crystal structure of a putative type I restriction-modification S subunit from Mycoplasma genitalium. J. Mol. Biol. 2005, 351:749-762.
7. Kim J.S., DeGiovanni A., Jancarik J., Adams P.D., Yokota H., Kim R., Kim S.H. Crystal structure of DNA sequence specificity subunit of a type I restriction-modification enzyme and its functional implications. Proc. Natl Acad. Sci. USA 2005, 102:3248-3253.
8. Lapkouski M., Panjikar S., Janscak P., Smatanova I.K., Carey J., Ettrich R., Csefalvay E. Structure of the motor subunit of type I restriction-modification complex EcoR124I. Nat. Struct. Mol. Biol. 2008, 16:94-95.
9. Uyen N.T., Park S.Y., Choi J.W., Lee H.J., Nishi K., Kim J.S. The fragment structure of a putative HsdR subunit of a type I restriction enzyme from Vibrio vulnificus YJ016: implications for DNA restriction and translocation activity. Nucleic Acids Res. 2009, 37:6960-6969.
10. Kennaway C.K., Obarska-Kosinska A., White J.H., Tuszynska I., Cooper L.P., Bujnicki J.M., et al. The structure of M.EcoKI Type I DNA methyltransferase with a DNA mimic antirestriction protein. Nucleic Acids Res. 2009, 37:762-770.
11. Obarska A., Blundell A., Feder M., Vejsadova S., Sisakova E., Weiserova M., et al. Structural model for the multi-subunit Type IC restriction-modification DNA methyltransferase M. EcoR124I in complex with DNA. Nucleic Acids Res. 2006, 34:1992-2005.
12. Davies G.P., Martin I., Sturrock S.S., Cronshaw A., Murray N.E., Dryden D.T.F. On the structure and operation of type I DNA restriction enzymes. J. Mol. Biol. 1999, 290:565-579.
13. Price C., Shepherd J.C.W., Bickle T.A. DNA recognition by a new family of type I restriction enzymes: a unique relationship between two different DNA specificities. EMBO J. 1987, 6:1493-1498.
14. Taylor I., Watts D., Kneale G. Substrate recognition and selectivity in the type-IC DNA modification methylase M.EcoR124I. Nucleic Acids Res. 1993, 21:4929-4935.
15. Patel J., Taylor I., Dutta C.F., Kneale G., Firman K. High-level expression of the cloned genes encoding the subunits of and intact DNA methyltransferase, M.EcoR124I. Gene 1992, 112:21-27.
16. Taylor I., Patel J., Firman K., Kneale G.G. Purification and biochemical-characterization of the EcoR124 type-I modification methylase. Nucleic Acids Res. 1992, 20:179-186.
17. Smith M.A., Mernagh D.R., Kneale G.G. Expression and characterisation of the N-terminal fragment of the HsdS subunit of M.EcoR124I. Biol. Chem. 1998, 379:505-509.
18. Abadjieva A., Patel J., Webb M., Zinkevich V., Firman K. A deletion mutant of the type-IC restriction-endonuclease EcoR124I expressing a novel DNA specificity. Nucleic Acids Res. 1993, 21:4435-4443.
19. Smith M.A., Read C.M., Kneale G.G. Domain structure and subunit interactions in the type I DNA methyltransferase M.EcoR124I. J. Mol. Biol. 2001, 314:41-50.
20. Marks P., McGeehan J.E., Kneale G.G. A novel strategy for the expression and purification of the DNA methyltransferase, M.AhdI. Protein Expr. Purif. 2004, 37:236-242.
21. Callow P., Sukhodub A., Taylor J.E., Kneale G.G. Shape and subunit organisation of the DNA methyltransferase M.AhdI by small-angle neutron scattering. J. Mol. Biol. 2007, 369:177-185.
22. Bandyopadhyay P.K., Studier F.W., Hamilton D.L., Yuan R. Inhibition of the type I restriction-modification enzymes EcoB and EcoK by the gene 0.3 protein of bacteriophage T7. J. Mol. Biol. 1985, 182:567-578.
23. Walkinshaw M.D., Taylor P., Sturrock S.S., Atanasiu C., Berge T., Henderson R.M., et al. Structure of Ocr from bacteriophage T7, a protein that mimics B-form DNA. Mol. Cell 2002, 9:187-194.
24. Schuck P. Size-distribution analysis of macromolecules by sedimentation velocity ultracentrifugation and lamm equation modeling. Biophys. J. 2000, 78:1606-1619.
25. Taylor I.A., Davis K.G., Watts D., Kneale G.G. DNA-binding induces a major structural transition in a type I methyltransferase. EMBO J. 1994, 13:5772-5778.
26. Laue T.M., Shah B.D., Ridgeway T.M., Pelletier S.L. Computer-aided interpretation of analytical sedimentation data for proteins. Analytical Ultracentrifugation in Biochemistry and Polymer Science 1992, 90-125. Royal Society of Chemistry, Cambridge, UK. S.E. Harding, A.J. Rowe, J.C. Horton (Eds.).
27. Petoukhov M.V., Volkov V.V., Svergun D.I. ATSAS 2.1, a program package for small-angle scattering data analysis. J. Appl. Crystallogr. 2006, 39:277-286.
28. Konarev P.V., Volkov V.V., Sokolova A.V., Koch M.H.J., Svergun D.I. PRIMUS: a Windows PC-based system for small-angle scattering data analysis. J. Appl. Crystallogr. 2003, 36:1277-1282.
29. Svergun D.I. Determination of the regularization parameter in indirect-transform methods using perceptual criteria. J. Appl. Crystallogr. 1992, 25:495-503.
30. Volkov V.V., Svergun D.I. Uniqueness of ab initio shape determination in small-angle scattering. J. Appl. Crystallogr. 2003, 36:860-864.
31. Kozin M.B., Svergun D.I. Automated matching of high- and low-resolution structural models. J. Appl. Crystallogr. 2001, 34:33-41.
32. Garcia de la Torre J., Huertas M.L., Carrasco B. Calculation of hydrodynamic properties of globular proteins from their atomic-level structure. Biophys. J. 2000, 78:719-730.
33. Svergun D.I., Richard S., Koch M.H.J., Sayers Z., Kuprin S., Zaccai G. Protein hydration in solution: experimental observation by X-ray and neutron scattering. Proc. Natl Acad. Sci. USA 1998, 95:2267-2272.