Structural basis for sequence-dependent DNA cleavage by nonspecific endonucleases

Nucleic Acids Research

Volumn 35, Issue 2, 2007, Pages 584-594

  Wang, Yi Ting ^a,b   Yang, Wei Jen ^a   Li, Chia Lung ^a   Doudeva, Lyudmila G ^a   Yuan, Hanna S ^a  

^a INSTITUTE OF MOLECULAR BIOLOGY   (Taiwan)

^b NATIONAL YANG MING UNIVERSITY   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

ENDONUCLEASE; ENDONUCLEASE CO1E7; ENDONUCLEASE VVN; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; CELL SPECIFICITY; CONTROLLED STUDY; CRYSTAL STRUCTURE; DNA CLEAVAGE; DNA CONFORMATION; DNA PURIFICATION; DNA SEQUENCE; DNA STRUCTURE; ENZYME ACTIVITY; ENZYME SPECIFICITY; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN STRUCTURE; SEQUENCE ANALYSIS;

AMINO ACID SUBSTITUTION; BACTERIAL PROTEINS; BASE SEQUENCE; BINDING SITES; COLICINS; CRYSTALLOGRAPHY, X-RAY; DEOXYRIBONUCLEASES; DNA; ENDONUCLEASES; ESCHERICHIA COLI PROTEINS; ESTERASES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; SUBSTRATE SPECIFICITY;

EID: 33846895418     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkl621     Document Type: Article

References (46)

1. Srinivasan,E. and Shankar,V. (2001) Sugar nonspecific endonucleases. FEMS Microbiol. Rev., 25, 583-613.
2. Widlak,P. and Garrard,W.T. (2005) Discovery, regulation and action of the major apoptotic nucleases DFF40/CAD and endonuclease G. J. Cell. Biochem., 94, 1078-1087.
3. Marti,T.M. and Fleck,O. (2004) DNA repair nucleases. Cell. Mol. Life Sci., 61, 336-354.
4. Parker,R. and Song,H. (2004) The enzymes and control fo eukaryotic mRNA turnover. Nature Struct. Mol. Biol., 11, 121-126.
5. Carmell,M.A. and Hannon,G.J. (2004) RNase III enzymes and the initiation of gene silencing. Nature Struct. Mol. Biol., 11, 214-218.
6. Lingel,A. and Sattler,M. (2005) Novel modes of protein-RNA recognition in the RNAi pathway. Curr. Opin. Struct. Biol., 15, 107-115.
7. Scheffler,I.E., Elson,E.L. and Baldwin,R.L. (1968) Helix formation by dAT oligomers. I. Hairpin and straight-chain helices. J. Mol. Biol., 36, 291-304.
8. Lomonossoff,G.P., Butler,P.J.G. and Klug,A. (1981) Sequence-dependent variation in the conformation of DNA. J. Mol. Biol., 149, 745-760.
9. Drew,H.R. and Travers,A.A. (1984) DNA structure variations in the E.coli tyrT promoter. Cell, 37, 491-502.
10. Suck,D., Lahm,A. and Oefner,C. (1988) Structure refined to 2 Angstrom of a nicked DNA octanucleotide complex with DNase I. Nature, 332, 464-468.
11. Lahm,A. and Suck,D. (1991) DNase I-induced DNA conformation. 2 Angstrom structure of a DNase I-octamer complex. J. Mol. Biol., 221, 645-667.
12. 2 complex at 2.3 Angstrom resolution. J. Mol. Biol., 226, 1237-1256.
13. Fox,K.R. (1992) Probing the conformation of eight cloned DNA dodecamers: CGCGAATTCGCG, CGCGTTAACGCG, CGCGTTATACGCG, CGCGATATCGCG, TCGCAAATTTGCG, GCGTTTAAAGCG, CGCGGATCCGCG and CGCGGTACCGCG. Nucleic Acid Res., 20, 6487-6493.
14. Herrera,J.E. and Jonathan,B.C. (1994) Characterization of preferred deoxyribonuclease I cleavage sites. J. Mol. Biol., 236, 405-411.
15. Meiss,G., Friedhoff,P., Hahn,M., Gimadutdinow,O. and Pingoud,A. (1995) Sequence preferences in cleavage of dsDNA and ssDNA by the extracellular Serratia marcescens endonuclease. Biochemistry, 34, 11979-11988.
16. Meiss,G., Franke,I., Gimadutdinow,O., Urbanke,C. and Pingoud,A. (1998) Biochemical characterization of Anabaena sp. strain PCC 7120 nonspecific nuclease NucA and its inhibitor NuiA. Eur. J. Biochem., 251, 924-934.
17. Pommer,A.J., Cal,S., Keeble,A.H., Walker,D., Evans,S.J., Kuhlmann,U.C., Cooper,A., Connolly,B.A., Hemmings,A.M., Moore,G.R. et al. (2001) Mechanism and cleavage specificity of the H-N-H endonuclease colicin E9. J. Mol. Biol., 314, 735-749.
18. Widlak,P., Li,P., Wang,X. and Garrard,W.T. (2000) Cleavage preferences of the apoptotic endonuclease DFF40 (Caspase-activated DNase or nuclease) on naked DNA and chromatin substrates. J. Biol. Chem., 275, 8226-8232.
19. Perez-Stable,C., Shen,C.C. and Shen,C.-K.J. (1988) Enrichment and depletion of Hela topoisomerase I recognition sites among specific types of DNA elements. Nucleic Acid Res., 16, 7975-7993.
20. Hogan,M.E. and Austin,R.H. (1987) Importance of DNA stiffness in protein-DNA binding specificity. Nature, 329, 263-266.
21. Chak,K.-F., Kuo,W.-S., Lu,F.-M. and James,R. (1991) Cloning and characterization of the ColE7 plasmid. J. Gen. Microbiol., 137, 91-100.
22. Hsia,K.-C., Chak,K.-F., Liang,P.-H., Cheng,Y.-S., Ku,W.-Y. and Yuan,H.S. (2004) DNA binding and degradation by the HNH endonuclease ColE7. Structure, 12, 205-214.
23. Wu,S.-I., Lo,S.-K., Shao,C.-P., Tsai,H.-W. and Hor,L.-I. (2001) Cloning and characterization of a periplasmic nuclease of Vibrio vulnificus and its role in preventing uptake of foreign DNA. Appl. Environ. Microbiol., 67, 82-88.
24. Li,C.-L., Hor,L.-I., Chang,Z.-F., Tsai,L.-C., Yang,W.-Z. and Yuan,H.S. (2003) DNA binding and cleavage by the periplasmic nuclease Vvn: A novel structure with a known active site. EMBO J., 22, 4014-4025.
25. Hsia,K.-C., Li,C.-L. and Yuan,H.S. (2005) Structural and functional insight into the sugar-nonspecific nucleases in host defense. Curr. Opin. Struct. Biol., 15, 126-134.
26. Gorbalenya,A.E. (1994) Self-splicing group I and group II introns encode homologous (putative) DNA endonucleases of a new family. Protein Sci., 3, 1117-1120.
27. Shub,D.A., Goodrich-Blair,H. and Eddy,S.R. (1994) Amino acid sequence motif of group I intron endonucleases is conserved in open reading frames of group II introns. Trends Biochem. Sci., 19, 402-404.
28. Chevalier,B.S. and Stoddard,B.L. (2001) Homing endonucleases: Structural and functional insight into the catalysts of intron/intein mobility. Nucleic Acid Res., 29, 3757-3774.
29. Sui,M.-J., Tsai,L.-C., Hsia,K.-C., Doudeva,L.-G., Chak,K.-F. and Yuan,H.S. (2002) 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, 2947-2957.
30. Cheng,Y.-S., Hsia,K.-C., Doudeva,L.G., Chak,K.-F. and Yuan,H.S. (2002) The crystal structure of the nuclease domain of ColE7 suggests a mechanism for binding to double-stranded DNA by the H-N-H endonucleases. J. Mol. Biol., 324, 227-236.
31. Ko,T.-P., Liao,C.-C., Ku,W.-Y., Chak,K.-F. and Yuan,H.S. (1999) The crystal structure of the DNase domain of colicin E7 in complex with its inhibitor Im7 protein. Structure, 7, 91-102.
32. 2+. Protein Sci., 15, 269-280.
33. Friedhoff,P., Franke,I., Meiss,G., Wende,W., Krause,K.L. and Pingoud,A. (1999) A similar active site for nonspecific and specific endonucleases. Nature Struct. Biol., 6, 112-113.
34. Miller,M.D., Cai,J. and Krause,K.L. (1999) The active site of Serratia endonuclease contains a conserved magnesium-water cluster. J. Mol. Biol., 288, 975-987.
35. Grishin,N.V. (2001) Treble clef finger - a functionally diverse zinc-binding structural motif. Nucleic Acids Res., 29, 1703-1714.
36. Brunger,A.T., Adams,P.D., Clore,G.M., Delano,W.L., Gros,P., Grosse-Kunstleve,R.W., Jiang,J.-S., Kuszewski,J., Nilges,N., Pannu,N.S. et al. (1998) Crystallography and NMR System (CNS): A new software system for macromolecular structure determination. Acta Cryst., D54, 905-921.
37. Lavery,R. and Sklenar,H. (1988) The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. J. Biomol. Struct. Dynam., 6, 63-91.
38. Djuranovic,D. and Hartmann,B. (2003) Conformational characteristics and correlations in crystal structures of nucleic acid oligonucleotides: evidence for sub-states. J. Biomol. Struct. Dyn., 20, 771-788.
39. Várnai,P., Djuranovic,D., Lavery,R. and Hartmann,B. (2002) α/γ transitions in the B-DNA backbone. Nucleic Acid Res., 30, 5398-5406.
40. Halford,S.E. and Marko,J.F. (2004) How do site-specific DNA-binding proteins find their targets? Nucleic Acid Res., 32, 3040-3052.
41. Kalodimos,C.G., Biris,N., Bonvin,A.M.J.J., Levandoski,M.M., Guennuegues,M., Boelens,R. and Kaptein,R. (2004) Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes. Science, 305, 386-389.
42. Pingoud,A. and Jeltsch,A. (2001) Structure and function of type II restriction endonucleases. Nucleic Acids Res., 29, 3705-3727.
43. Pingoud,A., Fuxreiter,M., Pingoud,V. and Wende,W. (2005) Type II restriction endonucleases: Structure and mechanism. Cell. Mol. Life Sci., 62, 685-707.
44. Winkler,F.K., Banner,D.W., Oefner,C., Tsernoglou,D., Brown,R.S., Heathman,S.P., Bryan,R.K., Martin,P.D., Petratos,K. and Wilson,K.S. (1993) The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments. EMBO J., 12, 1781-1795.
45. Newman,M., Strzelecka,T., Dorner,L.F., Schildkraut,I. and Aggarwal,A.K. (1995) Structure of Bam HI endonuclease bound to DNA: Partial folding and unfolding on DNA binding. Science, 269, 656-663.
46. Viadiu,H. and Aggarwal,A.K. (2000) Structure of BamHI bound to nonspecific DNA: A model for DNA sliding. Mol. Cell, 5, 889-895.