MnlI - The member of H-N-H subtype of Type IIS restriction endonucleases

Biochimica et Biophysica Acta - Proteins and Proteomics

Volumn 1751, Issue 2, 2005, Pages 194-204

  Kriukiene, Edita ^a   Lubiene, Judita ^a,b   Lagunavicius, Arunas ^a,b   Lubys, Arvydas ^a,b  

^a VILNIUS UNIVERSITY   (Lithuania)

^b Fermentas UAB   (Lithuania)

Author keywords

Colicin; H N H motif; MnlI; REase; Restriction endonuclease; Restriction modification system

Indexed keywords

6 N METHYLADENINE; ALANINE; BACTERIAL TOXIN; COLICIN; DOUBLE STRANDED DNA; ENDONUCLEASE MN1I; MAGNESIUM ION; METAL ION; NICKEL; SINGLE STRANDED DNA; TRANSFERASE; TRANSITION ELEMENT; TYPE II SITE SPECIFIC DEOXYRIBONUCLEASE; UNCLASSIFIED DRUG;

AMINO ACID SUBSTITUTION; ARTICLE; BIOCHEMISTRY; DNA CLEAVAGE; GENE MUTATION; GENE SEQUENCE; HYDROLYSIS; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; OLIGOMERIZATION; PRIORITY JOURNAL; PROTEIN DOMAIN;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; BACTERIOPHAGE LAMBDA; CATALYSIS; CATIONS, DIVALENT; CHROMATOGRAPHY, GEL; CLONING, MOLECULAR; DEOXYRIBONUCLEASES, TYPE II SITE-SPECIFIC; DNA RESTRICTION-MODIFICATION ENZYMES; DNA, BACTERIAL; DNA, SINGLE-STRANDED; KINETICS; MOLECULAR SEQUENCE DATA; MOLECULAR WEIGHT; MORAXELLA; MUTAGENESIS, SITE-DIRECTED; MUTATION; OPEN READING FRAMES; PROTEIN BINDING; RECOMBINANT PROTEINS; SEQUENCE ANALYSIS, PROTEIN; SEQUENCE HOMOLOGY, AMINO ACID; SUBSTRATE SPECIFICITY;

EID: 23444453714     PISSN: 15709639     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbapap.2005.06.006     Document Type: Article

References (58)

1. R.J. Roberts, T. Vincze, J. Posfai, and D. Macelis REBASE: restriction enzymes and methyltransferases Nucleic Acids Res. 31 2003 418 420
2. R.J. Roberts, M. Belfort, T. Bestor, A.S. Bhagwat, T.A. Bickle, J. Bitinaite, R.M. Blumenthal, S.Kh. Degtyarev, D.T. Dryden, and K. Dybvig A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes Nucleic Acids Res. 31 2003 1805 1812
3. V. Siksnys, A. Timinskas, S. Klimasauskas, V. Butkus, and A. Janulaitis Sequence similarity among type-II restriction endonucleases, related by their recognized 6-bp target and tetranucleotide-overhang cleavage Gene 157 1995 311 314
4. G. Tamulaitis, A.S. Solonin, and V. Siksnys Alternative arrangements of catalytic residues at the active sites of restriction enzymes FEBS Lett. 518 2002 17 22
5. J. Bitinaite, G. Mitkaite, V. Dauksaite, A. Jakubauskas, A. Timinskas, R. Vaisvila, A. Lubys, and A. Janulaitis Evolutionary relationship of Alw26I, Eco31I and Esp3I, restriction endonucleases that recognise overlapping sequences Mol. Genet. Genomics 267 2002 664 672
6. A. Pingoud, M. Fuxreiter, V. Pingoud, and W. Wende Type II restriction endonucleases: structure and mechanism Cell. Mol. Life Sci. 62 2005 685 707
7. R.A. Kovall, and B.W. Matthews Type II restriction endonucleases: structural, functional and evolutionary relationships Curr. Opin. Chem. Biol. 3 1999 578 583
8. J.M. Bujnicki Crystallographic and bioinformatic studies on restriction endonucleases: inference of evolutionary relationships in the "midnight zone" of homology Curr. Protein Pept. Sci. 4 2003 327 337
9. D.A. Wah, J. Bitinaite, I. Schildkraut, and A.K. Aggarwal Structure of FokI has implications for DNA cleavage Proc. Natl Acad. Sci. U. S. A. 95 1998 10564 10569
10. H. Kong Analyzing the functional organization of a novel restriction modification system, the BcgI system J. Mol. Biol. 279 1998 823 832
11. R. Rimseliene, and A. Janulaitis Mutational analysis of two putative catalytic motifs of the type IV restriction endonuclease Eco57I J. Biol. Chem. 276 2001 10492 10497
12. Q. Huai, J.D. Colandene, M.D. Topal, and H. Ke Structure of NaeI-DNA complex reveals dual-mode DNA recognition and complete dimer rearrangement Nat. Struct. Biol. 8 2001 665 669
13. X.E. Zhou, Y. Wang, M. Reuter, M. Mucke, D.H. Kruger, E.J. Meehan, and L. Chen Crystal structure of type IIE restriction endonuclease EcoRII reveals an autoinhibition mechanism by a novel effector-binding fold J. Mol. Biol. 335 2004 307 319
14. R. Skirgaila, S. Grazulis, D. Bozic, R. Huber, and V. Siksnys Structure-based redesign of the catalytic/metal binding site of Cfr10I restriction endonuclease reveals importance of spatial rather than sequence conservation of active centre residues J. Mol. Biol. 279 1998 473 481
15. M. Deibert, S. Grazulis, G. Sasnauskas, V. Siksnys, and R. Huber Structure of the tetrameric restriction endonuclease NgoMIV in complex with cleaved DNA Nat. Struct. Biol. 7 2000 92 799
16. K. Stankevicius, A. Lubys, A. Timinskas, D. Vaitkevicius, and A. Janulaitis Cloning and analysis of the four genes coding for Bpu10I restriction-modification enzymes Nucleic Acids Res. 26 1998 1084 1091
17. R. Sapranauskas, G. Sasnauskas, A. Lagunavicius, G. Vilkaitis, A. Lubys, and V. Siksnys Novel subtype of type IIs restriction enzymes. BfiI endonuclease exhibits similarities to the EDTA-resistant nuclease Nuc of Salmonella typhimurium J. Biol. Chem. 275 2000 30878 30885
18. A. Lagunavicius, G. Sasnauskas, S.E. Halford, and V. Siksnys The metal-independent type IIs restriction enzyme BfiI is a dimer that binds two DNA sites but has only one catalytic centre J. Mol. Biol. 326 2003 1051 1064
19. G. Sasnauskas, S.E. Halford, and V. Siksnys How the BfiI restriction enzyme uses one active site to cut two DNA strands Proc. Natl Acad. Sci. U. S. A. 100 2003 6410 6415
20. M. Zaremba, C. Urbanke, S.E. Halford, and V. Siksnys Generation of the BfiI restriction endonuclease from the fusion of a DNA recognition domain to a non-specific nuclease from the phospholipase D superfamily J. Mol. Biol. 336 2004 81 92
21. L. Aravind, K.S. Makarova, and E.V. Koonin Survey and Summary: Holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories Nucleic Acids Res. 28 2000 3417 3432
22. J.M. Bujnicki Understanding the evolution of restriction-modification systems: clues from sequence and structure comparisons Acta Biochim. Pol. 48 2001 935 967
23. P. Mehta, K. Katta, and S. Krishnaswamy HNH family subclassification leads to identification of commonality in the His-Me endonuclease superfamily Protein Sci. 13 2004 295 300
24. M. Saravanan, J.M. Bujnicki, I.A. Cymerman, D.N. Rao, and V. Nagaraja Type II restriction endonuclease R.KpnI is a member of the HNH nuclease superfamily Nucleic Acids Res. 32 2004 6129 6135
25. F. Bolivar, R.L. Rodriguez, P.J. Greene, M.C. Betlach, H.L. Heyneker, and H.W. Boyer Construction and characterization of new cloning vehicles: II. A multipurpose cloning system Gene 2 1977 95 113
26. F.W. Studier, A.H. Rosenberg, J.J. Dunn, and J.W. Dubendorff Use of T7 RNA polymerase to direct expression of cloned genes Methods Enzymol. 185 1990 60 89
27. E.A. Raleigh, N.E. Murray, H. Revel, R.M. Blumenthal, D. Westaway, A.D. Reith, P.W. Rigby, J. Elhai, and D. Hanahan McrA and McrB restriction phenotypes of some E. coli strains and implications for gene cloning Nucleic Acids Res. 16 1988 1563 1575
28. J. Sambrook, and D.W. Russell Molecular Cloning: A Laboratory Manual 3rd ed. 2001 Cold Spring Harbour Laboratory Press Cold Spring Harbour, NY
29. A. Lubys, J. Lubiene, S. Kulakauskas, K. Stankevicius, A. Timinskas, and A. Janulaitis Cloning and analysis of the genes encoding the type IIs restriction-modification system HphI from Haemophilus parahaemolyticus Nucleic Acids Res. 24 1996 2760 2766
30. A.C.Y. Chang, and S.N. Cohen Construction and characterization of amplifiable multicopy DNA cloning vehicles derived from the P15A cryptic mini plasmid J. Bacteriol. 134 1978 1141 1156
31. H.C. Birnboim, and J. Doly A rapid alkaline extraction procedure for screening recombinant plasmid DNA Nucleic Acids Res. 7 1979 1513 1523
32. M.A. Marko, R. Chipperfield, and H.C. Birnboim A procedure for the large scale isolation of highly purified plasmid DNA using alkaline extraction and binding glass powder Anal. Biochem. 121 1982 382 387
33. J. Marmur A procedure for the isolation of deoxyribonucleic acid from microorganisms J. Mol. Biol. 3 1961 208 218
34. P.R. Whitehead, and N.L. Brown A simple and rapid method for screening bacteria for type II restriction endonucleases: enzymes in Aphanothece halophytica Arch. Microbiol. 141 1985 70 74
35. G. Vilkaitis, and S. Klimasauskas Bisulfite sequencing protocol displays both 5-methylcytosine and N4-methylcytosine Anal Biochem. 271 1999 116 119
36. S. Barik Site-directed mutagenesis by double polymerase chain reaction Mol. Biotechnol. 3 1995 1 7
37. M.B. Mann, R.N. Rao, and H.O. Smith Cloning of restriction and modification genes in E. coli: the HbaII system from Haemophilus haemolyticus Gene 3 1978 97 112
38. J. Posfai, A.S. Bhagwat, G. Posfai, and R.J. Roberts Predictive motifs derived from cytosine methyltransferases Nucleic Acids Res. 17 1989 2421 2435
39. S. Kumar, X. Cheng, S. Klimasauskas, S. Mi, J. Posfai, R.J. Roberts, and G.G. Wilson The DNA (cytosine-5) methyltransferases Nucleic Acids Res. 22 1994 1 10
40. J.F. Tomb, O. White, A.R. Kerlavage, R.A. Clayton, G.G. Sutton, R.D. Fleischmann, K.A. Ketchum, H.P. Klenk, S. Gill, and B.A. Dougherty The complete genome sequence of the gastric pathogen Helicobacter pylori Nature 388 1997 539 547
41. J. Vitkute, K. Stankevicius, G. Tamulaitiene, Z. Maneliene, A. Timinskas, D.E. Berg, and A. Janulaitis Specificities of eleven different DNA methyltransferases of Helicobacter pylori strain 26695 J. Bacteriol. 183 2001 443 450
42. T. Malone, R.M. Blumenthal, and X. Cheng Structure-guided analysis reveals nine sequence motifs conserved among DNA amino-methyltransferases, and suggests a catalytic mechanism for these enzymes J. Mol. Biol. 253 1995 618 632
43. A. Timinskas, V. Butkus, and A. Janulaitis Sequence motifs characteristic for DNA [cytosine-N4] and DNA [adenine-N6] methyltransferases Gene 157 1995 3 11
44. Y. Patel, E. Van Cott, G.G. Wilson, and M. McClelland Cleavage at the twelve-base-pair sequence 5′-TCTAGATCTAGA-3′ using M.Xbal (TCTAGm6A) methylation and DpnI (Gm6A/TC) cleavage Nucleic Acids Res. 18 1990 1603 1607
45. T.P. Ko, C.C. Liao, W.Y. Ku, K.F. Chak, and H.S. Yuan The crystal structure of the DNase domain of colicin E7 in complex with its inhibitor Im7 protein Structure Fold Des. 7 1999 91 102
46. C. Kleanthous, U.C. Kuhlmann, A.J. Pommer, N. Ferguson, S.E. Radford, G.R. Moore, R. James, and M. Hemmings Structural and mechanistic basis of immunity toward endonuclease colicins Nat. Struc. Biol. 6 1999 243 252
47. U.C. Kuhlmann, A.J. Pommer, G.R. Moore, R. James, and C. Kleanthous Specificity in protein-protein interactions: the structural basis for dual recognition in endonuclease colicin-immunity protein complexes J. Mol. Biol. 301 2000 1163 1178
48. A.J. Pommer, S. Cal, A.H. Keeble, D. Walker, S.J. Evans, U.C. Kuhlmann, A. Cooper, A. Connolly, A.M. Hemmings, G.R. Moore, R. James, and C. Kleanthous Mechanism and cleavage specificity of the H-N-H endonuclease colicin E9 J. Mol. Biol. 314 2001 735 749
49. E.A. Galburt, and B.L. Stoddard Catalytic mechanisms of restriction and homing endonucleases Biochemistry 41 2002 13851 13860
50. D.C. Walker, T. Georgiou, A.J. Pommer, D. Walker, G.R. Moore, C. Kleanthous, and R. James Mutagenic scan of the H-N-H motif of colicin E9: implications for the mechanistic enzymology of colicins, homing enzymes and apoptotic endonucleases Nucleic Acids Res. 30 2002 3225 3234
51. W.Y. Ku, Y.W. Liu, Y.C. Hsu, C.C. Liao, P.H. Liang, H.S. Yuan, and K.F. Chak The zinc ion in the HNH motif of the endonuclease domain of colicin E7 is not required for DNA binding but is essential for DNA hydrolysis Nucleic Acids Res. 30 2002 1670 1678
52. K.C. Hsia, K.F. Chak, P.H. Liang, Y.S. Cheng, W.Y. Ku, and H.S. Yuan DNA binding and degradation by the HNH protein ColE7 Structure 12 2004 205 214
53. A.J. Pommer, R. Wallis, G.R. Moore, R. James, and C. Kleanthouse Enzymological characterisation of the nuclease domain from the bacterial toxin colicin E9 from Escherichia coli J. Biochem. 334 1998 387 392
54. M.J. Mate, and C. Kleanthous Structure-based analysis of the metal-dependent mechanism of H-N-H endonucleases J. Biol. Chem. 279 2004 34763 34769
55. M.J. Sui, L.C. Tsai, K.C. Hsia, L.G. Doudeva, W.Y. Ku, G.W. Han, and H.S. Yuan Metal ions and phosphate binding in the H-N-H motif: crystal structures of the nuclease domain of ColE7/Im7 in complex with a phosphate ion and different divalent metal ions Protein Sci. 11 2002 2947 2957
56. Y.S. Cheng, K.C. Hsia, L.G. Doudeva, K.F. Chak, and H.S. Yuan The crystal structure of the nuclease domain of colicin E7 suggests a mechanism for binding to double-stranded DNA by the H-N-H endonucleases J. Mol. Biol. 324 2002 227 236
57. A.J. Pommer, U.C. Kuhlmann, A. Cooper, A.M. Hemmings, G.R. Moore, R. James, and C. Kleanthous Homing in on the role of transition metals in the HNH motif of colicin endonucleases J. Biol. Chem. 274 1999 27153 27160
58. A.H. Keeble, A.M. Hemmings, R. James, G.R. Moore, and C. Kleanthous Multistep binding of transition metals to the H-N-H endonuclease toxin colicin E9 Biochemistry 41 2002 10234 10244