Monomeric Restriction Endonuclease BcnI in the Apo Form and in an Asymmetric Complex with Target DNA

Journal of Molecular Biology

Volumn 369, Issue 3, 2007, Pages 722-734

  Sokolowska, Monika ^a,b   Kaus Drobek, Magdalena ^a,b   Czapinska, Honorata ^a,b   Tamulaitis, Gintautas ^c   Szczepanowski, Roman H ^a,b   Urbanke, Claus ^d   Siksnys, Virginijus ^c   Bochtler, Matthias ^a,b  

^a INTERNATIONAL INSTITUTE OF MOLECULAR AND CELL BIOLOGY   (Poland)

^b MAX PLANCK INSTITUTE OF MOLECULAR CELL BIOLOGY AND GENETICS   (Germany)

^c VILNIUS UNIVERSITY   (Lithuania)

^d HANNOVER MEDICAL SCHOOL   (Germany)

Author keywords

1 nt 5 overhang; asymmetric recognition; BcnI, monomer; crystal structure; restriction endonuclease

Indexed keywords

DNA TOPOISOMERASE; DOUBLE STRANDED DNA; MONOMER; RESTRICTION ENDONUCLEASE; RESTRICTION ENDONUCLEASE BACNI; UNCLASSIFIED DRUG;

ARTICLE; COMPLEX FORMATION; CRYSTAL STRUCTURE; DIMERIZATION; DNA CLEAVAGE; DNA REPAIR; DNA SEQUENCE; DNA STRAND; GENE FUNCTION; GENE IDENTIFICATION; GENE INTERACTION; GENE STRUCTURE; GENE TARGETING; KINETICS; MOLECULAR RECOGNITION; NONHUMAN; PRIORITY JOURNAL;

EID: 34248153723     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2007.03.018     Document Type: Article

References (38)

1. Xu Q.S., Kucera R.B., Roberts R.J., and Guo H.C. An asymmetric complex of restriction endonuclease MspI on its palindromic DNA recognition site. Structure 12 (2004) 1741-1747
2. Yang Z., Horton J.R., Maunus R., Wilson G.G., Roberts R.J., and Cheng X. Structure of HinP1I endonuclease reveals a striking similarity to the monomeric restriction enzyme MspI. Nucl. Acids Res. 33 (2005) 1892-1901
3. Horton J.R., Zhang X., Maunus R., Yang Z., Wilson G.G., Roberts R.J., and Cheng X. DNA nicking by HinP1I endonuclease: bending, base flipping and minor groove expansion. Nucl. Acids Res. 34 (2006) 939-948
4. Petrusyte M., and Janulaitis A. Isolation and some properties of the restriction endonuclease BcnI from Bacillus centrosporus. Eur. J. Biochem. 121 (1982) 377-381
5. Janulaitis A., Povilionis P., and Sasnauskas K. Cloning of the modification methylase gene of Bacillus centrosporus in Escherichia coli. Gene 20 (1982) 197-204
6. Janulaitis A., Klimasauskas S., Petrusyte M., and Butkus V. Cytosine modification in DNA by BcnI methylase yields N4-methylcytosine. FEBS Letters 161 (1983) 131-134
7. Vilkaitis G., Lubys A., Merkiene E., Timinskas A., Janulaitis A., and Klimasauskas S. Circular permutation of DNA cytosine-N4 methyltransferases: in vivo coexistence in the BcnI system and in vitro probing by hybrid formation. Nucl. Acids Res. 30 (2002) 1547-1557
8. Lebowitz J., Lewis M.S., and Schuck P. Modern analytical ultracentrifugation in protein science: a tutorial review. Protein Sci. 11 (2002) 2067-2079
9. Kaus-Drobek, M., Czapinska, H., Sokolowska, M., Tamulaitis, G., Szczepanowski, R. H., Urbanke, C., Siksnys, V., & Bochtler, M. (2007). Restriction endonuclease MvaI is a monomer that recognizes its target sequence asymmetrically. Nucl. Acids Res. epub ahead of print, doi:10.1093/nar/gkm064.
10. Richardson J.S. β-Sheet topology and the relatedness of proteins. Nature 268 (1977) 495-500
11. Harding M.M. The geometry of metal-ligand interactions relevant to proteins. Acta Crystallog. sect. D 55 (1999) 1432-1443
12. Mordasini T., Curioni A., and Andreoni W. Why do divalent metal ions either promote or inhibit enzymatic reactions? The case of BamHI restriction endonuclease from combined quantum-classical simulations. J. Biol. Chem. 278 (2003) 4381-4384
13. Pingoud V., Sudina A., Geyer H., Bujnicki J.M., Lurz R., Luder G., et al. Specificity changes in the evolution of type II restriction endonucleases: a biochemical and bioinformatic analysis of restriction enzymes that recognize unrelated sequences. J. Biol. Chem. 280 (2005) 4289-4298
14. Seeman N.C., Rosenberg J.M., and Rich A. Sequence-specific recognition of double helical nucleic acids by proteins. Proc. Natl Acad. Sci. USA 73 (1976) 804-808
15. Holm L., and Sander C. The FSSP database: fold classification based on structure-structure alignment of proteins. Nucl. Acids Res. 24 (1996) 206-209
16. Welsh K.M., Lu A.L., Clark S., and Modrich P. Isolation and characterization of the Escherichia coli mutH gene product. J. Biol. Chem. 262 (1987) 15624-15629
17. Kupper D., Reuter M., Mackeldanz P., Meisel A., Alves J., Schroeder C., and Kruger D.H. Hyperexpressed EcoRII renatured from inclusion bodies and native enzyme both exhibit essential cooperativity with two DNA sites. Protein Expr. Purif. 6 (1995) 1-9
18. Zimbro M.J., and Power D.A. Difco and BBL Manual (2003), Becton Dickinson and Company, Sparks, MD
19. Van Duyne G.D., Standaert R.F., Karplus P.A., Schreiber S.L., and Clardy J. Atomic structures of the human immunophilin FKBP-12 complexes with FK506 and rapamycin. J. Mol. Biol. 229 (1993) 105-124
20. Schuck P. Size-distribution analysis of macromolecules by sedimentation velocity ultracentrifugation and lamm equation modeling. Biophys. J. 78 (2000) 1606-1619
21. Siksnys V., Skirgaila R., Sasnauskas G., Urbanke C., Cherny D., Grazulis S., and Huber R. The Cfr10I restriction enzyme is functional as a tetramer. J. Mol. Biol. 291 (1999) 1105-1118
22. Gasteiger E., Hoogland C., Gattiker A., Duvaud S., Wilkins M.R., Appel R.D., A., and B. Protein identification and analysis tools on the ExPASy server. The Proteomics Protocols Handbook (2005), Humana Press, Totowa, NJ, USA 571-607
23. Leslie A.W.G. Recent changes to the MOSFLM package for processing film and image plate data. Joint CCP4 + ESF-EAMCB Newsletter Protein Crystallog. 26 (1992)
24. Collaborative Computational Project Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallog. sect. D 50 (1994) 760-763
25. Terwilliger T.C., and Berendzen J. Evaluation of macromolecular electron-density map quality using the correlation of local r.m.s. density. Acta Crystallog. sect. D 55 (1999) 1872-1877
26. Terwilliger T.C., and Berendzen J. Discrimination of solvent from protein regions in native Fouriers as a means of evaluating heavy-atom solutions in the MIR and MAD methods. Acta Crystallog. sect. D 55 (1999) 501-505
27. Murshudov G.N., Vagin A.A., and Dodson E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallog. sect. D 53 (1997) 240-255
28. Uson I., and Sheldrick G.M. Advances in direct methods for protein crystallography. Curr. Opin. Struct. Biol. 9 (1999) 643-648
29. Sheldrick G.M. Macromolecular phasing with SHELXE. Zeitschrift Kristallog. 217 (2002) 644-650
30. Lu X.J., and Olson W.K. 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucl. Acids Res. 31 (2003) 5108-5121
31. Kleywegt G.J., and Jones T.A. Databases in protein crystallography. Acta Crystallog. sect. D 54 (1998) 1119-1131
32. Lee J.Y., Chang J., Joseph N., Ghirlando R., Rao D.N., and Yang W. MutH complexed with hemi- and unmethylated DNAs: coupling base recognition and DNA cleavage. Mol. Cell 20 (2005) 155-166
33. Joshi H.K., Etzkorn C., Chatwell L., Bitinaite J., and Horton N.C. Alteration of sequence specificity of the type II restriction endonuclease HincII through an indirect readout mechanism. J. Biol. Chem. 281 (2006) 23852-23869
34. Huai Q., Colandene J.D., Topal M.D., and Ke H. Structure of NaeI-DNA complex reveals dual-mode DNA recognition and complete dimer rearrangement. Nature Struct. Biol. 8 (2001) 665-669
35. Vanamee E.S., Viadiu H., Kucera R., Dorner L., Picone S., Schildkraut I., and Aggarwal A.K. A view of consecutive binding events from structures of tetrameric endonuclease SfiI bound to DNA. EMBO J. 24 (2005) 4198-4208
36. Horton N.C., and Perona J.J. Role of protein-induced bending in the specificity of DNA recognition: crystal structure of EcoRV endonuclease complexed with d(AAAGAT) + d(ATCTT). J. Mol. Biol. 277 (1998) 779-787
37. Newman M., Lunnen K., Wilson G., Greci J., Schildkraut I., and Phillips S.E. Crystal structure of restriction endonuclease BglI bound to its interrupted DNA recognition sequence. EMBO J. 17 (1998) 5466-5476
38. Horton J.R., and Cheng X. PvuII endonuclease contains two calcium ions in active sites. J. Mol. Biol. 300 (2000) 1049-1056