Cofactor requirement of HpyAV restriction endonuclease

PLoS ONE

Volumn 5, Issue 2, 2010, Pages

  Chan, Siu Hong ^a   Opitz, Lars ^a,b   Higgins, Lauren ^a   O'Loane, Diana ^a   Xu, Shuang Yong ^a  

^a NEW ENGLAND BIOLABS   (United States)

^b GLAXOSMITHKLINE   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ENDONUCLEASE; HPYAV ENZYME; MAGNESIUM; UNCLASSIFIED DRUG; BACTERIAL PROTEIN; COBALT; DIVALENT CATION; DNA; MANGANESE; METAL; NICKEL; RESTRICTION ENDONUCLEASE;

ARTICLE; DNA CLEAVAGE; DNA SEQUENCE; HELICOBACTER PYLORI; NONHUMAN; AMINO ACID SEQUENCE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; ENZYME ACTIVE SITE; ENZYMOLOGY; GENETICS; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PROTEIN TERTIARY STRUCTURE; SEQUENCE HOMOLOGY; SITE DIRECTED MUTAGENESIS;

HELICOBACTER PYLORI;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; BASE SEQUENCE; BINDING SITES; CATALYTIC DOMAIN; CATIONS, DIVALENT; COBALT; DNA; DNA RESTRICTION ENZYMES; DNA RESTRICTION-MODIFICATION ENZYMES; HELICOBACTER PYLORI; MANGANESE; METALS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTAGENESIS, SITE-DIRECTED; NICKEL; PROTEIN STRUCTURE, TERTIARY; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 77949345175     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0009071     Document Type: Article

References (80)

1. Roberts RJ, Vincze T, Posfai J, Macelis D (2007) REBASE - enzymes and genes for DNA restriction and modification. Nucleic Acids Res 35: D269-270.
2. Hatakeyama M (2009) Helicobacter pylori and gastric carcinogenesis. J Gastroenterol 44: 239-248.
3. Lin LF, Posfai J, Roberts RJ, Kong H (2001) Comparative genomics of the restriction-modification systems in Helicobacter pylori. Proc Natl Acad Sci U S A 98: 2740-2745.
4. Xu Q, Morgan RD, Roberts RJ, Blaser MJ (2000) Identification of type II restriction and modification systems in Helicobacter pylori reveals their substantial diversity among strains. Proc Natl Acad Sci U S A 97: 9671-9676.
5. Israel DA, Lou, Angele S, Blaser, Martin J (2000) Characteristics of Helicobacter pylori natural transformation. FEMS Microbiology Letters 188: 275-280.
6. Baltrus DA, Guillemin K, Phillips PC (2008) Natural transformation increases the rate of adaptation in the human pathogen Helicobacter pylori. Evolution 62: 39-49.
7. Skoglund A, Bjorkholm B, Nilsson C, Andersson AF, Jernberg C, et al. (2007) Functional analysis of the M.HpyAIV DNA methyltransferase of Helicobacter pylori. J Bacteriol 189: 8914-8921.
8. Heusipp G, Falker S, Schmidt MA (2007) DNA adenine methylation and bacterial pathogenesis. Int J Med Microbiol 297: 1-7.
9. Kahng LS, Shapiro L (2001) The CcrM DNA methyltransferase of Agrobacterium tumefaciens is essential, and its activity is cell cycle regulated. J Bacteriol 183: 3065-3075.
10. Morgan RD, Bhatia TK, Lovasco L, Davis TB (2008) MmeI: a minimal Type II restriction-modification system that only modifies one DNA strand for host protection. Nucleic Acids Res 36: 6558-6570.
11. Morgan RD, Dwinell EA, Bhatia TK, Lang EM, Luyten YA (2009) The MmeI family: type II restriction-modification enzymes that employ single-strand modification for host protection. Nucleic Acids Res 37: 5208-5221.
12. Chan SH, Zhu Z, Van Etten JL, Xu SY (2004) Cloning of CviPII nicking and modification system from chlorella virus NYs-1 and application of Nt.CviPII in random DNA amplification. Nucleic Acids Res 32: 6187-6199.
13. Stoddard BL (2005) Homing endonuclease structure and function. Q Rev Biophys 38: 49-95.
14. Shen BW, Landthaler M, Shub DA, Stoddard BL (2004) DNA binding and cleavage by the HNH homing endonuclease I-HmuI. J Mol Biol 342: 43-56.
15. Chandrashekaran S, Saravanan M, Radha DR, Nagaraja V (2004) Ca(2+)-mediated site-specific DNA cleavage and suppression of promiscuous activity of KpnI restriction endonuclease. J Biol Chem 279: 49736-49740.
16. Saravanan M, Vasu K, Kanakaraj R, Rao DN, Nagaraja V (2007) R.KpnI, an HNH superfamily REase, exhibits differential discrimination at non-canonical sequences in the presence of Ca2+ and Mg2+. Nucleic Acids Res 35: 2777-2786.
17. Horton JR, Blumenthal RM, Cheng X (2004) Restriction endonucleases: structure of the conserved catalytic core and the role of metal ions in DNA cleavage. In: Pingoud A, ed (2004) Restriction Endonucleases: Springer-Verlag Berlin Heidelberg. pp 316-392.
18. Pingoud A, Jeltsch A (2001) Structure and function of type II restriction endonucleases. Nucleic Acids Res 29: 3705-3727.
19. Kovall RA, Matthews BW (1999) Type II restriction endonucleases: structural, functional and evolutionary relationships. Curr Opin Chem Biol 3: 578-583.
20. Galburt EA, Stoddard BL (2002) Catalytic mechanisms of restriction and homing endonucleases. Biochemistry 41: 13851-13860.
21. Viadiu H, Aggarwal AK (1998) The role of metals in catalysis by the restriction endonuclease BamHI. Nat Struct Biol 5: 910-916.
22. Dunten PW, Little EJ, Gregory MT, Manohar VM, Dalton M, et al. (2008) The structure of SgrAI bound to DNA; recognition of an 8 base pair target. Nucleic Acids Res 36: 5405-5416.
23. Pingoud V, Wende W, Friedhoff P, Reuter M, Alves J, et al. (2009) On the divalent metal ion dependence of DNA cleavage by restriction endonucleases of the EcoRI family. J Mol Biol 393: 140-160.
24. Miller MD, Tanner J, Alpaugh M, Benedik MJ, Krause KL (1994) 2.1 A structure of Serratia endonuclease suggests a mechanism for binding to double-stranded DNA. Nat Struct Biol 1: 461-468.
25. Miller MD, Krause KL (1996) Identification of the Serratia endonuclease dimer: structural basis and implications for catalysis. Protein Sci 5: 24-33.
26. Cheng YS, Hsia KC, Doudeva LG, Chak KF, Yuan HS (2002) 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: 227-236.
27. Ku WY, Liu YW, Hsu YC, Liao CC, Liang PH, et al. (2002) 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: 1670-1678.
28. Walker DC, Georgiou T, Pommer AJ, Walker D, Moore GR, et al. (2002) 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: 3225-3234.
29. Mate MJ, Kleanthous C (2004) Structure-based analysis of the metal-dependent mechanism of H-N-H endonucleases. J Biol Chem 279: 34763-34769.
30. Biertumpfel C, Yang W, Suck D (2007) Crystal structure of T4 endonuclease VII resolving a Holliday junction. Nature 449: 616-620.
31. Mannino SJ, Jenkins CL, Raines RT (1999) Chemical mechanism of DNA cleavage by the homing endonuclease I-PpoI. Biochemistry 38: 16178-16186.
32. Galburt EA, Chevalier B, Tang W, Jurica MS, Flick KE, et al. (1999) A novel endonuclease mechanism directly visualized for I-PpoI. Nat Struct Biol 6: 1096-1099.
33. Pommer AJ, Kuhlmann UC, Cooper A, Hemmings AM, Moore GR, et al. (1999) Homing in on the role of transition metals in the HNH motif of colicin endonucleases. J Biol Chem 274: 27153-27160.
34. Pommer AJ, Cal S, Keeble AH, Walker D, Evans SJ, et al. (2001) Mechanism and cleavage specificity of the H-N-H endonuclease colicin E9. J Mol Biol 314: 735-749.
35. Sokolowska M, Czapinska H, Bochtler M (2009) Crystal structure of the beta beta alpha-Me type II restriction endonuclease Hpy99I with target DNA. Nucleic Acids Res 37: 3799-3810.
36. Saravanan M, Bujnicki JM, Cymerman IA, Rao DN, Nagaraja V (2004) Type II restriction endonuclease R.KpnI is a member of the HNH nuclease superfamily. Nucleic Acids Res 32: 6129-6135.
37. Kriukiene E, Lubiene J, Lagunavicius A, Lubys A (2005) MnlI - The member of H-N-H subtype of Type IIS restriction endonucleases. Biochim Biophys Acta 1751: 194-204.
38. Jakubauskas A, Sasnauskas G, Giedriene J, Janulaitis A (2008) Domain organization and functional analysis of type IIS restriction endonuclease Eco31I. Biochemistry 47: 8546-8556.
39. Jakubauskas A, Giedriene J, Bujnicki JM, Janulaitis A (2007) Identification of a single HNH active site in type IIS restriction endonuclease Eco31I. J Mol Biol 370: 157-169.
40. Cymerman IA, Obarska A, Skowronek KJ, Lubys A, Bujnicki JM (2006) Identification of a new subfamily of HNH nucleases and experimental characterization of a representative member, HphI restriction endonuclease. Proteins 65: 867-876.
41. Bujnicki JM, Radlinska M, Rychlewski L (2001) Polyphyletic evolution of type II restriction enzymes revisited: two independent sources of second-hand folds revealed. Trends Biochem Sci 26: 9-11.
42. Orlowski J, Bujnicki JM (2008) Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses. Nucleic Acids Res 36: 3552-3569.
43. Derbyshire V, Kowalski JC, Dansereau JT, Hauer CR, Belfort M (1997) Twodomain structure of the td intron-encoded endonuclease I-TevI correlates with the two-domain configuration of the homing site. J Mol Biol 265: 494-506.
44. Van Roey P, Meehan L, Kowalski JC, Belfort M, Derbyshire V (2002) Catalytic domain structure and hypothesis for function of GIY-YIG intron endonuclease I-TevI. Nat Struct Biol 9: 806-811.
45. Kaminska KH, Kawai M, Boniecki M, Kobayashi I, Bujnicki JM (2008) Type II restriction endonuclease R.Hpy188I belongs to the GIY-YIG nuclease superfamily, but exhibits an unusual active site. BMC Struct Biol 8: 48.
46. Ibryashkina EM, Zakharova MV, Baskunov VB, Bogdanova ES, Nagornykh MO, et al. (2007) Type II restriction endonuclease R.Eco29kI is a member of the GIY-YIG nuclease superfamily. BMC Struct Biol 7: 48.
47. Ibryashkina EM, Sasnauskas G, Solonin AS, Zakharova MV, Siksnys V (2009) Oligomeric structure diversity within the GIY-YIG nuclease family. J Mol Biol 387: 10-16.
48. Gasiunas G, Sasnauskas G, Tamulaitis G, Urbanke C, Razaniene D, et al. (2008) Tetrameric restriction enzymes: expansion to the GIY-YIG nuclease family. Nucleic Acids Res 36: 938-949.
49. Truglio JJ, Rhau B, Croteau DL, Wang L, Skorvaga M, et al. (2005) Structural insights into the first incision reaction during nucleotide excision repair. EMBO J 24: 885-894.
50. Eklund JL, Ulge UY, Eastberg J, Monnat RJ Jr (2007) Altered target site specificity variants of the I-PpoI His-Cys box homing endonuclease. Nucleic Acids Res 35: 5839-5850.
51. Kriukiene E (2006) Domain organization and metal ion requirement of the Type IIS restriction endonuclease MnlI. FEBS Lett 580: 6115-6122.
52. Wittmayer PK, Raines RT (1996) Substrate binding and turnover by the highly specific I-PpoI endonuclease. Biochemistry 35: 1076-1083.
53. Pommer AJ, Wallis R, Moore GR, James R, Kleanthous C (1998) Enzymological characterization of the nuclease domain from the bacterial toxin colicin E9 from Escherichia coli. Biochem J 334: 387-392.
54. Friedhoff P, Kolmes B, Gimadutdinow O, Wende W, Krause KL, et al. (1996) Analysis of the mechanism of the Serratia nuclease using site-directed mutagenesis. Nucleic Acids Res 24: 2632-2639.
55. Yang W, Lee JY, Nowotny M (2006) Making and breaking nucleic acids: two-Mg2+-ion catalysis and substrate specificity. Mol Cell 22: 5-13.
56. Yang W (2008) An equivalent metal ion in one- and two-metal-ion catalysis. Nat Struct Mol Biol 15: 1228-1231.
57. Hsu M, Berg P (1978) Altering the specificity of restriction endonuclease: effect of replacing Mg2+ with Mn2+. Biochemistry 17: 131-138.
58. Wei H, Therrien C, Blanchard A, Guan S, Zhu Z (2008) The Fidelity Index provides a systematic quantitation of star activity of DNA restriction endonucleases. Nucleic Acids Res 36: e50.
59. Vermote CL, Halford SE (1992) EcoRV restriction endonuclease: communication between catalytic metal ions and DNA recognition. Biochemistry 31: 6082-6089.
60. Izsvak Z, Duda E (1989) 'Star' activity and complete loss of specificity of CeqI endonuclease. Biochem J 258: 301-303.
61. Cirino NM, Cameron CE, Smith JS, Rausch JW, Roth MJ, et al. (1995) Divalent cation modulation of the ribonuclease functions of human immunodeficiency virus reverse transcriptase. Biochemistry 34: 9936-9943.
62. Vaisman A, Ling H, Woodgate R, Yang W (2005) Fidelity of Dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis. Embo J 24: 2957-2967.
63. Allingham JS, Haniford DB (2002) Mechanisms of metal ion action in Tn10 transposition. J Mol Biol 319: 53-65.
64. Taylor JD, Halford SE (1989) Discrimination between DNA sequences by the EcoRV restriction endonuclease. Biochemistry 28: 6198-6207.
65. Phillips ND, La T, Adams PJ, Harland BL, Fenwick SG, et al. (2009) Detection of Brachyspira hyodysenteriae, Lawsonia intracellularis and Brachyspira pilosicoli in feral pigs. Vet Microbiol 134: 294-299.
66. Thigpen JE, Cottew GS, Yeats F, McGhee CE, Rose DL (1983) Growth characteristics of large- and small-colony types of Mycoplasma mycoides subsp. mycoides on 5% sheep blood agar. J Clin Microbiol 18: 956-960.
67. Pilo P, Frey J, Vilei EM (2007) Molecular mechanisms of pathogenicity of Mycoplasma mycoides subsp. mycoides SC. Vet J 174: 513-521.
68. Harrington DJ, Sutcliffe IC, Chanter N (2002) The molecular basis of Streptococcus equi infection and disease. Microbes Infect 4: 501-510.
69. Nobusato A, Uchiyama I, Ohashi S, Kobayashi I (2000) Insertion with long target duplication: a mechanism for gene mobility suggested from comparison of two related bacterial genomes. Gene 259: 99-108.
70. Nobusato A, Uchiyama I, Kobayashi I (2000) Diversity of restrictionmodification gene homologues in Helicobacter pylori. Gene 259: 89-98.
71. Xu Q, Morgan RD, Roberts RJ, Xu SY, van Doorn LJ, et al. (2002) Functional analysis of iceA1, a CATG-recognizing restriction endonuclease gene in Helicobacter pylori. Nucleic Acids Res 30: 3839-3847.
72. Caner V, Yilmaz M, Yonetci N, Zencir S, Karagenc N, et al. (2007) H pylori iceA alleles are disease-specific virulence factors. World J Gastroenterol 13: 2581-2585.
73. Platt R, Drescher C, Park SK, Phillips GJ (2000) Genetic system for reversible integration of DNA constructs and lacZ gene fusions into the Escherichia coli chromosome. Plasmid 43: 12-23.
74. Samuelson J, Davis T, Raleigh E, Southworth M (2008) Expression of toxic genes in vivo in an non-natural host. WIPO WO/2008/073746.
75. Chiu J, March PE, Lee R, Tillett D (2004) Site-directed, Ligase-Independent Mutagenesis (SLIM): a single-tube methodology approaching 100% efficiency in 4 h. Nucleic Acids Res 32: e174.
76. Arnold K, Bordoli L, Kopp J, Schwede T (2006) The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics 22: 195-201.
77. Kiefer F, Arnold K, Kunzli M, Bordoli L, Schwede T (2009) The SWISSMODEL Repository and associated resources. Nucleic Acids Res 37: D387-392.
78. Zhang Y, Skolnick J (2005) TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res 33: 2302-2309.
79. Gille C, Frommel C (2001) STRAP: editor for STRuctural Alignments of Proteins. Bioinformatics 17: 377-378.
80. Azarinskas A, Maneliene Z, Jakubauskas A (2006) Hin4II, a new prototype restriction endonuclease from Haemophilus influenzae RFL4: discovery, cloning and expression in Escherichia coli. J Biotechnol 123: 288-296.